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Lee YY, Guler M, Chigumba DN, Wang S, Mittal N, Miller C, Krummenacher B, Liu H, Cao L, Kannan A, Narayan K, Slocum ST, Roth BL, Gurevich A, Behsaz B, Kersten RD, Mohimani H. HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search. Nat Commun 2023; 14:4219. [PMID: 37452020 PMCID: PMC10349150 DOI: 10.1038/s41467-023-39905-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes.
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Affiliation(s)
- Yi-Yuan Lee
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Cornell University, Ithaca, NY, 14850, USA
| | - Mustafa Guler
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Shen Wang
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Neel Mittal
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | | | | | - Haodong Liu
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Liu Cao
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Aditya Kannan
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | | | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
- Department of Computer Science, Saarland University, Saarbrücken, Germany
| | - Bahar Behsaz
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
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Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E, Stokke R, Bødtker G, Steen IH. Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System. Microorganisms 2018; 6:E63. [PMID: 29973550 PMCID: PMC6163223 DOI: 10.3390/microorganisms6030063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.
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Affiliation(s)
- Anders Schouw
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Francesca Vulcano
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Irene Roalkvam
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - William Peter Hocking
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Eoghan Reeves
- Department of Earth Science and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Runar Stokke
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
| | - Gunhild Bødtker
- Centre for Integrated Petroleum Research (CIPR), Uni Research AS, Nygårdsgaten 112, N-5008 Bergen, Norway.
| | - Ida Helene Steen
- Department of Biological Sciences and KG Jebsen Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway.
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3
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Chen X, Ma A, McDermaid A, Zhang H, Liu C, Cao H, Ma Q. RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis. Genes (Basel) 2018; 9:genes9060278. [PMID: 29849014 PMCID: PMC6027394 DOI: 10.3390/genes9060278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/19/2018] [Accepted: 05/25/2018] [Indexed: 11/16/2022] Open
Abstract
Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as promising candidates for better acid tolerance engineering in Lactococcus lactis. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation, and has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
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Affiliation(s)
- Xin Chen
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China.
| | - Anjun Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Adam McDermaid
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
| | - Hanyuan Zhang
- College of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE 68588, USA.
| | - Chao Liu
- Shandong Provincial Hospital affiliated to Shandong University, Jinan 250021, China.
| | - Huansheng Cao
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Qin Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57006, USA.
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD 57006, USA.
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4
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Repka LM, Chekan JR, Nair SK, van der Donk WA. Mechanistic Understanding of Lanthipeptide Biosynthetic Enzymes. Chem Rev 2017; 117:5457-5520. [PMID: 28135077 PMCID: PMC5408752 DOI: 10.1021/acs.chemrev.6b00591] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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5
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Cintas LM, Casaus MP, Herranz C, Nes IF, Hernández PE. Review: Bacteriocins of Lactic Acid Bacteria. FOOD SCI TECHNOL INT 2016. [DOI: 10.1106/r8de-p6hu-clxp-5ryt] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the last few years, a large number of new bacteriocins produced by lactic acid bacteria (LAB) have been identified and characterized. LAB-bacteriocins comprise a heterogeneous group of physicochemically diverse ribosomally-synthesized peptides or proteins showing a narrow or broad antimicrobial activity spectrum against Gram-positive bacteria. Bacteriocins are classified into separate groups such as the lantibiotics (Class I); the small (<10 kDa) heat-stable postranslationally unmodified non-lantibiotics (Class II), further subdivided in the pediocin-like and anti Listeria bacteriocins (subclass IIa), the two-peptide bacteriocins (subclass IIb), and the sec-dependent bacteriocins (subclass IIc); and the large (>30 kDa) heat-labile non-lantibiotics (Class III). Most bacteriocins characterized to date belong to Class II and are synthesized as precursor peptides (preprobacteriocins) containing an N-terminal double-glycine leader peptide, which is cleaved off concomitantly with externalization of biologically active bacteriocins by a dedicated ABC-transporter and its accessory protein. However, the recently identified sec-dependent bacteriocins contain an N-terminal signal peptide that directs bacteriocin secretion through the general secretory pathway (GSP). Most LAB-bacteriocins act on sensitive cells by destabilization and permeabilization of the cytoplasmic membrane through the formation of transitory poration complexes or ionic channels that cause the reduction or dissipation of the proton motive force (PMF). Bacteriocin producing LAB strains protect themselves against the toxicity of their own bacteriocins by the expression of a specific immunity protein which is generally encoded in the bacteriocin operon. Bacteriocin production in LAB is frequently regulated by a three-component signal transduction system consisting of an induction factor (IF), and histidine protein kinase (HPK) and a response regulator (RR). This paper presents an updated review on the general knowledge about physicochemical properties, molecular mode of action, biosynthesis, regulation and genetics of LAB-bacteriocins.
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Affiliation(s)
- L. M. Cintas
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - M. P. Casaus
- Carrefour, Departamento de Marcas Propias, Área de Calidad, Campezo 16, 28022 Madrid
| | - C. Herranz
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - I. F. Nes
- Laboratory of Microbial Gene Technology, Department of Chemistry and Biotechnology, Agricultural University of Norway, P.O. Box 5051, N-1432 Ås, Norway
| | - P. E. Hernández
- Departamento de Nutrición y Bromatología III (Higiene y Tecnología de los Alimentos), Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
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Kong W, Kapuganti VS, Lu T. A gene network engineering platform for lactic acid bacteria. Nucleic Acids Res 2016; 44:e37. [PMID: 26503255 PMCID: PMC4770204 DOI: 10.1093/nar/gkv1093] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 11/28/2022] Open
Abstract
Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
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Affiliation(s)
- Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Venkata S Kapuganti
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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7
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Heterologous Processing and Export of the Bacteriocins Pediocin PA-1 and Lactococcin A in Lactococcus Lactis: A Study with Leader Exchange. Probiotics Antimicrob Proteins 2016; 2:66-76. [PMID: 26781115 DOI: 10.1007/s12602-009-9023-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The bacteriocins pediocin PA-1 and lactococcin A are synthesized as precursors carrying N-terminal extensions with a conserved cleavage site preceded by two glycine residues in positions -2 and -1. Each bacteriocin is translocated through the cytoplasmic membrane by an integral membrane protein of the ABC cassette superfamily which, in the case of pediocin PA-1, has been shown to possess peptidase activity responsible for proteolytic cleavage of the pre-bacteriocin. In each case, another integral membrane protein is essential for bacteriocin production. In this study, a two-step PCR approach was used to permutate the leaders of pediocin PA-1 and lactococcin A. Wild-type and chimeric pre-bacteriocins were assayed for maturation by the processing/export machinery of pediocin PA-1 and lactococcin A. The results show that pediocin PA-1 can be efficiently exported by the lactococcin machinery whether it carries the lactococcin or the pediocin leader. It can also compete with wild-type lactococcin A for the lactococcin machinery. Pediocin PA-1 carrying the lactococcin A leader or lactococcin A carrying that of pediocin PA-1 was poorly secreted when complemented with the pediocin PA-1 machinery, showing that the pediocin machinery is more specific for its bacteriocin substrate. Wild-type pre-pediocin and chimeric pre-pediocin were shown to be processed by the lactococcin machinery at or near the double-glycine cleavage site. These results show the potential of the lactococcin LcnC/LcnD machinery as a maturation system for peptides carrying double-glycine-type amino-terminal leaders.
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8
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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9
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Fallico V, Ross R, Fitzgerald G, McAuliffe O. Novel conjugative plasmids from the natural isolate Lactococcus lactis subspecies cremoris DPC3758: A repository of genes for the potential improvement of dairy starters. J Dairy Sci 2012; 95:3593-608. [DOI: 10.3168/jds.2011-5255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/10/2012] [Indexed: 11/19/2022]
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10
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Stoyanova LG, Ustyugova EA, Netrusov AI. Antibacterial metabolites of lactic acid bacteria: Their diversity and properties. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812030143] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Fundamental functionality: recent developments in understanding the structure–activity relationships of lantibiotic peptides. J Antibiot (Tokyo) 2010; 64:27-34. [DOI: 10.1038/ja.2010.136] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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McIntosh JA, Donia MS, Schmidt EW. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat Prod Rep 2009; 26:537-59. [PMID: 19642421 PMCID: PMC2975598 DOI: 10.1039/b714132g] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Ribosomally synthesized bacterial natural products rival the nonribosomal peptides in their structural and functional diversity. The last decade has seen substantial progress in the identification and characterization of biosynthetic pathways leading to ribosomal peptide natural products with new and unusual structural motifs. In some of these cases, the motifs are similar to those found in nonribosomal peptides, and many are constructed by convergent or even paralogous enzymes. Here, we summarize the major structural and biosynthetic categories of ribosomally synthesized bacterial natural products and, where applicable, compare them to their homologs from nonribosomal biosynthesis.
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Affiliation(s)
- John A. McIntosh
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
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13
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Sahl HG, Jack RW, Bierbaum G. Biosynthesis and Biological Activities of Lantibiotics with Unique Post-Translational Modifications. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1432-1033.1995.0827g.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Furgerson Ihnken LA, Chatterjee C, van der Donk WA. In vitro reconstitution and substrate specificity of a lantibiotic protease. Biochemistry 2008; 47:7352-63. [PMID: 18570436 DOI: 10.1021/bi800278n] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lacticin 481 is a lanthionine-containing bacteriocin (lantibiotic) produced by Lactococcus lactis subsp. lactis. The final steps of lacticin 481 biosynthesis are proteolytic removal of an N-terminal leader sequence from the prepeptide LctA and export of the mature lantibiotic. Both proteolysis and secretion are performed by the dedicated ATP-binding cassette (ABC) transporter LctT. LctT belongs to the family of AMS (ABC transporter maturation and secretion) proteins whose prepeptide substrates share a conserved double-glycine type cleavage site. The in vitro activity of a lantibiotic protease has not yet been characterized. This study reports the purification and in vitro activity of the N-terminal protease domain of LctT (LctT150), and its use for the in vitro production of lacticin 481. The G(-2)A(-1) cleavage site and several other conserved amino acid residues in the leader peptide were targeted by site-directed mutagenesis to probe the substrate specificity of LctT as well as shed light upon the role of these conserved residues in lantibiotic biosynthesis. His 10-LctT150 did not process most variants of the double glycine motif and processed mutants of Glu-8 only very slowly. Furthermore, incorporation of helix-breaking residues in the leader peptide resulted in greatly decreased proteolytic activity by His 10-LctT150. On the other hand, His 10-LctT150 accepted all peptides containing mutations in the propeptide or at nonconserved positions of LctA. In addition, the protease domain of LctT was investigated by site-directed mutagenesis of the conserved residues Cys12, His90, and Asp106. The proteolytic activities of the resulting mutant proteins are consistent with a cysteine protease.
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Affiliation(s)
- L A Furgerson Ihnken
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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15
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Martin NI, Breukink E. Expanding role of lipid II as a target for lantibiotics. Future Microbiol 2007; 2:513-25. [PMID: 17927474 DOI: 10.2217/17460913.2.5.513] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Lipid II is an essential cell-wall precursor required for the growth and replication of both Gram-positive and Gram-negative bacteria. Compounds that use lipid II to selectively target bacterial cells for destruction represent an important class of antibiotics. Clinically, vancomycin is the most important example of an antibiotic that operates in this manner. Despite being considered the 'antibiotic drug of last resort', significant bacterial resistance to vancomycin now manifests itself worldwide. In this paper we review recent progress made in understanding the lipid II-associated antibacterial characteristics of various naturally occurring compounds, with particular focus on the lantibiotic peptides.
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Affiliation(s)
- Nathaniel I Martin
- Utrecht University, Department of Medicinal Chemistry & Chemical Biology, 3584 CA Utrecht, The Netherlands.
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16
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Paul M, Patton GC, van der Donk WA. Mutants of the zinc ligands of lacticin 481 synthetase retain dehydration activity but have impaired cyclization activity. Biochemistry 2007; 46:6268-76. [PMID: 17480057 PMCID: PMC2517114 DOI: 10.1021/bi7000104] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lantibiotics are ribosomally synthesized and post-translationally modified peptide antibiotics. The modifications involve dehydration of Ser and Thr residues to generate dehydroalanines and dehydrobutyrines, followed by intramolecular attack of cysteines onto the newly formed dehydro amino acids to produce cyclic thioethers. LctM performs both processes during the biosynthesis of lacticin 481. Mutation of the zinc ligands Cys781 and Cys836 to alanine did not affect the dehydration activity of LctM. However, these mutations compromised cyclization activity when investigated with full length or truncated peptide substrates. Mutation of His725, another residue that is fully conserved in lantibiotic cyclases, to Asn resulted in a protein that still catalyzed dehydration of the substrate peptide and also retained cyclization activity, but at a decreased level compared to that of the wild type enzyme. Collectively, these results show that the C-terminal domain of LctM is responsible for cyclization, that the zinc ligands are critical for cyclization, and that dehydration takes place independently from the cyclization activity. Furthermore, these mutant proteins are excellent dehydratases and provide useful tools to investigate the dehydration activity as well as generate dehydrated peptides for study of the cyclization reaction by wild type LctM.
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17
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You YO, van der Donk WA. Mechanistic investigations of the dehydration reaction of lacticin 481 synthetase using site-directed mutagenesis. Biochemistry 2007; 46:5991-6000. [PMID: 17455908 PMCID: PMC2517115 DOI: 10.1021/bi602663x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lantibiotic synthetases catalyze the dehydration of Ser and Thr residues in their peptide substrates to dehydroalanine (Dha) and dehydrobutyrine (Dhb), respectively, followed by the conjugate addition of Cys residues to the Dha and Dhb residues to generate the thioether cross-links lanthionine and methyllanthionine, respectively. In this study ten conserved residues were mutated in the dehydratase domain of the best characterized family member, lacticin 481 synthetase (LctM). Mutation of His244 and Tyr408 did not affect dehydration activity with the LctA substrate whereas mutation of Asn247, Glu261, and Glu446 considerably slowed down dehydration and resulted in incomplete conversion. Mutation of Lys159 slowed down both steps of the net dehydration: phosphorylation of Ser/Thr residues and the subsequent phosphate elimination step to form the dehydro amino acids. Mutation of Arg399 to Met or Leu resulted in mutants that had phosphorylation activity but displayed greatly decreased phosphate elimination activity. The Arg399Lys mutant retained both activities, however. Similarly, the Thr405Ala mutant phosphorylated the LctA substrate but had compromised elimination activity. Finally, mutation of Asp242 or Asp259 to Asn led to mutant enzymes that lacked detectable dehydration activity. Whereas the Asp242Asn mutant retained phosphate elimination activity, the Asp259Asn mutant was not able to eliminate phosphate from a phosphorylated substrate peptide. A model is presented that accounts for the observed phenotypes of these mutant enzymes.
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Affiliation(s)
- Young Ok You
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois, telephone (217) 244 5360, FAX (217) 244 8533
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois, telephone (217) 244 5360, FAX (217) 244 8533
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, Illinois, telephone (217) 244 5360, FAX (217) 244 8533
- To whom correspondence should be addressed. Phone: (217) 244-5360 FAX (217) 244 8024 E-mail:
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18
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Chatterjee C, Patton GC, Cooper L, Paul M, van der Donk WA. Engineering dehydro amino acids and thioethers into peptides using lacticin 481 synthetase. ACTA ACUST UNITED AC 2006; 13:1109-17. [PMID: 17052615 DOI: 10.1016/j.chembiol.2006.08.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 08/23/2006] [Accepted: 08/23/2006] [Indexed: 11/28/2022]
Abstract
Lantibiotics are peptide antimicrobials containing the thioether-bridged amino acids lanthionine (Lan) and methyllanthionine (MeLan) and often the dehydrated residues dehydroalanine (Dha) and dehydrobutyrine (Dhb). While biologically advantageous, the incorporation of these residues into peptides is synthetically daunting, and their production in vivo is limited to peptides containing proteinogenic amino acids. The lacticin 481 synthetase LctM offers versatile control over the installation of dehydro amino acids and thioether rings into peptides. In vitro processing of semisynthetic substrates unrelated to the prelacticin 481 peptide demonstrated the broad substrate tolerance of LctM. Furthermore, a chemoenzymatic strategy was employed to generate novel thioether linkages by cyclization of peptidic substrates containing the nonproteinogenic cysteine analogs homocysteine and beta-homocysteine. These findings are promising with respect to the utility of LctM toward preparation of conformationally constrained peptide therapeutics.
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Affiliation(s)
- Champak Chatterjee
- Department of Chemistry and University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
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19
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Dufour A, Hindré T, Haras D, Le Pennec JP. The biology of lantibiotics from the lacticin 481 group is coming of age. FEMS Microbiol Rev 2006; 31:134-67. [PMID: 17096664 DOI: 10.1111/j.1574-6976.2006.00045.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lantibiotics are antimicrobial peptides from the bacteriocin family, secreted by Gram-positive bacteria. These peptides differ from other bacteriocins by the presence of (methyl)lanthionine residues, which result from enzymatic modification of precursor peptides encoded by structural genes. Several groups of lantibiotics have been distinguished, the largest of which is the lacticin 481 group. This group consists of at least 16 members, including lacticin 481, streptococcin A-FF22, mutacin II, nukacin ISK-1, and salivaricins. We present the first review devoted to this lantibiotic group, knowledge of which has increased significantly within the last few years. After updating the group composition and defining the common properties of these lantibiotics, we highlight the most recent developments. The latter concern: transcriptional regulation of the lantibiotic genes; understanding the biosynthetic machinery, in particular the ability to perform in vitro prepeptide maturation; characterization of a novel type of immunity protein; and broad application possibilities. This group differs in many aspects from the best known lantibiotic group (nisin group), but shares properties with less-studied groups such as the mersacidin, cytolysin and lactocin S groups.
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Affiliation(s)
- Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, EA3884, Université de Bretagne Sud, Lorient, France.
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20
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Cotter PD, Draper LA, Lawton EM, McAuliffe O, Hill C, Ross RP. Overproduction of wild-type and bioengineered derivatives of the lantibiotic lacticin 3147. Appl Environ Microbiol 2006; 72:4492-6. [PMID: 16751576 PMCID: PMC1489664 DOI: 10.1128/aem.02543-05] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lacticin 3147 is a broad-spectrum two-peptide lantibiotic whose genetic determinants are located on two divergent operons on the lactococcal plasmid pMRC01. Here we introduce each of 14 subclones, containing different combinations of lacticin 3147 genes, into MG1363 (pMRC01) and determine that a number of them can facilitate overproduction of the lantibiotic. Based on these studies it is apparent that while the provision of additional copies of genes encoding the biosynthetic/production machinery and the regulator LtnR is a requirement for high-level overproduction, the presence of additional copies of the structural genes (i.e., ltnA1A2) is not.
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Affiliation(s)
- Paul D Cotter
- Department of Microbiology, University College Cork, Cork, Ireland
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21
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Guardabassi L, Perichon B, van Heijenoort J, Blanot D, Courvalin P. Glycopeptide resistance vanA operons in Paenibacillus strains isolated from soil. Antimicrob Agents Chemother 2006; 49:4227-33. [PMID: 16189102 PMCID: PMC1251550 DOI: 10.1128/aac.49.10.4227-4233.2005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sequence and gene organization of the van operons in vancomycin (MIC of >256 microg/ml)- and teicoplanin (MIC of > or =32 microg/ml)-resistant Paenibacillus thiaminolyticus PT-2B1 and Paenibacillus apiarius PA-B2B isolated from soil were determined. Both operons had regulatory (vanR and vanS), resistance (vanH, vanA, and vanX), and accessory (vanY, vanZ, and vanW) genes homologous to the corresponding genes in enterococcal vanA and vanB operons. The vanA(PT) operon in P. thiaminolyticus PT-2B1 had the same gene organization as that of vanA operons whereas vanA(PA) in P. apiarius PA-B2B resembled vanB operons due to the presence of vanW upstream from the vanHAX cluster but was closer to vanA operons in sequence. Reference P. apiarius strains NRRL B-4299 and NRRL B-4188 were found to harbor operons indistinguishable from vanA(PA) by PCR mapping, restriction fragment length polymorphism, and partial sequencing, suggesting that this operon was species specific. As in enterococci, resistance was inducible by glycopeptides and associated with the synthesis of pentadepsipeptide peptidoglycan precursors ending in D-Ala-D-Lac, as demonstrated by D,D-dipeptidase activities, high-pressure liquid chromatography, and mass spectrometry. The precursors differed from those in enterococci by the presence of diaminopimelic acid instead of lysine in the peptide chain. Altogether, the results are compatible with the notion that van operons in soil Paenibacillus strains and in enterococci have evolved from a common ancestor.
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Affiliation(s)
- Luca Guardabassi
- Unité des Agents Antibactériens, Institut Pasteur, Paris, France.
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22
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Nagao JI, Harada Y, Shioya K, Aso Y, Zendo T, Nakayama J, Sonomoto K. Lanthionine introduction into nukacin ISK-1 prepeptide by co-expression with modification enzyme NukM in Escherichia coli. Biochem Biophys Res Commun 2005; 336:507-13. [PMID: 16143300 DOI: 10.1016/j.bbrc.2005.08.125] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2005] [Accepted: 08/17/2005] [Indexed: 11/20/2022]
Abstract
We demonstrated lanthionine introduction into hexa-histidine-tagged (His-tagged) nukacin ISK-1 prepeptide NukA by modification enzyme NukM in Escherichia coli. Co-expression of nukA and nukM, purification of the resulting His-tagged prepeptide by affinity chromatography, and subsequent mass spectrometry analysis showed that the prepeptide was converted into a postulated peptide with decrease in mass of 72Da which resulted from dehydration of four amino acids. Characterization of the resultant prepeptide indicated the presence of unusual amino acids, such as dehydrated amino acid, lanthionine or 3-methyllanthionine, in its C-terminal propeptide moiety. The modified prepeptide encompassing the leader peptide attached to the post-translationally modified propeptide moiety was readily obtained by one-step purification. Our findings will thus be a powerful tool for introducing unusual amino acids aimed at peptide engineering and also helpful to provide new insight for further understanding of lanthionine-forming enzymes for lantibiotics.
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Affiliation(s)
- Jun-Ichi Nagao
- Laboratory of Microbial Technology, Division of Microbial Science and Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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23
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Madsen SM, Hindré T, Le Pennec JP, Israelsen H, Dufour A. Two acid-inducible promoters from Lactococcus lactis require the cis-acting ACiD-box and the transcription regulator RcfB. Mol Microbiol 2005; 56:735-46. [PMID: 15819628 DOI: 10.1111/j.1365-2958.2005.04572.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously characterized three Lactococcus lactis promoters, P170, P1 and P3, which are induced by low pH. Here, we identified a novel 14 bp regulatory DNA region centred at around -41.5 and composed of three tetranucleotide sequences, boxes A, C and D. Boxes A and C contribute to P1 activity, whereas box D and the position of boxes ACD (renamed ACiD-box) are essential to P1 activity and acid response. We also identified a trans -acting protein, RcfB, which is involved in P170 and P1 basal activity and is essential for their pH induction. The regulator belongs to the Crp-Fnr family of transcription regulators. Overexpression of rcfB resulted in increased beta-galactosidase activities and lantibiotic lacticin 481 production from P170- and P1-controlled genes, respectively, in acid condition. RcfB is thus probably activated when cells encounter an acid environment. rcfB is co-transcribed with genes encoding an universal stress-like protein and a multidrug transporter. RcfB plays a role in acid adaptation, as the survival rate of an rcfB mutant after a lethal acid challenge was 130-fold lower than that of the wild-type strain, when the bacteria were first grown in acidic medium. The groESL promoter includes a sequence resembling an ACiD-box and the chaperone GroEL production is partly RcfB dependent in acid condition. Our results suggest that the ACiD-box could be the DNA target site of RcfB.
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24
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Chatterjee C, Paul M, Xie L, van der Donk WA. Biosynthesis and mode of action of lantibiotics. Chem Rev 2005; 105:633-84. [PMID: 15700960 DOI: 10.1021/cr030105v] [Citation(s) in RCA: 563] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Champak Chatterjee
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, USA
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25
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Uguen P, Hindré T, Didelot S, Marty C, Haras D, Le Pennec JP, Vallée-Réhel K, Dufour A. Maturation by LctT is required for biosynthesis of full-length lantibiotic lacticin 481. Appl Environ Microbiol 2005; 71:562-5. [PMID: 15640237 PMCID: PMC544215 DOI: 10.1128/aem.71.1.562-565.2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In lantibiotic lacticin 481 biosynthesis, LctT cleaves the precursor peptide and exports mature lantibiotic. Matrix-assisted laser desorption ionization-time of flight mass spectrometry revealed that a truncated form of lacticin 481 is produced in the absence of LctT or after cleavage site inactivation. Production of truncated lacticin 481 is 4-fold less efficient, and its specific activity is about 10-fold lower.
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Affiliation(s)
- Patricia Uguen
- Laboratoire de Biotechnologie et Chimie Marines, EA 3884, Université de Bretagne Sud, BP 92116, 56321 Lorient Cedex, France
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26
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Papagianni M. Ribosomally synthesized peptides with antimicrobial properties: biosynthesis, structure, function, and applications. Biotechnol Adv 2004; 21:465-99. [PMID: 14499150 DOI: 10.1016/s0734-9750(03)00077-6] [Citation(s) in RCA: 173] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ribosomally synthesized peptides with antimicrobial properties (antimicrobial peptides-AMPs) are produced by eukaryotes and prokaryotes and represent crucial components of their defense systems against microorganisms. Although they differ in structure, they are nearly all cationic and very often amphiphilic, which reflects the fact that many of them attack their target cells by permeabilizing the cell membrane. They can be roughly categorized into those that have a high content of a certain amino acid, most often proline, those that contain intramolecular disulfide bridges, and those with an amphiphilic region in their molecule if they assume an alpha-helical structure. Most of the known ribosomally synthesized peptides with antimicrobial functions have been identified and studied during the last 20 years. As a result of these studies, new knowledge has been acquired into biology and biochemistry. It has become evident that these peptides may be developed into useful antimicrobial additives and drugs. The use of two-peptide antimicrobial peptides as replacement for clinical antibiotics is promising, though their applications in preservation of foods (safe and effective for use in meat, vegetables, and dairy products), in veterinary medicine, and in dentistry are more immediate. This review focuses on the current status of some of the main types of ribosomally synthesized AMPs produced by eucaryotes and procaryotes and discusses the novel antimicrobial functions, new developments, e.g. heterologous production of bacteriocins by lactic acid bacteria, or construction of multibacteriocinogenic strains, novel applications related to these peptides, and future research paradigms.
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Affiliation(s)
- Maria Papagianni
- Department of Hygiene and Technology of Food of Animal Origin, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54006, Greece.
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27
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Hindré T, Le Pennec JP, Haras D, Dufour A. Regulation of lantibiotic lacticin 481 production at the transcriptional level by acid pH. FEMS Microbiol Lett 2004; 231:291-8. [PMID: 14987777 DOI: 10.1016/s0378-1097(04)00010-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Revised: 12/17/2003] [Accepted: 12/29/2003] [Indexed: 10/26/2022] Open
Abstract
The lantibiotic lacticin 481 operon (lctAMTFEG) is mainly transcribed from P1 and P3, two promoters lying upstream of lctA. A weak additional promoter allows independent expression of the immunity genes (lctFEG). Lacticin 481 production by Lactococcus lactis is stimulated by the acidification due to lactic acid production, and by artificially lowering the pH of the medium. This regulation occurs at the transcriptional level, since P1 and P3 are both acid-induced. P1 is weaker but more tightly regulated than P3. As no specific regulator is encoded by the lacticin 481 operon, P1 and P3 are likely controlled by a general regulator.
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Affiliation(s)
- Thomas Hindré
- Laboratoire de Biologie et Chimie Moléculaires, EA 2594, Université de Bretagne Sud, P.O. Box 92116, 56321 Lorient, France
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28
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Aso Y, Nagao JI, Koga H, Okuda KI, Kanemasa Y, Sashihara T, Nakayama J, Sonomoto K. Heterologous expression and functional analysis of the gene cluster for the biosynthesis of and immunity to the lantibiotic, nukacin ISK-1. J Biosci Bioeng 2004; 98:429-36. [PMID: 16233732 DOI: 10.1016/s1389-1723(05)00308-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2004] [Accepted: 09/11/2004] [Indexed: 11/18/2022]
Abstract
Nukacin ISK-1 is a lantibiotic produced by Staphylococcus warneri ISK-1. The gene cluster of nukacin ISK-1 consists of at least nukAMTFEG, ORF1 and ORF7. In this study, we demonstrated the heterologous production of nukacin ISK-1 in Lactococcus lactis by the artificial polycistronic expression of nukAMTFEG-ORF7 under the control of the nisin-controlled expression (NICE) system. Consequently, the recombinant L. lactis showed antimicrobial activity. Mass analysis clarified the presence of nukacin ISK-1 produced in the culture supernatant. These results suggested that the recombinant L. lactis produced nukacin ISK-1 heterologously. Inactivation of nukA, -M or -T resulted in the complete loss of the nukacin ISK-1 production phenotype. This finding suggested that nukAMT are indispensably associated with the biosynthesis of nukacin ISK-1. To our knowledge, this is the first report of the heterologous production of lantibiotic using the NICE system.
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Affiliation(s)
- Yuji Aso
- Laboratory of Microbial Technology, Division of Microbial Science and Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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29
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O'Sullivan L, Ryan MP, Ross RP, Hill C. Generation of food-grade lactococcal starters which produce the lantibiotics lacticin 3147 and lacticin 481. Appl Environ Microbiol 2003; 69:3681-5. [PMID: 12788782 PMCID: PMC161475 DOI: 10.1128/aem.69.6.3681-3685.2003] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2002] [Accepted: 02/25/2003] [Indexed: 11/20/2022] Open
Abstract
Transconjugant lactococcal starters which produce both lantibiotics lacticin 3147 and lacticin 481 were generated via conjugation of large bacteriocin-encoding plasmids. A representative of one of the resultant strains proved more effective at killing Lactobacillus fermentum and inhibiting the growth of Listeria monocytogenes LO28H than either of the single bacteriocin-producing parental strains, demonstrating the potential of these transconjugants as protection cultures for food safety applications.
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Affiliation(s)
- Lisa O'Sullivan
- Dairy Products Research Centre, Teagasc, Moorepark, Fermoy, County Cork, Republic of Ireland
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30
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Corvey C, Stein T, Düsterhus S, Karas M, Entian KD. Activation of subtilin precursors by Bacillus subtilis extracellular serine proteases subtilisin (AprE), WprA, and Vpr. Biochem Biophys Res Commun 2003; 304:48-54. [PMID: 12705882 DOI: 10.1016/s0006-291x(03)00529-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide. To identify subtilin processing activities, we used antimicrobial inactive subtilin precursors consisting of the leader peptide which was still attached to the fully matured propeptide. Two extracellular B. subtilis proteases were able to activate subtilin precursors, the commercially available serine protease prototype subtilisin (AprE) and WprA. The latter was isolated from B. subtilis WB600, a strain deficient in six extracellular proteases. Surprisingly, the aprE wprA double mutant of the ATCC 6633 strain was still able to produce active subtilin, however, with a reduced production rate. No subtilin processing was found within the culture supernatant of the WB800 strain, which is deficient in eight extracellular proteases. Vpr was identified as the third protease capable to process subtilin.
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Affiliation(s)
- Carsten Corvey
- Institut für Pharmazeutische Chemie, Johann Wolfgang Goethe-Universität, Marie-Curie-Str. 9-11, 60439, Frankfurt/M, Germany
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31
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Hindré T, Didelot S, Le Pennec JP, Haras D, Dufour A, Vallée-Réhel K. Bacteriocin detection from whole bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 2003; 69:1051-8. [PMID: 12571028 PMCID: PMC143663 DOI: 10.1128/aem.69.2.1051-1058.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Class I bacteriocins (lantibiotics) and class II bacteriocins are antimicrobial peptides secreted by gram-positive bacteria. Using two lantibiotics, lacticin 481 and nisin, and the class II bacteriocin coagulin, we showed that bacteriocins can be detected without any purification from whole producer bacteria grown on plates by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS). When we compared the results of MALDI-TOF-MS performed with samples of whole cells and with samples of crude supernatants of liquid cultures, the former samples led to more efficient bacteriocin detection and required less handling. Nisin and lacticin 481 were both detected from a mixture of their producer strains, but such a mixture can yield additional signals. We used this method to determine the masses of two lacticin 481 variants, which confirmed at the peptide level the effect of mutations in the corresponding structural gene.
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Affiliation(s)
- Thomas Hindré
- Laboratoire de Biologie et Chimie Moléculaires, EA 2594, Université de Bretagne Sud, 56321 Lorient, France
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32
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Abstract
Preservation of food and beverages resulting from fermentation has been an effective form of extending the shelf-life of foods for millennia. Traditionally, foods were preserved through naturally occurring fermentations, however, modern large scale production generally now exploits the use of defined strain starter systems to ensure consistency and quality in the final product. This review will mainly focus on the use of lactic acid bacteria (LAB) for food improvement, given their extensive application in a wide range of fermented foods. These microorganisms can produce a wide variety of antagonistic primary and secondary metabolites including organic acids, diacetyl, CO2 and even antibiotics such as reuterocyclin produced by Lactobacillus reuteri. In addition, members of the group can also produce a wide range of bacteriocins, some of which have activity against food pathogens such as Listeria monocytogenes and Clostridium botulinum. Indeed, the bacteriocin nisin has been used as an effective biopreservative in some dairy products for decades, while a number of more recently discovered bacteriocins, such as lacticin 3147, demonstrate increasing potential in a number of food applications. Both of these lactococcal bacteriocins belong to the lantibiotic family of posttranslationally modified bacteriocins that contain lanthionine, beta-methyllanthionine and dehydrated amino acids. The exploitation of such naturally produced antagonists holds tremendous potential for extension of shelf-life and improvement of safety of a variety of foods.
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O'Sullivan L, Morgan SM, Ross RP, Hill C. Elevated enzyme release from lactococcal starter cultures on exposure to the lantibiotic lacticin 481, produced by Lactococcus lactis DPC5552. J Dairy Sci 2002; 85:2130-40. [PMID: 12362444 DOI: 10.3168/jds.s0022-0302(02)74291-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A Lactococcus lactis subsp. lactis strain (DPC5552), which causes the lysis of other lactococcal cultures, was isolated during a screening of raw milk samples for bacteriocin producers. Purification of the bacteriocin produced revealed that production of the lantibiotic, lacticin 481, was associated with the bacteriolytic capability of the strain. However, unlike bacteriocin-induced lysis observed with bacteriocins such as lacticin 3147 and lactococcins A, B, and M (where the target strain is killed), the DPC5552 supernatant gave rise to a situation whereby the target strain continued to grow (albeit at a lower rate) with simultaneous release of the intracellular enzymes lactate dehydrogenase (LDH) and post-proline dipeptidyl aminopeptidase (Pep X). In parallel experiments, 32 AU/ml of the inhibitory activity from L. lactis DPC5552 resulted in a 10- and 6-fold-higher LDH release after 5 h than that with 32 AU/ml of either lacticin 3147 or lactococcin A, B, and M. Laboratory-scale Cheddar cheese-making trials also demonstrated that lacticin 481-producing cultures induced the release of elevated levels of LDH from the starter L. lactis HP, without severely compromising its acid-producing capabilities. These results indicate that lacticin 481-producing strains may provide improved adjuncts for delivering lactococcal intracellular enzymes into the cheese matrix and, thus, improve cheese quality and flavor.
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Affiliation(s)
- L O'Sullivan
- Dairy Products Research Centre, Teagasc, Moorepark, Fermoy, County Cork, Republic of Ireland
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Mills S, Coffey A, O'Sullivan L, Stokes D, Hill C, Fitzgerald GF, Ross RP. Use of lacticin 481 to facilitate delivery of the bacteriophage resistance plasmid, pCBG104 to cheese starters. J Appl Microbiol 2002; 92:238-46. [PMID: 11849351 DOI: 10.1046/j.1365-2672.2002.01527.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS Use of lacticin 481 to facilitate the conjugal transfer of the bacteriophage resistance plasmid pCBG104 to various starter cultures. METHODS AND RESULTS A raw milk isolate of Lactococcus was found to harbour determinants for lacticin 481 production and immunity and phage resistance on a plasmid designated pCBG104. The lacticin 481 was successfully used to mobilize the phage resistance determinant to a variety of cheese starters enabling the formation of highly phage resistant starters. In addition, it facilitated the stacking of a number of phage resistance genes, namely a type I restriction modification system, a phage abortive infection system and a phage adsorption blocking system in a single Lactococcus strain without the use of recombinant techniques. The transconjugants were all shown to produce lacticin 481 and to contain the entire 481 operon. Subsequently one transconjugant was selected and successfully used for large-scale cheddar cheese manufacture. CONCLUSIONS Lacticin 481 could be used as a food-grade selectable marker to facilitate the introduction of advantageous traits to starter cultures for industrial food fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY Food-grade selectable markers greatly facilitate the introduction of various advantageous traits to starter cultures for industrial food fermentation. Indeed self-cloning which is becoming increasingly important for strain improvement has a requirement for the identification and demonstration of the utility of tools such as lacticin 481.
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Affiliation(s)
- S Mills
- TEAGASC Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork, Ireland, Department of Microbiology, University College, Cork, Ireland
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35
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Stein T, Borchert S, Conrad B, Feesche J, Hofemeister B, Hofemeister J, Entian KD. Two different lantibiotic-like peptides originate from the ericin gene cluster of Bacillus subtilis A1/3. J Bacteriol 2002; 184:1703-11. [PMID: 11872722 PMCID: PMC134901 DOI: 10.1128/jb.184.6.1703-1711.2002] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A lantibiotic gene cluster was identified in Bacillus subtilis A1/3 showing a high degree of homology to the subtilin gene cluster and occupying the same genetic locus as the spa genes in B. subtilis ATCC 6633. The gene cluster exhibits diversity with respect to duplication of two subtilin-like genes which are separated by a sequence similar to a portion of a lanC gene. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analyses of B. subtilis A1/3 culture extracts confirmed the presence of two lantibiotic-like peptides, ericin S (3,442 Da) and ericin A (2,986 Da). Disruption of the lanB-homologous gene eriB resulted in loss of production of both peptides, demonstrating that they are processed in an eriB-dependent manner. Although precursors of ericins S and A show only 75% of identity, the matured lantibiotic-like peptides reveal highly similar physical properties; separation was only achieved after multistep, reversed-phase high-performance liquid chromatography. Based on Edman and peptidase degradation in combination with MALDI-TOF MS, for ericin S a subtilin-like, lanthionine-bridging pattern is supposed. For ericin A two C-terminal rings are different from the lanthionine pattern of subtilin. Due to only four amino acid exchanges, ericin S and subtilin revealed similar antibiotic activities as well as similar properties in response to heat and protease treatment. For ericin A only minor antibiotic activity was found.
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Affiliation(s)
- Torsten Stein
- Institut für Mikrobiologie, Johann-Wolfgang-Goethe-Universität, D-60439 Frankfurt am Main, Germany
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36
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Abstract
Lacticin 481 is produced by Lactococcus lactis subsp. lactis and belongs to subgroup AII of the lanthionine-containing bacteriocins. The putative homodimeric LctT involved in lacticin 481 production shares significant similarities with the 'LcnC' protein encoded by 'lcnC', located on the chromosome of the lactic acid bacterium, L. lactis IL1403. LctT and 'LcnC' belong to the recently defined family of AMS (ABC transporter maturation and secretion) proteins. Inactivation of the 'lcnC' gene demonstrates that it is not responsible for the weak lacticin 481 production observed in a strain expressing only the precursor peptide LctA, and the modification enzyme LctM. This result indicates that the two AMS proteins, 'LcnC' and LctT, are not interchangeable in the machinery of processing/export of lacticin 481.
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Affiliation(s)
- Marilyne Uguen
- Laboratoire de Biologie et Chimie Moléculaires, EA 2594, Université de Bretagne Sud, Centre de Recherche Yves Coppens, P.O. Box 573, 56017, Vannes, France
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37
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Skaugen M, Andersen EL, Christie VH, Nes IF. Identification, characterization, and expression of a second, bicistronic, operon involved in the production of lactocin S in Lactobacillus sakei L45. Appl Environ Microbiol 2002; 68:720-7. [PMID: 11823212 PMCID: PMC126710 DOI: 10.1128/aem.68.2.720-727.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Through the analysis of spontaneous insertion mutants of Lactobacillus sakei L45, a second operon involved in lactocin S production was identified and characterized. The new, bicistronic unit, termed lasXY, is situated immediately upstream of the previously characterized nine-open reading frame (ORF) lactocin S operon (lasA-W) and is transcribed in the opposite direction. The proximal of the two newly identified genes, lasX, specifies a 285-residue protein that is similar to a group of proteins with reported gene regulation functions in gram-positive bacteria. It was demonstrated that the lasX mutants have a strongly reduced level of lasA and lasA-W mRNA, thus indicating the likely cause of the Bac(-) phenotype of these mutants. The second ORF in the operon, lasY, specifies a 300-residue ABC transporter homolog, the function of which is currently obscure. Transcription initiation mapping of the lasXY operon demonstrates that the two lactocin S promoters overlap such that both transcripts initiate within the -35 region of the oppositely oriented promoter. This organization of promoters is unique among this group of regulons and may constitute a modulatory site in the proposed LasX-dependent expression of lasA and downstream genes.
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Affiliation(s)
- Morten Skaugen
- Laboratory of Microbial Gene Technology, Agricultural University of Norway, P.O. Box 5051, N-1432 As-NLH, Norway.
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38
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Kleerebezem M, Quadri LE. Peptide pheromone-dependent regulation of antimicrobial peptide production in Gram-positive bacteria: a case of multicellular behavior. Peptides 2001; 22:1579-96. [PMID: 11587786 DOI: 10.1016/s0196-9781(01)00493-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Quorum sensing enables unicellular organisms to behave in a multicellular way by allowing population-wide synchronized adaptive responses that involve modulation of a wide range of physiological responses in a cell density-, cell proximity- or growth phase-dependent manner. Examples of processes modulated by quorum sensing are the development of genetic competence, conjugative plasmid transfer, sporulation and cell differentiation, biofilm formation, virulence response, production of antibiotics, antimicrobial peptides and toxins, and bioluminescence (for reviews see [38]). The cell-to-cell communication strategies involved in these processes are based on the utilization of small signal molecules produced and released into the environment by the microorganisms. These communication molecules are referred to as pheromones and act as chemical messengers that transmit information across space. The extracellular pheromones accumulate in the environment and trigger a response in the target cells when its concentration reaches a certain threshold value. Elucidation of the chemical nature of the pheromones modulating the processes mentioned above reveals that most of them are unmodified peptides, post-translationally modified peptides, N-acyl homoserine lactones, or butyrolactones. Lactone-based pheromones are the preferred communication signals in Gram-negative bacteria (for review see [47,48]), whereas peptide-based pheromones are the predominant extracellular signals among Gram-positive bacteria (for review see [37,61]). However, lactone-based pheromones are utilized as signals that modulate differentiation and secondary metabolism production in Streptomyces (for review see [20]). This review focuses on the major advances and current views of the peptide-pheromone dependent regulatory circuits involved in production of antimicrobial peptides in Gram-positive bacteria.
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Affiliation(s)
- M Kleerebezem
- Wageningen Centre for Food Sciences, The Netherlands.
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39
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Upton M, Tagg JR, Wescombe P, Jenkinson HF. Intra- and interspecies signaling between Streptococcus salivarius and Streptococcus pyogenes mediated by SalA and SalA1 lantibiotic peptides. J Bacteriol 2001; 183:3931-8. [PMID: 11395456 PMCID: PMC95275 DOI: 10.1128/jb.183.13.3931-3938.2001] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus salivarius 20P3 produces a 22-amino-acid residue lantibiotic, designated salivaricin A (SalA), that inhibits the growth of a range of streptococci, including all strains of Streptococcus pyogenes. Lantibiotic production is associated with the sal genetic locus comprising salA, the lantibiotic structural gene; salBCTX genes encoding peptide modification and export machinery proteins; and salYKR genes encoding a putative immunity protein and two-component sensor-regulator system. Insertional inactivation of salB in S. salivarius 20P3 resulted in abrogation of SalA peptide production, of immunity to SalA, and of salA transcription. Addition of exogenous SalA peptide to salB mutant cultures induced dose-dependent expression of salA mRNA (0.2 kb), demonstrating that SalA production was normally autoregulated. Inactivation of salR encoding the response regulator of the SalKR two-component system led to reduced production of, and immunity to, SalA. The sal genetic locus was also present in S. pyogenes SF370 (M type 1), but because of a deletion across the salBCT genes, the corresponding lantibiotic peptide, designated SalA1, was not produced. However, in S. pyogenes T11 (M type 4) the sal locus gene complement was apparently complete, and active SalA1 peptide was synthesized. Exogenously added SalA1 peptide from S. pyogenes T11 induced salA1 transcription in S. pyogenes SF370 and in an isogenic S. pyogenes T11 salB mutant and salA transcription in S. salivarius 20P3 salB. Thus, SalA and SalA1 are examples of streptococcal lantibiotics whose production is autoregulated. These peptides act as intra- and interspecies signaling molecules, modulating lantibiotic production and possibly influencing streptococcal population ecology in the oral cavity.
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Affiliation(s)
- M Upton
- Department of Oral and Dental Science, University of Bristol Dental School, Bristol, BS1 2LY, United Kingdom
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40
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Abstract
The lantibiotics are a group of ribosomally synthesised, post-translationally modified peptides containing unusual amino acids, such as dehydrated and lanthionine residues. This group of bacteriocins has attracted much attention in recent years due to the success of the well characterised lantibiotic, nisin, as a food preservative. Numerous other lantibiotics have since been identified and can be divided into two groups on the basis of their structures, designated type-A and type-B. To date, many of these lantibiotics have undergone extensive characterisation resulting in an advanced understanding of them at both the structural and mechanistic level. This review outlines some of the more recent developments in the biochemistry, genetics and mechanism of action of these peptides.
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Affiliation(s)
- O McAuliffe
- Department of Microbiology, University College Cork, Ireland
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41
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Sablon E, Contreras B, Vandamme E. Antimicrobial peptides of lactic acid bacteria: mode of action, genetics and biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2001; 68:21-60. [PMID: 11036685 DOI: 10.1007/3-540-45564-7_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A survey is given of the main classes of bacteriocins, produced by lactic acid bacteria: I. lantibiotics II. small heat-stable non-lanthionine containing membrane-active peptides and III. large heat-labile proteins. First, their mode of action is detailed, with emphasis on pore formation in the cytoplasmatic membrane. Subsequently, the molecular genetics of several classes of bacteriocins are described in detail, with special attention to nisin as the most prominent example of the lantibiotic-class. Of the small non-lanthionine bacteriocin class, the Lactococcus lactococcins, and the Lactobacillus sakacin A and plantaricin A-bacteriocins are discussed. The principles and mechanisms of immunity and resistance towards bacteriocins are also briefly reported. The biosynthesis of bacteriocins is treated in depth with emphasis on response regulation, post-translational modification, secretion and proteolytic activation of bacteriocin precursors. To conclude, the role of the leader peptides is outlined and a conceptual model for bacteriocin maturation is proposed.
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Affiliation(s)
- E Sablon
- Innogenetics N.V., Ghent, Belgium
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42
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Dufour A, Rincé A, Uguen P, Le Pennec JP. IS1675, a novel lactococcal insertion element, forms a transposon-like structure including the lacticin 481 lantibiotic operon. J Bacteriol 2000; 182:5600-5. [PMID: 10986268 PMCID: PMC111008 DOI: 10.1128/jb.182.19.5600-5605.2000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two copies of IS1675, a novel lactococcal insertion element from the IS4 family, are present on a 70-kb plasmid, where they frame the lantibiotic lacticin 481 operon. The whole structure could be a composite transposon designated Tn5721. This study shows that the lacticin 481 operon does not include any regulatory gene and provides a new example of a transposon-associated bacteriocin determinant. We identified five other IS1675 copies not associated with the lacticin 481 operon. The conservation of IS1675 flanking sequences suggested a 24-bp target site.
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Affiliation(s)
- A Dufour
- Laboratoire de Biologie et Chimie Moléculaires, EA 2594, Université de Bretagne Sud, Vannes, France.
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43
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McAuliffe O, Hill C, Ross RP. Each peptide of the two-component lantibiotic lacticin 3147 requires a separate modification enzyme for activity. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 9):2147-2154. [PMID: 10974102 DOI: 10.1099/00221287-146-9-2147] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genetic determinants for production and immunity to the two-component lantibiotic lacticin 3147 are encoded by a 12.6 kb region of the plasmid pMRC01. This region contains ten genes arranged in two divergent clusters; these include the structural genes and a number of genes whose products show significant similarity to proteins involved in the biosynthesis of other lantibiotics. Using a strategy of deletion and mutational analysis, the effect of disruption of a number of these genes was investigated. Inactivation of either of the structural genes, ltnA1 or ltnA2, resulted in mutants that were incapable of producing active lacticin 3147; however, the combination of the cell-free supernatant from both mutants resulted in a restoration of bacteriocin activity, confirming that processing and export of the structural peptides can occur independently. An unusual feature of the lacticin 3147 gene cluster is the presence of two lanM homologues, whose gene products are proposed to be involved in the dehydration and thioether-forming reactions which result in lanthionine bridge formation. Mutants created in the ltnM1 and ltnM2 genes were also incapable of lantibiotic production, confirming an essential role for these enzymes in the lacticin 3147 biosynthetic pathway and supporting the assertion that these proteins are modification enzymes. Interestingly, addition of purified LtnA1, but not purified LtnA2, to the cell-free supernatant of the ltnM1 mutant restored bacteriocin activity; in contrast, only purified LtnA2 could complement the cell-free supernatant of the ltnM2 mutant. Creation of a number of double mutants supported these findings, and confirmed that LtnM1 is required to produce mature LtnA1, while LtnM2 is required to produce mature LtnA2.
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Affiliation(s)
- Olivia McAuliffe
- Department of Microbiology and National Food Biotechnology Centre, University College Cork, Ireland1
| | - Colin Hill
- Department of Microbiology and National Food Biotechnology Centre, University College Cork, Ireland1
| | - R Paul Ross
- National Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork, Ireland2
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44
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Uguen P, Le Pennec JP, Dufour A. Lantibiotic biosynthesis: interactions between prelacticin 481 and its putative modification enzyme, LctM. J Bacteriol 2000; 182:5262-6. [PMID: 10960114 PMCID: PMC94678 DOI: 10.1128/jb.182.18.5262-5266.2000] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2000] [Accepted: 06/21/2000] [Indexed: 11/20/2022] Open
Abstract
Class AII and AIII lantibiotics and mersacidin are antibacterial peptides containing unusual residues obtained by posttranslational modifications of prepeptides, presumably catalyzed by LanM. LctM, the LanM for lacticin 481, is essential for the production of this class AII lantibiotic. Using the yeast two-hybrid system, we showed direct contact between the prelacticin 481 and LctM, supporting the proposed LctM function. Sixteen domains are conserved between the 10 known LanM proteins, whereas three additional domains were found only in class AII LanM proteins and in MrsM, the LanM for mersacidin. All the truncated LctM proteins that we tested presented impaired LctA-binding activity.
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Affiliation(s)
- P Uguen
- Laboratoire de Biologie et Chimie Moléculaires, Université de Bretagne Sud, Vannes, France
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45
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Qi F, Chen P, Caufield PW. Purification and biochemical characterization of mutacin I from the group I strain of Streptococcus mutans, CH43, and genetic analysis of mutacin I biosynthesis genes. Appl Environ Microbiol 2000; 66:3221-9. [PMID: 10919773 PMCID: PMC92137 DOI: 10.1128/aem.66.8.3221-3229.2000] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously, we reported isolation and characterization of mutacin III and genetic analysis of mutacin III biosynthesis genes from the group III strain of Streptococcus mutans, UA787 (F. Qi, P. Chen, and P. W. Caufield, Appl. Environ. Microbiol. 65:3880-3887, 1999). During the same process of isolating the mutacin III structural gene, we also cloned the structural gene for mutacin I. In this report, we present purification and biochemical characterization of mutacin I from the group I strain CH43 and compare mutacin I and mutacin III biosynthesis genes. The mutacin I biosynthesis gene locus consists of 14 genes in the order mutR, -A, -A', -B, -C, -D, -P, -T, -F, -E, -G, orfX, orfY, orfZ. mutA is the structural gene for mutacin I, while mutA' is not required for mutacin I activity. DNA and protein sequence analysis revealed that mutacins I and III are homologous to each other, possibly arising from a common ancestor. The mature mutacin I is 24 amino acids in size and has a molecular mass of 2, 364 Da. Ethanethiol modification and peptide sequencing of mutacin I revealed that it contains six dehydrated serines, four of which are probably involved with thioether bridge formation. Comparison of the primary sequence of mutacin I with that of mutacin III and epidermin suggests that mutacin I likely has the same bridging pattern as epidermin.
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Affiliation(s)
- F Qi
- Department of Oral Biology, School of Dentistry, University of Alabama at Birmingham, 35294, USA.
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46
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Altena K, Guder A, Cramer C, Bierbaum G. Biosynthesis of the lantibiotic mersacidin: organization of a type B lantibiotic gene cluster. Appl Environ Microbiol 2000; 66:2565-71. [PMID: 10831439 PMCID: PMC110582 DOI: 10.1128/aem.66.6.2565-2571.2000] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biosynthetic gene cluster (12.3 kb) of mersacidin, a lanthionine-containing antimicrobial peptide, is located on the chromosome of the producer, Bacillus sp. strain HIL Y-85,54728 in a region that corresponds to 348 degrees on the chromosome of Bacillus subtilis 168. It consists of 10 open reading frames and contains, in addition to the previously described mersacidin structural gene mrsA (G. Bierbaum, H. Brötz, K.-P. Koller, and H.-G. Sahl, FEMS Microbiol. Lett. 127:121-126, 1995), two genes, mrsM and mrsD, coding for enzymes involved in posttranslational modification of the prepeptide; one gene, mrsT, coding for a transporter with an associated protease domain; and three genes, mrsF, mrsG, and mrsE, encoding a group B ABC transporter that could be involved in producer self-protection. Additionally, three regulatory genes are part of the gene cluster, i.e., mrsR2 and mrsK2, which encode a two-component regulatory system which seems to be necessary for the transcription of the mrsFGE operon, and mrsR1, which encodes a protein with similarity to response regulators. Transcription of mrsA sets in at early stationary phase (between 8 and 16 h of culture).
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Affiliation(s)
- K Altena
- Institut für Medizinische Mikrobiologie und Immunologie der Universität Bonn, D-53105 Bonn, Germany
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47
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Krull RE, Chen P, Novak J, Kirk M, Barnes S, Baker J, Krishna NR, Caufield PW. Biochemical structural analysis of the lantibiotic mutacin II. J Biol Chem 2000; 275:15845-50. [PMID: 10821848 DOI: 10.1074/jbc.275.21.15845] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutacin II is a post-translationally modified lantibiotic peptide secreted by Streptococcus mutans T8, which inhibits the energy metabolism of sensitive cells. The deduced amino acid sequence of promutacin II is NRWWQGVVPTVSYECRMNSWQHVFTCC, which is capable of forming three thioether bridges. It was not obvious, however, how the three thioether bridges are organized. To examine the bridging, the cyanogen bromide cleavage products of mutacin II and its variants generated by protein engineering, C15A, C26A, and C15A/C26A, were analyzed by mass spectrometry. Analysis of the wild type molecule and the C15A variant excluded several possibilities and also indicated a high fidelity of formation of the thioether bridges. This allowed us to further resolve the structure by analysis (mass spectrometry and tandem mass spectrometry) of the cyanogen bromide cleavage fragments of the C26A and C15A/C26A mutants. Nuclear magnetic resonance analysis established the presence of one and two dehydrobutyrine residues in mutacin II and the C15A variant, respectively, thus yielding the final structure. The results of this investigation showed that the C-terminal part contains three thioether bridges connecting Cys residues 15, 26, and 27 to Ser/Thr residues 10, 12 and 19, respectively, with Thr(25) being modified to dehydrobutyrine.
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Affiliation(s)
- R E Krull
- Department of Oral Biology, Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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48
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McAuliffe O, Hill C, Ross RP. Identification and overexpression of ltnl, a novel gene which confers immunity to the two-component lantibiotic lacticin 3147. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 1):129-138. [PMID: 10658659 DOI: 10.1099/00221287-146-1-129] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Production and immunity of the two-component lantibiotic lacticin 3147 is encoded by the 60-2 kb lactococcal plasmid pMRC01. A 12.6 kb region of this plasmid, containing ten genes in two divergently arranged gene clusters, has been subcloned in Lactococcus lactis subsp. cremoris MG1363 and has been shown to confer both lacticin 3147 production and immunity. Further subcloning revealed that the smaller of the two clusters (ItnRIFE) confers immunity. Although the ItnF and E genes are homologous to ABC transporters which confer immunity to other lantibiotics, deletion analysis indicates that they do not play a role in the immunity exhibited by this subclone in L. lactis subsp. cremoris MG1363. Also, a deletion in ItnR (which resembles a family of transcriptional repressors) had no effect on immunity. The remaining gene, Itnl, encodes a 116 amino acid protein with a predicted membrane location which bears no homology to other bacteriocin immunity proteins. Confirmation of its role in immunity was obtained when it was observed that disruption of Itnl resulted in a complete loss of immunity. When Itnl was cloned into the expression vector pMG36e, the resulting construct conferred levels of immunity comparable to pMRC01. This confirmed that under the control of a strong promoter, the Itnl gene product alone is sufficient to confer lacticin immunity. In addition, heterologous expression of Itnl was observed in Enterococcus faecalis OG1X. On cloning Itnl behind a nisin-inducible promoter, it was observed that the level of immunity was dependent on nisin concentration. Using this construct, the authors have demonstrated a potential role for Itnl as food-grade selectable marker. Thus, Ltnl appears to represent a new class of lantibiotic immunity proteins.
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Affiliation(s)
- Olivia McAuliffe
- Department of Microbiology and National Food Biotechnology Centre, University College Cork, Republic of Ireland1
| | - Colin Hill
- Department of Microbiology and National Food Biotechnology Centre, University College Cork, Republic of Ireland1
| | - R Paul Ross
- National Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork, Republic of Ireland2
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49
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Navaratna MA, Sahl HG, Tagg JR. Identification of genes encoding two-component lantibiotic production in Staphylococcus aureus C55 and other phage group II S. aureus strains and demonstration of an association with the exfoliative toxin B gene. Infect Immun 1999; 67:4268-71. [PMID: 10417203 PMCID: PMC96736 DOI: 10.1128/iai.67.8.4268-4271.1999] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The production of exfoliative toxin B (ET-B), but not ET-A, was shown to be specifically associated with production of a highly conserved two-component lantibiotic peptide system in phage group II Staphylococcus aureus. Two previously studied but incompletely characterized S. aureus bacteriocins, staphylococcins C55 and BacR1, were found to be members of this lantibiotic system, and considerable homology was also found with the two-component Lactococcus lactis bacteriocin, lacticin 3147. sacalphaA and sacbetaA, the structural genes of the lantibiotics staphylococcins C55alpha and C55beta and two putative lantibiotic processing genes, sacM1 and sacT, were localized together with the ET-B structural gene to a single 32-kb plasmid in strain C55. Irreversible loss of both ET-B and two-component lantibiotic production occurs during laboratory passage of ET-B-positive S. aureus strains, particularly at elevated temperatures.
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Affiliation(s)
- M A Navaratna
- Department of Microbiology, University of Otago, Dunedin, New Zealand
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50
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McLaughlin RE, Ferretti JJ, Hynes WL. Nucleotide sequence of the streptococcin A-FF22 lantibiotic regulon: model for production of the lantibiotic SA-FF22 by strains of Streptococcus pyogenes. FEMS Microbiol Lett 1999; 175:171-7. [PMID: 10386366 DOI: 10.1111/j.1574-6968.1999.tb13616.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Streptococcin A-FF22 (SA-FF22) is a type AII linear lantibiotic produced by Streptococcus pyogenes strain FF22. Sequence analysis of an approximate 10 kb region of DNA showed it to contain nine open reading frames arranged in three operons responsible for regulation, biosynthesis and immunity of SA-FF22. This region is organized similarly to the Lactococcus lactis lacticin 481 region, however, unlike lacticin 481, a two-component regulatory system is essential for SA-FF22 production. Located immediately downstream of the scn region is a putative transposase gene, the presence of which supports earlier data that indicated a mobile nature to this region.
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Affiliation(s)
- R E McLaughlin
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, USA
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