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A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins [article]

James T Morton, Stefan D Freed, Shaun W Lee, Iddo Friedberg
2015 arXiv   pre-print
We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: https://github.com/idoerg/BOA  ...  To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones.  ...  Acknowledgments We are grateful to Sean Eddy and Rob Finn for the use of the HMMER logo. Some images used in Figure 1 are reproduced from Wikimedia Commons under CC-BY 3.0 or 4.0 license.  ... 
arXiv:1510.06008v1 fatcat:7rc5ijuppvhi3abekutzvgpnvu

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg
2015 BMC Bioinformatics  
We also discover that several phyla have a strong preference for bacteriocin genes, suggesting distinct functions for this group of molecules. Software Availability: https://github.com/idoerg/BOA  ...  Results and conclusions: We provide a novel dataset of predicted bacteriocins and context genes.  ...  Acknowledgements We are grateful to Sean Eddy and Rob Finn for the use of the HMMER logo. Some images used in Fig. 1 are reproduced from Wikimedia Commons under CC-BY 3.0 or 4.0 license.  ... 
doi:10.1186/s12859-015-0792-9 pmid:26558535 pmcid:PMC4642626 fatcat:fi5cmh354ze23ojo6xqpvupipe

Circular and Leaderless Bacteriocins: Biosynthesis, Mode of Action, Applications, and Prospects

Rodney H. Perez, Takeshi Zendo, Kenji Sonomoto
2018 Frontiers in Microbiology  
RP is a JSPS International Fellow.  ...  ACKNOWLEDGMENTS The studies described here were supported in part by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS KAKENHI Grant Number JP17H03797).  ...  In the case of enterocin NKR-5-3B, production of the mature circular bacteriocin was blocked when the phenotype is devoid of a single gene in its biosynthetic gene cluster.  ... 
doi:10.3389/fmicb.2018.02085 pmid:30233551 pmcid:PMC6131525 fatcat:2nfolbkd55hqrckqrpjwxoi5ai

Using bacterial genomes and essential genes for the development of new antibiotics

Francisco R. Fields, Shaun W. Lee, Michael J. McConnell
2017 Biochemical Pharmacology  
Whole genome mutagenesis studies can also identify genes necessary for bacterial growth and survival under different environmental conditions, making them attractive targets for the development of novel  ...  In addition, transcriptomic and proteomic approaches can be used to characterize RNA and protein levels on a cellular scale, providing information on bacterial physiology that can be applied to antibiotic  ...  Network for the Research in Infectious Diseases (REIPI RD06/0008/0000).  ... 
doi:10.1016/j.bcp.2016.12.002 pmid:27940263 pmcid:PMC5411290 fatcat:uxo2repznbhfrmaqatr3hpkdzy

Bacteriocins of gram-positive bacteria

R W Jack, J R Tagg, B Ray
1995 Microbiological reviews  
Although a large number of these bacteriocins (or bacteriocin-like inhibitory substances) have been reported, only a few have been studied in detail for their mode of action, amino acid sequence, genetic  ...  Some suggestions for improved standardization of nomenclature are offered.  ...  We are also grateful for the help of Deb Rogers, Mary Beth Hanlin, and Soumen Ghosh for their work in completing this review.  ... 
pmid:7603408 pmcid:PMC239359 fatcat:xdjicpo6i5agpj4ejyip7qbfdm

Bacteriocins of gram-positive bacteria

R W Jack, J R Tagg, B Ray
1995 Microbiological reviews  
We are also grateful for the help of Deb Rogers, Mary Beth Hanlin, and Soumen Ghosh for their work in completing this review.  ...  ACKNOWLEDGMENTS We are grateful to Kim Harmark for helpful discussion and critical appraisal of the manuscript.  ...  (6) have developed a commercially viable procedure for the large-scale production of epidermin and gallidermin.  ... 
doi:10.1128/mmbr.59.2.171-200.1995 fatcat:b4yynfxvl5gpnkeszhytboizye

Bacteriocins of gram-positive bacteria

J R Tagg, A S Dajani, L W Wannamaker
1976 Bacteriological reviews  
We are also grateful for the help of Deb Rogers, Mary Beth Hanlin, and Soumen Ghosh for their work in completing this review.  ...  ACKNOWLEDGMENTS We are grateful to Kim Harmark for helpful discussion and critical appraisal of the manuscript.  ...  (6) have developed a commercially viable procedure for the large-scale production of epidermin and gallidermin.  ... 
pmid:791239 pmcid:PMC413978 fatcat:bxui2wsx5fhxncucpze2heu5ne

Expression in eukaryotic cells and purification of synthetic gene encoding enterocin P: a bacteriocin with broad antimicrobial spectrum

Abbas Tanhaeian, Mohammad Sadegh Damavandi, Davood Mansury, Kiarash Ghaznini
2019 AMB Express  
We evaluated the cloning, functional expression, and antimicrobial activities of enterocin P (EntP), a class II bacteriocin member, in Chinese hamster ovary (CHO) cells.  ...  A synthetic gene matching CHO cell codon usage was designed from the known mature amino acid sequence of EntP and cloned into the protein expression vector pcDNA™3.1(+).  ...  We have demonstrated activity against a wide variety of bacteria, including pathogenic species known to account for a large number nosocomial infections, often with multidrug-resistant activities, suggesting  ... 
doi:10.1186/s13568-018-0729-6 pmid:30617751 pmcid:PMC6323060 fatcat:6uazqjr3tbc5vfzi3vvxz3ztu4

Ferredoxin Containing Bacteriocins Suggest a Novel Mechanism of Iron Uptake in Pectobacterium spp

Rhys Grinter, Joel Milner, Daniel Walker, Pierre Cornelis
2012 PLoS ONE  
Two sequenced strains of the phytopathogenic bacterium Pectobacterium carotovorum carry genes encoding putative bacteriocins which have seemingly evolved through a recombination event to encode proteins  ...  In this work, we show that these genes encode active bacteriocins, pectocin M1 and M2, which target strains of Pectobacterium carotovorum and Pectobacterium atrosepticum with increased potency under iron  ...  Alette Brinth for kindly supplying purified human adrenodoxin, Dr Nick Tucker (Strathclyde) for P. aeruginosa strains and Philip Younger for creation and characterisation of pectocin M1 D222A.  ... 
doi:10.1371/journal.pone.0033033 pmid:22427936 pmcid:PMC3302902 fatcat:z4p6jp55a5aczaqbu3qou5i7uy

Localized Recombination Drives Diversification of Killing Spectra for Phage Derived Syringacins [article]

David Baltrus, Meara Clark, Caitlin Smith, Kevin Hockett
2017 bioRxiv   pre-print
To better understand the potential for detrimental interactions between strains of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen  ...  Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types.  ...  The copyright holder for this preprint . http://dx.doi.org/10.1101/240762 doi: bioRxiv preprint first posted online Dec. 29, 2017; Caveats We have presented a large-scale screen of general bacteriocin  ... 
doi:10.1101/240762 fatcat:dflqdtujx5bnrmnnvudtjgw73e

The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element

Yukun Sun, Iva A. Veseli, Katy Vaillancourt, Michel Frenette, Daniel Grenier, Jean-François Pombert, Axel Cloeckaert
2019 PLoS ONE  
Furthermore, the S. suis 90-1330 genome was found to code for genes involved in blood survival, suggesting that strain may not be a benign as previously thought.  ...  This bacteriocin locus was also found to be widely distributed across several streptococcal species and in a few Staphylococcus aureus strains.  ...  Acknowledgments This work was supported by funds from the Illinois Institute of Technology to Jean-François Pombert. Iva A.  ... 
doi:10.1371/journal.pone.0216002 pmid:31039174 pmcid:PMC6490898 fatcat:d5wmgrrovbevdmqxkxhgx34wmm

Localized recombination drives diversification of killing spectra for phage-derived syringacins

David A. Baltrus, Meara Clark, Caitlin Smith, Kevin L. Hockett
2018 The ISME Journal  
To better understand the potential for detrimental interactions between strains of the same bacterial species, we have surveyed bacteriocin killing activity across a diverse suite of strains of the phytopathogen  ...  Despite a high overall diversity of bacteriocin activity, strains can broadly be classified into five main killing types and two main sensitivity types.  ...  a large-scale screen of general bacteriocin activity across diverse P. syringae strains, followed by selection of R-type syringacin activity from these same samples.  ... 
doi:10.1038/s41396-018-0261-3 pmid:30171255 fatcat:h5rgmmwywjdrthqdaq7pbcsqr4

The Genes Coding for Enterocin EJ97 Production by Enterococcus faecalis EJ97 Are Located on a Conjugative Plasmid

M. Sanchez-Hidalgo, M. Maqueda, A. Galvez, H. Abriouel, E. Valdivia, M. Martinez-Bueno
2003 Applied and Environmental Microbiology  
These data suggest that EJ97 could represent a new class of bacteriocins with a novel secretion mechanism and that the whole structure could be a composite transposon.  ...  The gene ej97A translated as a 44-amino-acid residue mature protein lacking a leader peptide with no homology to other bacteriocins described so far.  ...  We thank Enrique Méndez and Emilio Camafeita for peptide sequencing of EJ97 fragments.  ... 
doi:10.1128/aem.69.3.1633-1641.2003 pmid:12620853 pmcid:PMC150074 fatcat:md56mint3rchfbmslxlcqzitjm

Novel Lectin-Like Bacteriocins of Biocontrol Strain Pseudomonas fluorescens Pf-5

A. H. A. Parret, K. Temmerman, R. De Mot
2005 Applied and Environmental Microbiology  
Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired  ...  Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.  ...  The llpA1 Pf-5 gene was expressed without the upstream region due to the presence of a predicted phage-like gene immediately upstream of the bacteriocin gene.  ... 
doi:10.1128/aem.71.9.5197-5207.2005 pmid:16151105 pmcid:PMC1214683 fatcat:j47mo67shbhx3cndiotqba5fz4

Ribosomally encoded antibacterial proteins and peptides fromPseudomonas

Maarten G.K. Ghequire, René De Mot
2014 FEMS Microbiology Reviews  
enable further divergence of the both bacteriocin genes toward a broader antagonistic spectrum.  ...  These are part of a large group of c. 70 different putative bacteriocins that were retrieved through a search of pseudomonad genomic sequences for gene product pairs consisting of a protein with a HNH  ...  Many thanks for your assistance. Query reference Query Remarks 1 AUTHOR: Genes should be set it italics and proteins should be set in roman.  ... 
doi:10.1111/1574-6976.12079 pmid:24923764 fatcat:gzko3bc56jczteeukol2zbny5a
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