Summary: Bacteriocin (Lactococcin_972)
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Bacteriocin Edit Wikipedia article
Bacteriocins are proteinaceous or peptidic toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are similar to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse. Applications of bacteriocins are being tested to assess their application as narrow-spectrum antibiotics.
Bacteriocins were first discovered by AndrÃ© Gratia in 1925. He was involved in the process of searching for ways to kill bacteria, which also resulted in the development of antibiotics and the discovery of bacteriophage, all within a span of a few years. He called his first discovery a colicine because it killed E. coli.
- 1 Classification
- 2 Uses
- 3 Relevance to human health
- 4 Research
- 5 By name
- 6 See also
- 7 References
- 8 External links
Bacteriocins are categorized in several ways, including producing strain, common resistance mechanisms, and mechanism of killing. There are several large categories of bacteriocin which are only phenomenologically related. These include the bacteriocins from gram-positive bacteria, the colicins, the microcins, and the bacteriocins from Archaea. The bacteriocins from E. coli are called colicins (formerly called 'colicines', meaning 'coli killers'). They are the longest studied bacteriocins. They are a diverse group of bacteriocins and do not include all the bacteriocins produced by E. coli. In fact, one of the oldest known so-called colicins was called colicin V and is now known as microcin V. It is much smaller and produced and secreted in a different manner than the classic colicins.
This naming system is problematic for a number of reasons. First, naming bacteriocins by what they putatively kill would be more accurate if their killing spectrum were contiguous with genus or species designations. The bacteriocins frequently possess spectra that exceed the bounds of their named taxa and almost never kill the majority of the taxa for which they are named. Further, the original naming is generally derived not from the sensitive strain the bacteriocin kills, but instead the organism that produces the bacteriocin. This makes the use of this naming system a problematic basis for theory; thus the alternative classification systems.
Bacteriocins that contain the modified amino acid lanthionine as part of their structure are called lantibiotics. However, efforts to reorganize the nomenclature of the family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products have led to the differentiation of lantipeptides from bacteriocins based on biosynthetic genes.
Methods of classification
Alternative methods of classification include: method of killing (pore-forming, nuclease activity, peptidoglycan production inhibition, etc.), genetics (large plasmids, small plasmids, chromosomal), molecular weight and chemistry (large protein, peptide, with/without sugar moiety, containing atypical amino acids such as lanthionine), and method of production (ribosomal, post-ribosomal modifications, non-ribosomal).
From Gram negative bacteria
Gram negative bacteriocins are typically classified by size. Microcins are less than 20 kDa in size, colicin-like bacteriocins are 20 to 90 kDa in size and tailocins or so called high molecular weight bacteriocins which are multi subunit bacteriocins that resemble the tails of bacteriophages. This size classification also coincides with genetic, structural and functional similarities.
See main article on microcins.
Colicins are bacteriocins (CLBs) found in the Gram-negative E. coli. Similar bacteriocins occur in other Gram-negative bacteria. These CLBs are distinct from Gram-positive bacteriocins. They are modular proteins between 20 and 90 kDa in size. They often consist of a receptor binding domain, a translocation domain and a cytotoxic domain. Combinations of these domains between different CLBs occur frequently in nature and can be created in the laboratory. Due to these combinations further subclassification can be based on either import mechanism (group A and B) or on cytotoxic mechanism (nucleases, pore forming, M-type, L-type).
From Gram positive bacteria
Bacteriocins from Gram positive bacteria are typically classified into Class I, Class IIa/b/c, and Class III. 
Class I bacteriocins
Class II bacteriocins
The class II bacteriocins are small (<10 kDa) heat-stable proteins. This class is subdivided into five subclasses. The class IIa bacteriocins (pediocin-like bacteriocins) are the largest subgroup and contain an N-terminal consensus sequence -Tyr-Gly-Asn-Gly-Val-Xaa-Cys across this group. The C-terminal is responsible for species-specific activity, causing cell-leakage by permeabilizing the target cell wall.
- Class IIa bacteriocins have a large potential for use in food preservation as well medical applications due to their strong anti-Listeria activity and broad range of activity. One example of Class IIa bacteriocin is pediocin PA-1.
- The class IIb bacteriocins (two-peptide bacteriocins) require two different peptides for activity. One such an example is lactococcin G, which permeabilizes cell membranes for monovalent sodium and potassium cations, but not for divalent cations. Almost all of these bacteriocins have a GxxxG motifs. This motif is also found in transmembrane proteins, where they are involved in helix-helix interactions. Accordingly, the bacteriocin GxxxG motifs can interact with the motifs in the membranes of the bacterial cells, killing the cells.
- Class IIc encompasses cyclic peptides, in which the N-terminal and C-terminal regions are covalentely linked. Enterocin AS-48 is the prototype of this group.
- Class IId cover single-peptide bacteriocins, which are not post-translationally modified and do not show the pediocin-like signature. The best example of this group is the highly stable aureocin A53. This bacteriocin is stable under highly acidic conditions, high temperatures, and is not affected by proteases.
The most recently proposed subclass is the Class IIe, which encompasses those bacteriocins composed of three or four non-pediocin like peptides. The best example is aureocin A70, a four-peptide bacteriocin, highly active against Listeria monocytogenes, with potential biotechnological applications.
Class III bacteriocins
Class III bacteriocins are large, heat-labile (>10 kDa) protein bacteriocins. This class is subdivided in two subclasses: subclass IIIa (bacteriolysins) and subclass IIIb. Subclass IIIa comprises those peptides that kill bacterial cells by cell wall degradation, thus causing cell lysis. The best studied bacteriolysin is lysostaphin, a 27 kDa peptide that hydrolyzes the cell walls of several Staphylococcus species, principally S. aureus. Subclass IIIb, in contrast, comprises those peptides that do not cause cell lysis, killing the target cells by disrupting plasma membrane potential.
Class IV bacteriocins
Class IV bacteriocins are defined as complex bacteriocins containing lipid or carbohydrate moieties. Confirmation by experimental data was established with the characterisation of sublancin and glycocin F (GccF) by two independent groups.
As of 2016, nisin was the only bacteriocin generally recognized as safe by the FDA and was used as a food preservative in several countries. Generally bacteriocidins are not useful as food preservatives because they are expensive to make, are broken down in food products, they harm some proteins in food, and they target too narrow a range of microbes.
Relevance to human health
Bacteriocins have been proposed as a replacement for antibiotics to which pathogenic bacteria have become resistant. Potentially, the bacteriocins could be produced by bacteria intentionally introduced into the patient to combat infection. There are several strategies by which new bacteriocins can be discovered. In the past, bacteriocins had to be identified by intensive culture-based screening for antimicrobial activity against suitable targets and subsequently purified using fastidious methods prior to testing. However, since the advent of the genomic era, the availability of the bacterial genome sequences has revolutionized the approach to identifying bacteriocins. Recently developed in silico-based methods can be applied to rapidly screen thousands of bacterial genomes in order to identify novel antimicrobial peptides.
As of 2014 some bacteriocins had been studied in in vitro studies to see if they can stop viruss from replicating, namely staphylococcin 188 against Newcastle disease virus, influenza virus, and coliphage HSA virus; each of enterocin AAR-71 class IIa, enterocin AAR-74 class IIa, and erwiniocin NA4 against coliphage HSA virus; each of enterocin ST5Ha, enterocin NKR-5-3C, and subtilosine against HSV-1; each of enterocin ST4V and enterocin CRL35 class IIa against HSV-1 and HSV-2; labyrinthopeptin A1 against HIV-1 and HSV-1; and bacteriocin from Lactobacillus delbrueckii against influenza virus.
As of 2009, some bacteriocins, cytolysin, pyocyn S2, colicins A and E1, and the microcin MccE492 had been tested on cancer cell lines and in a mouse model of cancer.
- aureocin A53
- aureocin A70
- circularin A
- gassericin A
- lactocin S
- microcin S
- reutericin 6
- thuricin 17
- Cotter, Paul D.; Ross, R. Paul; Hill, Colin (2012). "Bacteriocins â€” a viable alternative to antibiotics?". Nature Reviews Microbiology. 11 (2): 95â€“105. doi:10.1038/nrmicro2937. ISSN 1740-1526. PMID 23268227.
- Gratia A (1925). "Sur un remarquable example d'antagonisme entre deux souches de colibacille". Compt. Rend. Soc. Biol. 93: 1040â€“2.
- Gratia JP (October 2000). "AndrÃ© Gratia: a forerunner in microbial and viral genetics". Genetics. 156 (2): 471â€“6. PMC 1461273. PMID 11014798.
- Cascales E, Buchanan SK, DuchÃ© D, et al. (March 2007). "Colicin Biology". Microbiol. Mol. Biol. Rev. 71 (1): 158â€“229. doi:10.1128/MMBR.00036-06. PMC 1847374. PMID 17347522.
- Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, GÃ¶ransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, MÃ¼ller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJ, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, SÃ¼ssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA (2013). "Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature". Nat Prod Rep. 30 (1): 108â€“60. doi:10.1039/c2np20085f. PMC 3954855. PMID 23165928.
- Eric Cascales and others, â€˜Colicin Biologyâ€™, MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 71.1 (2007), 158â€“229 <https://dx.doi.org/10.1128/MMBR.00036-06>.
- Maarten G K Ghequire and RenÃ© De Mot, 'Ribosomally Encoded Antibacterial Proteins and Peptides from Pseudomonas', FEMS Microbiology Reviews, 38.4 (2014), 523â€“68 <https://dx.doi.org/10.1111/1574-6976.12079>.
- Cotter PD, Hill C, Ross RP (2006). "What's in a name? Class distinction for bacteriocins". Nature Reviews Microbiology. 4 (2): 160. doi:10.1038/nrmicro1273-c2. is author reply to comment on article :Cotter PD, Hill C, Ross RP (2005). "Bacteriocins: developing innate immunity for food". Nature Reviews Microbiology. 3 (?): 777â€“88. doi:10.1038/nrmicro1273. PMID 16205711.
- HENG, C. K. N., WESCOMBE, P. A., BURTON, J. P., JACK, R. W., & TAGG, J. R. (2007). The diversity of bacteriocins in Gram-positive bacteria. In: Bacteriocins: Ecology and Evolution. 1st ed., Riley, M. A. & Chavan, M. A., Eds. Springer, Hildberg, p. 45-83.
- Nissen-Meyer, J; Rogne, P; OppegÃ¥rd, C; Haugen, HS; Kristiansen, PE (2013-08-12). "Structure-function relationships of the non-lanthionine-containing peptide (class II) bacteriocins produced by gram-positive bacteria". Curr Pharm Biotechnol. 10 (1): 19â€“37. doi:10.2174/138920109787048661. PMID 19149588.
- NETZ D. J., POHL , BECK-SICKINGER A. G., SELMER , PIERIK , SAHL H. G. (2002). "Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus". J. Mol. Biol. 319 (3): 745â€“756. doi:10.1016/s0022-2836(02)00368-6. PMID 12054867.CS1 maint: uses authors parameter (link)
- NETZ D. J. A., SAHL , NASCIMENTO , OLIVEIRA , SOARES , BASTOS M. C. F. (2001). "Molecular characterisation of aureocin A70, a multiple-peptide bacteriocin isolated from Staphylococcus aureus". J. Mol. Biol. 311 (5): 939â€“949. doi:10.1006/jmbi.2001.4885. PMID 11531330.CS1 maint: uses authors parameter (link)
- Bastos M.C.F., Coutinho B.G., Coelho M.L.V. Lysostaphin: A Staphylococcal Bacteriolysin with Potential Clinical Applications. Pharmaceuticals. 2010; 3(4):1139-1161.
- Oman T. J., Boettcher J. M., Wang H., Okalibe X. N., Van der Donk W. A (2011). "Sublancin is not a Lantibiotic but an s-Linked Glycopeptide". Nat Chem Biol. 7 (2): 78â€“80. doi:10.1038/nchembio.509. PMC 3060661. PMID 21196935.CS1 maint: uses authors parameter (link)
- Stepper J.; Shastri S.; Loo T. S.; Preston J. C.; Novak P.; Man P.; Moore C. H.; HavlÃÄek V.; Patchett M. L.; Norris G. E (2011). "Cysteine s-Glycosylation, A New Post-Translational Modification Found In Glycopeptide Bacteriocins". FEBS Letters. 585 (4): 645â€“650. doi:10.1016/j.febslet.2011.01.023. PMID 21251913.
- de Jong A; van Hijum S A F T; Bijlsma J J E; Kok J; Kuipers O P (2006). "BAGEL: a web-based bacteriocin genome mining tool". Nucleic Acids Research. 34 (Web Server issue): W273â€“W279. doi:10.1093/nar/gkl237. PMC 1538908. PMID 16845009.
- Hammami R, Zouhir A, Ben Hamida J, Fliss I (2007). "BACTIBASE: a new web-accessible database for bacteriocin characterization". BMC Microbiology. 7: 89. doi:10.1186/1471-2180-7-89. PMC 2211298. PMID 17941971.
- Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (2010). "BACTIBASE second release: a database and tool platform for bacteriocin characterization". BMC Microbiology. 10: 22. doi:10.1186/1471-2180-10-22. PMC 2824694. PMID 20105292.
- Fahim, Hazem A.; Khairalla, Ahmed S.; El-Gendy, Ahmed O. (2016-01-01). "Nanotechnology: A Valuable Strategy to Improve Bacteriocin Formulations". Frontiers in Microbiology. 7: 1385. doi:10.3389/fmicb.2016.01385. PMC 5026012. PMID 27695440.
- Nardis, C.; Mastromarino, P.; Mosca, L. (Sepâ€“Oct 2013). "Vaginal microbiota and viral sexually transmitted diseases". Annali di Igiene. 25 (5): 443â€“56. doi:10.7416/ai.2013.1946. PMID 24048183.
- Cotter, PD; Ross, RP; Hill, C (February 2013). "Bacteriocins - a viable alternative to antibiotics?". Nature Reviews. Microbiology. 11 (2): 95â€“105. doi:10.1038/nrmicro2937. PMID 23268227.
- Rezaei Javan, Reza; Van Tonder, Andries; King, James; Harrold, Caroline; Brueggemann, Angela (August 2018). "Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides". Frontiers in Microbiology. 2012 (9): 2012. doi:10.3389/fmicb.2018.02012. PMC 6120550. PMID 30210481.
- Al Kassaa, I; Hober, D; Hamze, M; Chihib, NE; Drider, D (December 2014). "Antiviral potential of lactic acid bacteria and their bacteriocins". Probiotics and Antimicrobial Proteins. 6 (3â€“4): 177â€“85. doi:10.1007/s12602-014-9162-6. PMID 24880436.
- Lagos, R; Tello, M; Mercado, G; GarcÃa, V; Monasterio, O (January 2009). "Antibacterial and antitumorigenic properties of microcin E492, a pore-forming bacteriocin". Current Pharmaceutical Biotechnology. 10 (1): 74â€“85. doi:10.2174/138920109787048643. PMID 19149591.
- Naclerio, G; Ricca, E; Sacco, M; De Felice, M (December 1993). "Antimicrobial activity of a newly identified bacteriocin of Bacillus cereus". Appl Environ Microbiol. 59 (12): 4313â€“6. PMC 195902. PMID 8285719.
- Kawai Y, Kemperman R, Kok J, Saito T (2004). "The circular bacteriocins gassericin A and circularin A". Current Protein & Peptide Science. 5 (5): 393â€“8. doi:10.2174/1389203043379549. PMID 15544534.
- Pandey N, Malik RK, Kaushik JK, Singroha G (2013). "Gassericin A: a circular bacteriocin produced by lactic acid bacteria Lactobacillus gasseri". World Journal of Microbiology & Biotechnology. 29 (11): 1977â€“87. doi:10.1007/s11274-013-1368-3. PMID 23712477.
- MÃ¸rtvedt, C. I.; Nissen-Meyer, J.; Sletten, K.; Nes, I. F. (1991). "Purification and amino acid sequence of lactocin S, a bacteriocin produced by Lactobacillus sake L45". Applied and Environmental Microbiology. 57 (6): 1829â€“1834. PMC 183476. PMID 1872611.
- Bogaardt, C.; van Tonder, A. J.; Brueggemann, A. (2015). "Genomic analyses of pneumococci reveal a wide diversity of bacteriocins â€“ including pneumocyclicin, a novel circular bacteriocin". BMC Genomics. 16: 554. doi:10.1186/s12864-015-1729-4. PMC 4517551. PMID 26215050.
- Michel-Briand, Y.; Baysse, C. (2002). "The pyocins of Pseudomonas aeruginosa". Biochimie. 84 (5â€“6): 499â€“510. doi:10.1016/s0300-9084(02)01422-0. PMID 12423794.
- Kabuki T, Saito T, Kawai Y, Uemura J, Itoh T (1997). "Production, purification and characterization of reutericin 6, a bacteriocin with lytic activity produced by Lactobacillus reuteri LA6". International Journal of Food Microbiology. 34 (2): 145â€“56. doi:10.1016/s0168-1605(96)01180-4. PMID 9039561.
- Wescombe, PA; Upton, M; Dierksen, KP; Ragland, NL; Sivabalan, S; Wirawan, RE; Inglis, MA; Moore, CJ; Walker, GV; Chilcott, CN; Jenkinson, HF; Tagg, JR (February 2006). "Production of the lantibiotic salivaricin A and its variants by oral streptococci and use of a specific induction assay to detect their presence in human saliva". Applied and Environmental Microbiology. 72 (2): 1459â€“66. doi:10.1128/aem.72.2.1459-1466.2006. PMC 1392966. PMID 16461700.
- MÃ¼ller, Ina; Lurz, Rudi; Geider, Klaus (25 July 2012). "Tasmancin and lysogenic bacteriophages induced from Erwinia tasmaniensis strains". Microbiological Research. 167 (7): 381â€“387. doi:10.1016/j.micres.2012.01.005. PMID 22381912.
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Bacteriocin (Lactococcin_972) Provide feedback
These sequences represent bacteriocins related to lactococcin. Members tend to be found in association with a seven transmembrane putative immunity protein.
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|Author:||TIGRFAMs, Coggill P|
|Number in seed:||16|
|Number in full:||186|
|Average length of the domain:||63.50 aa|
|Average identity of full alignment:||28 %|
|Average coverage of the sequence by the domain:||56.02 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lactococcin_972 domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
Loading structure mapping...