Bacteriocin

Bacteriocin
Lactococcin-like family
Identifiers Symbol Pfam Pfam clan InterPro TCDB Lactococcin PF04369 CL0400 [1]

[2] [3]

IPR007464 1.C.22 [4]

Available protein structures: Pfam PDB structures [5] [6] ; PDBe [7] ; PDBj [8]

RCSB PDB

PDBsum structure summary [9]

Bacteriocin (Lactococcin_972)
Identifiers Symbol Pfam InterPro Lactococcin_972 PF09683 [10] [11]

IPR006540

Available protein structures: Pfam PDB structures [12] [13] ; PDBe [14] ; PDBj [15]

RCSB PDB

PDBsum structure summary [16]

Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are typically considered to be narrow spectrum antibiotics, though this has been debated. They are phenomenologically analogous to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse. Bacteriocins were first discovered by A. 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.

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Classification of bacteriocins
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. For example the bacteriocins produced by Staphylococcus warneri are called as warnerin or warnericin. 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.

Methods of classification
Alternative methods of classification include: method of killing (pore forming, dnase, nuclease, murein production inhibition, etc.), genetics (large plasmids, small plasmids, chromosomal), molecular weight and chemistry (large protein, polypeptide, with/without sugar moiety, containing atypical amino acids like lanthionine) and method of production (ribosomal, post ribosomal modifications, non-ribosomal). One method of classification fits the bacteriocins into Class I, Class IIa/b/c, and Class III. [17]

Class I bacteriocins
The class I bacteriocins are small peptide inhibitors and include nisin and other lantibiotics.

Class II bacteriocins
The class II bacteriocins are small (<10 kDa) heat-stable proteins. This class is subdivided into five subclassses. 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 antilisterial activity, and broad range of activity. One example of Class IIa bacteriocin is pediocin PA-1.[18] 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 ions such as Na and K, but not for divalents ones. Almost all of this bacteriocins have a GxxxG motifs. This motif is also found in transmembrane proteins where they are involved in helix-helix interactions. The bacteriocins GxxxG motifs can interact with the motifs in the membranes of the bacterial cells and kill the bacteria by doing so. Class IIc encompasses cyclic peptides, which possesses the N-terminal and C-terminal regions covalentely linked. Enterocin AS-48 is the prototype of this group. Class IId cover single-peptide bacteriocins, which are not post-translated 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 environment (HCl 6 N), not affected by proteases and thermoresistant.

Bacteriocin The most recently proposed subclass is the Class IIe, which encompasses those bacteriocins composed by three or four non-pediocin like peptides. The best example is aureocin A70, a four-peptides bacteriocin, highly active against L. 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 or 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 hydrolises several Staphylococcus spp. cell walls, principally S. aureus.[19] Subclass IIIb, in contrast, comprises those peptides that do not cause cell lysis, killing the target cells by disrupting the membrane potential, which causes ATP efflux .

Class IV bacteriocins
Class IV bacteriocins are defined as complex bacteriocins containing lipid or carbohydrate moities. Confirmatory experimental data was only recently established with the characterisation of Sublancin and Glycocin F (GccF) by two independent groups.[20][21]

Databases
Two databases of bacteriocins are available: BAGEL and BACTIBASE.

Medical significance
Bacteriocins are of interest in medicine because they are made by non-pathogenic bacteria that normally colonize the human body. Loss of these harmless bacteria following antibiotic use may allow opportunistic pathogenic bacteria to invade the human body [citation needed]. Bacteriocins have also been suggested as a cancer treatment. They have shown distinct promise as a diagnostic agent for some cancers, but their status as a form of therapy remains experimental and outside the main thread of cancer research. Partly this is due to questions about their mechanism of action and the presumption that anti-bacterial agents have no obvious connection to killing mammalian tumor cells. Some of these questions have been addressed, at least in part. Bacteriocins Wikipedia:Avoid weasel words were tested as AIDS drugs around 1990, but did not progress beyond in-vitro tests on cell lines. Bacteriocins can target individual bacterial species, or provide broad-spectrum killing of many microbes. As with today's antibiotics, bacteria can evolve to resist bacteriocins. However, they can be bioengineered to regain their effectiveness. Further, they could be produced in the body by intentionally introduced beneficial bacteria, as some probiotics do.

Production
There are many ways to demonstrate bacteriocin production, depending on the sensitivity and labor intensiveness desired. To demonstrate their production, technicians stab inoculate multiple strains on separate multiple nutrient agar Petri dishes, incubate at 30 C for 24 h., overlay each plate with one of the strains (in soft agar), incubate again at 30 C for 24 h. After this process, the presence of bacteriocins can be inferred if there are zones of growth inhibition around stabs. This is the simplest and least sensitive way. It will often mistake phage for bacteriocins. Some methods prompt production with UV radiation, Mitomycin C, or heat shock. UV radiation and Mitomycin C are used because the DNA damage they produce stimulates the SOS response. Cross streaking may be substituted for lawns. Similarly, production in broth may be followed by dripping the broth on a nascent bacterial lawn, or even filtering it. Precipitation (ammonium sulfate) and some purification (e.g. column or HPLC) may help exclude

Bacteriocin lysogenic and lytic phage from the assay.

Bacteriocins by name
acidocin actagardine agrocin alveicin aureocin aureocin A53 aureocin A70 carnocin carnocyclin colicin curvaticin divercin duramycin enterocin enterolysin epidermin/gallidermin erwiniocin glycinecin halocin haloduracin Lactocin S, a bacteriocin produced by strain L45 of Lactobacillus sakei. lactococin lacticin leucoccin macedocin mersacidin mesentericin microbisporicin Microcin S mutacin nisin paenibacillin planosporicin pediocin pentocin plantaricin pyocin reutericin sakacin salivaricin subtilin sulfolobicin thuricin 17 trifolitoxin variacin vibriocin warnericin warnerin

References
[1] http:/ / pfam. sanger. ac. uk/ family?acc=PF04369 [2] http:/ / pfam. sanger. ac. uk/ clan/ CL0400 [3] http:/ / www. ebi. ac. uk/ interpro/ entry/ IPR007464 [4] http:/ / www. tcdb. org/ search/ result. php?tc=1. C. 22 [5] http:/ / pfam. sanger. ac. uk/ family/ PF04369?tab=pdbBlock [6] http:/ / www. rcsb. org/ pdb/ search/ smartSubquery. do?smartSearchSubtype=PfamIdQuery& pfamID=PF04369 [7] http:/ / www. ebi. ac. uk/ pdbe-srv/ PDBeXplore/ pfam/ ?pfam=PF04369 [8] http:/ / pdbj. org/ searchFor?query=PF04369 [9] http:/ / www. ebi. ac. uk/ thornton-srv/ databases/ cgi-bin/ pdbsum/ GetPfamStr. pl?pfam_id=PF04369 [10] http:/ / pfam. sanger. ac. uk/ family?acc=PF09683 [11] http:/ / www. ebi. ac. uk/ interpro/ entry/ IPR006540 [12] http:/ / pfam. sanger. ac. uk/ family/ PF09683?tab=pdbBlock [13] http:/ / www. rcsb. org/ pdb/ search/ smartSubquery. do?smartSearchSubtype=PfamIdQuery& pfamID=PF09683 [14] http:/ / www. ebi. ac. uk/ pdbe-srv/ PDBeXplore/ pfam/ ?pfam=PF09683 [15] http:/ / pdbj. org/ searchFor?query=PF09683 [16] http:/ / www. ebi. ac. uk/ thornton-srv/ databases/ cgi-bin/ pdbsum/ GetPfamStr. pl?pfam_id=PF09683 [17] is author reply to comment on article : [18] 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. [19] 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. [20] Oman T. J., Boettcher J. M., Wang H., Okalibe X. N., & Van der Donk W. A: Sublancin is not a Lantibiotic but an s-Linked Glycopeptide. Nat Chem Biol. 2011; 7(2):78-80. [21] Stepper J., Shastri S., Loo T. S., Preston J. C., Novak P., Man P., Moore C. H., Havlek V., Patchett M. L., and Norris G. E:Cysteine s-Glycosylation, A New Post-Translational Modification Found In Glycopeptide Bacteriocins. FEBS letters. 2011; 585:645-650.

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External links
Bagel Bacteriocin Database (http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php) BACTIBASE Database (http://bactibase.pfba-lab-tun.org/)

External links
Bacteriocins (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Bacteriocins) at the US National Library of Medicine Medical Subject Headings (MeSH)

Article Sources and Contributors

Article Sources and Contributors

Bacteriocin Source: http://en.wikipedia.org/w/index.php?oldid=593944308 Contributors: AManWithNoPlan, AerobicFox, Ajh20, Animeronin, Anrnusna, Arcadian, Bckirkup, Bobblewik, Bonnifac, Bryan Derksen, Can't sleep, clown will eat me, CanisRufus, Chester Markel, Derek Ross, Eleassar777, Eog1916, Erik Zachte, Fringlis, Gregory dj, Hequba, Hodja Nasreddin, Hoffmeier, JLaTondre, JWSchmidt, John of Reading, Kupirijo, Kzarifes, Lchiarav, Lfstevens, Magnus Manske, Mathrick, Mav, Michael Hardy, My very best wishes, Netha Hussain, Nihiltres, Nina, Ninjatacoshell, NotWith, Ohwell32, Orenburg1, Patrikd, Pqrstuv, RDBrown, RE73, Reedy, Rhlozier, Rich Farmbrough, Rjwilmsi, Rod57, Sabedon, Sobsisabeast, Sun Creator, THEN WHO WAS PHONE?, Tabletop, Taxman, TimVickers, Tuganax, Uitbreiding, Vbenedetti, Viking59, Zaqette, 64 anonymous edits

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