Editing Bacteriocin (section)

== Classification ==
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]],<ref name="Colicin biology">{{cite journal | vauthors = Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, Riley M, Slatin S, Cavard D | display-authors = 6 | title = Colicin biology | journal = Microbiology and Molecular Biology Reviews | volume = 71 | issue = 1 | pages = 158–229 | date = March 2007 | pmid = 17347522 | pmc = 1847374 | doi = 10.1128/MMBR.00036-06 }}</ref> the [[microcins]], and the bacteriocins from [[Archaea]].  The bacteriocins from ''[[Escherichia coli|E. coli]]'' are called ''[[colicins]]'' (formerly called 'colicines', meaning 'coli killers').  These 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.{{Citation needed|date=May 2024|reason=None of this has any citation for it, and should be backed up by a source.}}

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 peptides|ribosomally synthesized and post-translationally modified peptide]] (RiPP) natural products have led to the differentiation of lantipeptides from bacteriocins based on biosynthetic genes.<ref>{{cite journal | vauthors = 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, Göransson 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, Müller 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, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA | display-authors = 6 | title = Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature | journal = Natural Product Reports | volume = 30 | issue = 1 | pages = 108–60 | date = January 2013 | pmid = 23165928 | pmc = 3954855 | doi = 10.1039/c2np20085f }}</ref>

===Methods of classification===
Alternative methods of classification include: method of killing ([[Pore-forming toxin|pore-forming]], [[nuclease]] activity, [[peptidoglycan]] production inhibition, etc.), genetics (large [[plasmid]]s, small plasmids, [[Bacterial chromosome|chromosomal]]), molecular weight and chemistry (large protein, [[peptide]], with/without [[sugar]] moiety, containing atypical amino acids such as lanthionine), and method of production ([[bacterial translation|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.

====Microcins====
See main article on [[microcin]]s.

====Colicin-like bacteriocins====
[[Colicins]] are bacteriocins found in the Gram-negative ''E. coli''. Similar bacteriocins (CLBs, colicin-like bacteriocins) occur in other Gram-negative bacteria. CLBs typically target same species and have species-specific names: klebicins from ''Klebsiella'' and pesticins from ''Yersinia pestis''.<ref>{{cite journal | vauthors = Behrens HM, Six A, Walker D, Kleanthous C | title = The therapeutic potential of bacteriocins as protein antibiotics | journal = Emerging Topics in Life Sciences | volume = 1 | issue = 1 | pages = 65–74 | date = April 2017 | pmid = 33525816 | pmc = 7243282 | doi = 10.1042/ETLS20160016 | veditors = Walker D }}</ref> ''Pseudomonas'' -genus produces bacteriocins called [[pyocin]]s. S-type pyocins belong to CLBs, but R- and F-type pyocins belong to tailocins.<ref>{{cite journal | vauthors = Michel-Briand Y, Baysse C | title = The pyocins of Pseudomonas aeruginosa | journal = Biochimie | volume = 84 | issue = 5–6 | pages = 499–510 | date = May 2002 | pmid = 12423794 | doi = 10.1016/S0300-9084(02)01422-0 }}</ref>

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).<ref name="Colicin biology" />

====Tailocins====
Most well studied are the tailocins of ''[[Pseudomonas aeruginosa]]''. They can be further subdivided into R-type and F-type pyocins.<ref>{{cite journal | vauthors = Ghequire MG, De Mot R | title = Ribosomally encoded antibacterial proteins and peptides from Pseudomonas | journal = FEMS Microbiology Reviews | volume = 38 | issue = 4 | pages = 523–68 | date = July 2014 | pmid = 24923764 | doi = 10.1111/1574-6976.12079 | doi-access = free }}</ref>
Some research was made to identify the pyocins and show how they are involved in the “cell-to-cell” competition of the closely related Pseudomonas bacteria.

The two types of tailocins differ by their structure; they are both composed of a sheath and a hollow tube forming a long helicoidal hexameric structure attached to a baseplate. There are multiple tail fibers that allow the viral particle to bind to the target cell. However, the R-pyocins are a large, rigid contractile tail-like structure whereas the F-pyocins are a small flexible, non-contractile tail-like structure.

The tailocins are coded by prophage sequences in the bacteria genome, and the production will happen when kin bacteria are spotted in the environment of the producer. 
The particles are synthesized in the center of the cells and after maturation they will migrate to the cell pole via tubulin structure. The tailocins will then be ejected in the medium with the cell lysis. They can be projected up to several tens of micrometers thanks to a very high turgor pressure of the cell. The tailocins released will then recognize and bind to the kin bacteria to kill them.<ref>{{cite journal | vauthors = Vacheron J, Heiman CM, Keel C| title = Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion | journal = Communications Biology | volume = 87 | issue = 4 | date = January 2021 | page = 87 | doi =10.1038/s42003-020-01581-1 | pmid = 33469108 | pmc = 7815802 }}</ref>

===From Gram positive bacteria===

Bacteriocins from Gram positive bacteria are typically classified into Class I, Class IIa/b/c, and Class III.
<ref>{{cite journal | vauthors = Cotter PD, Hill C, Ross RP |title=What's in a name? Class distinction for bacteriocins |journal=Nature Reviews Microbiology |date=February 2006 |volume=4 |issue=2 |pages=160 |doi=10.1038/nrmicro1273-c2 |s2cid=29421506 |doi-access=free }} is author reply to comment on article :{{cite journal | vauthors = Cotter PD, Hill C, Ross RP | title = Bacteriocins: developing innate immunity for food | journal = Nature Reviews. Microbiology | volume = 3 | issue = 10 | pages = 777–88 | date = October 2005 | pmid = 16205711 | doi = 10.1038/nrmicro1273 | s2cid = 19040535 }}</ref>

====Class I bacteriocins====
The [[lantibiotics|class I bacteriocins]] are small peptide inhibitors and include [[nisin]] and other [[lantibiotic]]s.

====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-terminus|N-terminal]] consensus sequence -Tyr-Gly-Asn-Gly-Val-Xaa-Cys across this group.<ref>{{Cite journal |last1=Zhu |first1=Liyan |last2=Zeng |first2=Jianwei |last3=Wang |first3=Chang |last4=Wang |first4=Jiawei |date=2022-02-08 |title=Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1 |journal=Applied and Environmental Microbiology |volume=88 |issue=3 |pages=e0199221 |doi=10.1128/AEM.01992-21 |issn=1098-5336 |pmc=8824269 |pmid=34851716}}</ref><ref>{{Cite journal |last1=Zhu |first1=Liyan |last2=Zeng |first2=Jianwei |last3=Wang |first3=Jiawei |date=2022-06-15 |title=Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins |journal=Applied and Environmental Microbiology |volume=88 |issue=13 |pages=e0048122 |doi=10.1128/aem.00481-22 |issn=1098-5336 |pmid=35703550|pmc=9275228 }}</ref> 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''.<ref>{{cite book |doi=10.1007/978-3-540-36604-1_4 |chapter=The Diversity of Bacteriocins in Gram-Positive Bacteria |title=Bacteriocins |year=2007 | vauthors = Heng NC, Wescombe PA, Burton JP, Jack RW, Tagg JR |pages=45–92 |isbn=978-3-540-36603-4 }}</ref>
: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 protein]]s, 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.<ref>{{cite journal | vauthors = Nissen-Meyer J, Rogne P, Oppegård C, Haugen HS, Kristiansen PE | title = Structure-function relationships of the non-lanthionine-containing peptide (class II) bacteriocins produced by gram-positive bacteria | journal = Current Pharmaceutical Biotechnology | volume = 10 | issue = 1 | pages = 19–37 | date = January 2009 | pmid = 19149588 | doi = 10.2174/138920109787048661 }}</ref>
:Class IIc encompasses [[cyclic peptide]]s, in which the N-terminal and [[C-terminus|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 [[protease]]s.<ref>{{cite journal | vauthors = Netz DJ, Pohl R, Beck-Sickinger AG, Selmer T, Pierik AJ, Bastos M, Sahl HG | title = Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus | journal = Journal of Molecular Biology | volume = 319 | issue = 3 | pages = 745–56 | date = June 2002 | pmid = 12054867 | doi = 10.1016/S0022-2836(02)00368-6 }}</ref>

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.<ref>{{cite journal | vauthors = Netz DJ, Sahl HG, Marcelino R, dos Santos Nascimento J, de Oliveira SS, Soares MB, do Carmo de Freire Bastos M, Marcolino R | display-authors = 6 | title = Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus | journal = Journal of Molecular Biology | volume = 311 | issue = 5 | pages = 939–49 | date = August 2001 | pmid = 11531330 | doi = 10.1006/jmbi.2001.4885 }}</ref> Recent work has identified that these bacteriocins are widespread across the bacterial domain and are present in the phylum [[Actinomycetota]]. <ref>{{Cite journal |last=Hourigan |first=David |last2=Miceli de Farias |first2=Felipe |last3=O’Connor |first3=Paula M. |last4=Hill |first4=Colin |last5=Ross |first5=R. Paul |date=2024-10-15 |editor-last=Galperin |editor-first=Michael Y. |title=Discovery and synthesis of leaderless bacteriocins from the Actinomycetota |url=https://journals.asm.org/doi/10.1128/jb.00298-24 |journal=Journal of Bacteriology |language=en |doi=10.1128/jb.00298-24 |issn=0021-9193|doi-access=free |pmc=11580447 }}</ref>

====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#Bacterial cell walls|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 ''[[Staphylococcus aureus|S. aureus]]''.<ref>{{cite journal | vauthors = Bastos MD, Coutinho BG, Coelho ML | title = Lysostaphin: A Staphylococcal Bacteriolysin with Potential Clinical Applications | journal = Pharmaceuticals | volume = 3 | issue = 4 | pages = 1139–1161 | date = April 2010 | pmid = 27713293 | pmc = 4034026 | doi = 10.3390/ph3041139 | doi-access = free }}</ref> 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.<ref>{{cite journal | vauthors = Oman TJ, Boettcher JM, Wang H, Okalibe XN, van der Donk WA | title = Sublancin is not a lantibiotic but an S-linked glycopeptide | journal = Nature Chemical Biology | volume = 7 | issue = 2 | pages = 78–80 | date = February 2011 | pmid = 21196935 | pmc = 3060661 | doi = 10.1038/nchembio.509 }}</ref><ref>{{cite journal | vauthors = Stepper J, Shastri S, Loo TS, Preston JC, Novak P, Man P, Moore CH, Havlíček V, Patchett ML, Norris GE | display-authors = 6 | title = Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins | journal = FEBS Letters | volume = 585 | issue = 4 | pages = 645–50 | date = February 2011 | pmid = 21251913 | doi = 10.1016/j.febslet.2011.01.023 | s2cid = 29992601 }}</ref>

===Databases===
Two databases of bacteriocins are available: BAGEL<ref name=deJong_2006>{{cite journal | vauthors = de Jong A, van Hijum SA, Bijlsma JJ, Kok J, Kuipers OP | title = BAGEL: a web-based bacteriocin genome mining tool | journal = Nucleic Acids Research | volume = 34 | issue = Web Server issue | pages = W273-9 | date = July 2006 | pmid = 16845009 | pmc = 1538908 | doi = 10.1093/nar/gkl237 }}</ref> and BACTIBASE.<ref name=Hammami_2007>{{cite journal | vauthors = Hammami R, Zouhir A, Ben Hamida J, Fliss I | title = BACTIBASE: a new web-accessible database for bacteriocin characterization | journal = BMC Microbiology | volume = 7 | issue = 1 | pages = 89 | date = October 2007 | pmid = 17941971 | pmc = 2211298 | doi = 10.1186/1471-2180-7-89 | doi-access = free }}</ref><ref name=Hammami_2010>{{cite journal | vauthors = Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I | title = BACTIBASE second release: a database and tool platform for bacteriocin characterization | journal = BMC Microbiology | volume = 10 | issue = 1 | pages = 22 | date = January 2010 | pmid = 20105292 | pmc = 2824694 | doi = 10.1186/1471-2180-10-22 | doi-access = free }}</ref>