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'). 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. 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.
Microcins See main article on
microcins.
Colicin-like bacteriocins Colicins are bacteriocins found in the gram-negative
E. coli. Similar bacteriocins (colicin-like bacteriocins, or CLBs) occur in other gram-negative bacteria. CLBs typically target same species and have species-specific names: klebicins from
Klebsiella and pesticins from
Yersinia pestis.
Pseudomonas -genus produces bacteriocins called
pyocins. S-type pyocins belong to CLBs, but R- and F-type pyocins belong to tailocins. 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). 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.
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 The
class I bacteriocins are small peptide inhibitors and include
nisin and other
lantibiotics.
Class II bacteriocins The
class II bacteriocins are small (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. :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 bacteriocins are 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. :Class IIe is the most recently proposed subclass and 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. Recent work has identified that these bacteriocins are widespread across the bacterial domain and are present in the phylum
Actinomycetota.
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.
Databases Two databases of bacteriocins are available: BAGEL and BACTIBASE. ==Uses==