1.C.24 The Pediocin (Pediocin) Family

Many organisms synthesize proteins (or peptides) which are degraded to relatively small hydrophobic or amphipathic, bioactive peptides. These peptides exhibit antibiotic, fungicidal, virucidal, hemolytic and/or tumoricidal activities by interacting with membranes and forming transmembrane channels that allow the free flow of electrolytes, metabolites and water across the phospholipid bilayers. Most of these peptides appear to function in biological warfare. There are many designations given to these bioactive peptides. They include the magainins, cecropins, melittins, defensins, bacteriocidins, etc. The proteins in each family within this functional superfamily are homologous, but they exhibit little or no significant sequence similarity with members of the other families. Thus, each family may have evolved independently. However, certain common structural features observed between members of distinct families suggest that at least some of these families share a common ancestry.

Bacteriocins are bacterially produced peptide antibiotics with the ability to kill a limited range of bacteria, usually but not always those that are closely related to the producer bacterium. Many of them exhibit structural features typical of members of the eukaryotic channel-forming amphipathic peptides. That is, they are usually synthesized as small precursor proteins or peptides which are processed with proteolytic elimination of their N-terminal leader sequences, and the resultant mature peptides form one, two or more putative amphipathic transmembrane α-helical spanners (TMSs). For those with two TMSs, a characteristic hinge region that separates the two putative transmembrane segments is usually observed. A similar structural arrangement occurs in the two-TMS Cecropin A proteins (TC #1.C.17).

Many bacteriocins are encoded in operons that also encode an immunity protein and an ABC transport system (TC #3.A.1) with a protease domain at the N-terminus. The ABC systems export the bacteriocins while the protease domains cleave the N-terminal leader sequence. A few bacteriocins are exported by the type II general secretory pathway rather than by ABC-type export systems. In some cases, expression of the bacteriocin-encoding operon is induced by a bacteriocin-like peptide which acts in conjunction with a two component sensor kinase-response regulator to effect induction.

Peptide bacteriocins produced by lactic acid bacteria are categorized into two different classes according to their biochemical and genetic properties (Drider et al., 2006; Nes et al., 2007). Class I peptides are the lantibiotics, which are small, posttranslationally modified peptides that contain unusual amino acids such as lanthionine (1.C.20). Class II includes unmodified bacteriocins which are subdivided into three subclasses, namely, class IIa (pediocin-like bacteriocins), class IIb (two-peptide bacteriocins), and IIc (other [i.e., non-pediocin-like], one-peptide bacteriocins).

Class II non lanthionine-containing heat-stable bacteriocins are small membrane active peptides of less than 10 kDa characterized by a Gly-Gly-1 Xaa+1 processing site in the bacteriocin precursor, processed by the protease domain linked to the ABC-type bacteriocin export permease (e.g., TC #3.A.1.42.2). The mature bacteriocins are predicted to form amphipathic helices with varying amounts of hydrophobicity. Subgroups in Class II bacteriocins include: class IIa, Listeria-active peptides with a consensus sequence in the N-terminus of Y-G-N-G-V-X-C. Many other homologous peptides, not tabulated, are also members of this family. Pediocin PA-1 and Sakacin P are members of this family (TC #1.C.24.1.1 and 1.C.24.1.2, respectively). While Pediocin PA-1 has a C-terminal disulfide bridge, Sakacin P does not. Introducing such a bridge in Sakacin P broadened its target cell specificity and rendered it 10-20x more potent against many bacterial strains but not others. The disulfide bridge also increased its heat stability.

Many bacteriocins have been identified in addition to those tabulated in the TC system, but those listed are among the best characterized, with respect to evidence for channel formation in target bacterial membranes. Some members of the family have additional functions. For example, one member of the Pediocin family, Divergicin M35 activates K+ channels, particularly of the K(v) and BK(Ca) types and to a lesser extent the K(ATP) type. This causes K+ efflux and consequently cell death (Naghmouchi et al., 2008). Class III and IV bacteriocins (Klaenhammer, 1993) are large heat-labile proteins that function by mechanisms unrelated to those of the bacteriocins listed here.

In a review, Ríos Colombo et al. 2018 analyzed the mechanism of action and immunity of class IIa bacteriocins which act on the membranes of Gram-positive bacterial cells, dissipating the transmembrane electrical potential by forming pores.The mannose phosphotransferase system (man-PTS) is the receptor for class IIa bacteriocins and the membrane composition influences their activities. A model suggests that the non-specific binding of the bacteriocin to the negatively charged membrane of target bacteria facilitates the specific binding to the receptor protein, altering its functionality and forming an independent pore in which the bacteriocin is inserted in the membrane. An immunity protein could specifically recognize and block the pore (Ríos Colombo et al. 2018).

Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic membranes of Gram-positive cells by dissipating the transmembrane electrical potential through pore formation with the mannose phosphotransferase system (man-PTS) as the target/receptor. Bacteriocin-producing strains also synthesize a cognate immunity protein that protects them against their own bacteriocins. Zhu et al. 2022 reported the cryo-EM structure of the bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. The complex structure reveals that pediocin-like bacteriocins bind to the same position on the Core domain of the man-PTS, while the C-terminal helical tails of bacteriocins delimit the opening range of the Core domain away from the V-motif domain to facilitate transmembrane pore formation. Upon attack of bacteriocins from the extracellular side, the man-PTS exposes its cytosolic side for recognition of the N-terminal four-helix bundle of the immunity protein. The C-terminal loop of the immunity protein then inserts into the pore and blocks leakage induced by bacteriocins (Zhu et al. 2022).

The generalized transport reaction catalyzed by channel-forming amphipathic peptides is:

Small solutes, electrolytes and water (in) small solutes, electrolytes and water (out)



This family belongs to the Bacterial Bacteriocin (BB) Superfamily.

 

References:

Allison, G.E., C. Fremaux, and T.R. Klaenhammer. (1994). Expansion of bacteriocin activity and host range upon complementation of two peptides encoded within the lactacin F operon. J. Bacteriol. 176: 2235-2241.

Diep, D.B., L.S. Håvarstein, and I.F. Nes. (1995). A bacteriocin-like peptide induces bacteriocin synthesis in Lactobacillus plantarum C11. Mol. Microbiol. 18: 631-639.

Drider D., G. Fimland, Y. Héchard, L.M. McMullen, H. Prévost. (2006). The continuing story of class IIa bacteriocins. Microbiol Mol Biol Rev. 70: 564-582.

Ennahar, S., T. Sashihara, K. Sonomoto, and A. Ishizaki. (2000). Class IIa bacteriocins: biosynthesis, structure, and activity. FEMS Microbiol. Rev. 24: 85-106.

Ferchichi, M., J. Frère, K. Mabrouk, and M. Manai. (2001). Lactococcin MMFII, a novel class IIa bacteriocin produced by Lactococcus lactis MMFII, isolated from a Tunisian dairy product. FEMS Microbiol. Lett. 205: 49-55.

Fimland, G., L. Johnsen, L. Axelsson, M.B. Brurberg, I.F. Nes, V.G.H. Eijsink, and J. Nissen-Meyer. (2000). A C-terminal disulfide bridge in pediocin-like bacteriocins renders bacteriocin activity less temperature dependent and is a major determnant of the antimicrobial spectrum. J. Bacteriol. 182: 2643-2648.

Haugen, H.S., P.E. Kristiansen, G. Fimland, and J. Nissen-Meyer. (2008). Mutational analysis of the class IIa bacteriocin curvacin A and its orientation in target cell membranes. Appl. Environ. Microbiol. 74: 6766-6773.

Heng, N.C., G.A. Burtenshaw, R.W. Jack, and J.R. Tagg. (2007). Ubericin A, a class IIa bacteriocin produced by Streptococcus uberis . Appl. Environ. Microbiol. 73: 7763-7766.

Kaiser, A.L. and T.J. Montville. (1996). Purification of the bacteriocin bavaricin MN and characterization of its mode of action against Listeria monocytogenes Scott A cells and lipid vesicles. Appl. Environ. Microbiol. 62: 4529-4535.

Klaenhammer, T.R. (1993). Genetics of bacteriocins produced by lactic acid bacteria. FEMS Microbiol. Rev. 12: 39-85.

Moll, G.N., W.N. Konings, and A.J.M. Driessen. (1999). Bacteriocins: mechanism of membrane insertion and pore formation. Antonie van Leeuwenhoek 76: 185-198.

Naghmouchi, K., D. Drider, R. Hammami, and I. Fliss. (2008). Effect of Antimicrobial Peptides Divergicin M35 and Nisin A on Listeria monocytogenes LSD530 Potassium Channels. Curr. Microbiol. 56: 609-612.

Nes I.F., D.B. Diep, H. Holo H. (2007). Bacteriocin diversity in Streptococcus and Enterococcus. J Bacteriol. 189: 1189-1198.

Nes, I.F., D.B. Diep, L.S. Håvarstein, M.B. Brurberg, V. Eijsink, and H. Holo. (1996). Biosynthesis of bacteriocins in lactic acid bacteria. Antonie van Leeuwenhoek 70: 113-128.

Ríos Colombo, N.S., M.C. Chalón, F.G. Dupuy, C.F. Gonzalez, and A. Bellomio. (2019). The case for class II bacteriocins: a biophysical approach using "suicide probes" in receptor-free hosts to study their mechanism of action. Biochimie. [Epub: Ahead of Print]

Ríos Colombo, N.S., M.C. Chalón, S.A. Navarro, and A. Bellomio. (2018). Pediocin-like bacteriocins: new perspectives on mechanism of action and immunity. Curr. Genet. 64: 345-351.

Sahl, H.-G. and G. Bierbaum. (1998). Lantibiotics: biosynthesis and biological activities of uniquely modified peptides from Gram-positive bacteria. Annu. Rev. Microbiol. 52: 41-79.

Tomita, H., E. Kamei, and Y. Ike. (2008). Cloning and genetic analyses of the bacteriocin 41 determinant encoded on the Enterococcus faecalis pheromone-responsive conjugative plasmid pYI14: a novel bacteriocin complemented by two extracellular components (lysin and activator). J. Bacteriol. 190: 2075-2085.

Venema, K., G. Venema, and J. Kok. (1995). Lactococcal bacteriocins: mode of action and immunity. Trends Microbiol. 3: 299-304.

Venema, K., J. Kok, J.D. Marugg, M.Y. Toonen, A.M. Ledeboer, G. Venema, and M.L. Chikindas. (1995). Functional analysis of the pediocin operon of Pediococcus acidilactici PAC1.0: PedB is the immunity protein and PedD is the precursor processing enzyme. Mol. Microbiol. 17: 515-522.

Zhu, L., J. Zeng, and J. Wang. (2022). Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins. Appl. Environ. Microbiol. 88: e0048122.

Examples:

TC#NameOrganismal TypeExample
1.C.24.1.1

Class IIa bacteriocin Pediocin PA-1 precursor of 62 aas.  Class II bacteriocins are unmodified membrane-active peptides that act over a narrow spectrum of target bacteria. They bind a specific receptor protein on the membrane to form a pore, leading to membrane permeabilization and cell death. The specific receptor acts as a docking molecule, not as a structural piece of the pore, if the bacteriocin is anchored to the membrane (Ríos Colombo et al. 2019).

Gram-positive bacteria

Pediocin PA-1 precursor of Pediococcus acidilactici

 
1.C.24.1.10Class IIc sec-secreted bacteriocin Enterocin P precursor, EntP Gram-positive bacteria EntP of Enterococcus faecium
 
1.C.24.1.11Class IIa bacteriocin, Ubericin A (Heng et al., 2007)Gram-positive bacteriaUbericin A of Streptococcus uberis (A9Q0M7)
 
1.C.24.1.12Bacteriocin 41 precursor, BacA (pore-forming ability not demonstrated; Tomita et al., 2008)Gram-positive bacteriaBacA of Enterococcus faecalis (B1NRV2)
 
1.C.24.1.13Divergicin M35 (43aas) (Naghmouchi et al., 2008) (The C-terminal residues most resemble BacA (TC#1.C.24.1.12)).BacteriaDivergicin M35 of Carnobacterium divergens (P84962)
 
1.C.24.1.14Listeria-active class IIa peptide, Lactococcin MMFII (may form pores in lipid bilayers, but also in combination with proteins of the mannose phosphotransferase system (PTS)) (Ferchichi et al., 2001).

Gram-positive bacteria

Loctococcin MMFII of Lactococcus lactis (P83002)

 
1.C.24.1.15

Enterocin CRL35 of 58 aas, MunA. Class II bacteriocins are unmodified membrane-active peptides that act over a narrow spectrum of target bacteria. They bind a specific receptor protein on the membrane to form a pore, leading to membrane permeabilization and cell death. The specific receptor acts as a docking molecule, not as a structural part of the pore, but the bacteriocin must be anchored to the membrane (Ríos Colombo et al. 2019).  The ABC efflux porter is MunB (TC# 3.A.1.112.11).  The enterocin CR35 immunity protein is MunC (98 aas; possibly 2 TMSs; Q6TGQ5).

Enterocin ARL35 of Enterococcus mundtii

 
1.C.24.1.16

Uncharacterized protein of 70 aas and 2 TMSs.

UP of Chlamydia trachomatis

 
1.C.24.1.2Class IIa bacteriocin Sakacin P precursor Gram-positive bacteria Sakacin P of Lactobacillus sake
 
1.C.24.1.3Class IIa bacteriocin Pisciolin 126 precursor Gram-positive bacteria Pisciolin 126 precursor of Carnobacterium piscicola
 
1.C.24.1.4Class IIa bacteriocin Enterocin A Gram-positive bacteria Enterocin A of Enterococcus faecium
 
1.C.24.1.5Class IIa bacteriocin Mesentericin Y105 precursor Gram-positive bacteria Mesentericin Y105 precursor of Leuconostoc mesenteroides
 
1.C.24.1.6Class IIa bacteriocin Leucocin A precursor Gram-positive bacteria Leucocin A precursor of Leuconostoc gelidum
 
1.C.24.1.7Class IIa bacteriocin Carno(bacterio)cin B2 precursor Gram-positive bacteria Carnocin B2 of Carnobacterium piscicola
 
1.C.24.1.8Class IIa bacteriocin Sakacin A precursor (Identical to Curvacin A of Lactobacillus curvatus; P0A311) (Haugen et al. 2008).

Gram-positive bacteria

Sakacin A precursor of Lactobacillus sakei ( P0A310)

 
1.C.24.1.9Class IIa bacteriocin Bavaricin MN precursor Gram-positive bacteria Bavaricin MN of Lactobacillus sakei