Lactococcin-like family
Identifiers
SymbolLactococcin
PfamPF04369
Pfam clanCL0400
InterProIPR007464
TCDB1.C.22
OPM superfamily141
OPM protein6gnz
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
Bacteriocin (Lactococcin_972)
7.4 kDa Lactococcin 972 PDB: 2LGN​
Identifiers
SymbolLactococcin_972
PfamPF09683
InterProIPR006540
TCDB1.C.37
OPM superfamily457
OPM protein2lgn
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

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.[1]

Bacteriocins were first discovered by André Gratia in 1925.[2][3] 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 had made by E. coli.

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,[4] 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.[5]

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 (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 Yersia pestis.[6] Pseudomonas -genus produces bacteriocins called pyocins. S-type pyocins belong to CLBs, but R- and F-type pyocins belong to tailocins.[7]

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).[4]

Tailocins

Most well studied are the tailocins of Pseudomonas aeruginosa. They can be further subdivided into R-type and F-type pyocins.[8] 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 a kin bacteria is spotted in the environment of the competitive bacteria. 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.[9]

From Gram positive bacteria

Bacteriocins from Gram positive bacteria are typically classified into Class I, Class IIa/b/c, and Class III. [10]

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 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.[11][12] 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.[13]
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.[14]
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.[15]

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.[16]

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.[17] 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.[18][19]

Databases

Two databases of bacteriocins are available: BAGEL[20] and BACTIBASE.[21][22]

Uses

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.[23] Generally bacteriocins 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.[23]

Furthermore, bacteriocins active against E. coli, Salmonella and Pseudomonas aeruginosa have been produced in plants with the aim for them to be used as food additives.[24][25][26] The use of bacteriocins in food has been generally regarded as safe by the FDA.[24]

Moreover, has been recently demonstrated that bacteriocins active against plant pathogenic bacteria can be expressed in plants to provide robust resistance against plant disease.[27]

Relevance to human health

Bacteriocins are made by non-pathogenic Lactobacilli in the vagina and help maintain the stability of the vaginal microbiome.[28]

Research

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.[1] 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.[29]

As of 2014 some bacteriocins had been studied in in vitro studies to see if they can stop viruses 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 subtilosin 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.[30]

As of 2009, some bacteriocins, cytolysin, pyocin S2, colicins A and E1, and the microcin MccE492[31] had been tested on eukaryotic cell lines and in a mouse model of cancer.[32]

By name

See also

References

  1. 1 2 Cotter PD, Ross RP, Hill C (February 2013). "Bacteriocins - a viable alternative to antibiotics?". Nature Reviews. Microbiology. 11 (2): 95–105. doi:10.1038/nrmicro2937. PMID 23268227. S2CID 37563756.
  2. ↑ Gratia A (1925). "Sur un remarquable exemple d'antagonisme entre deux souches de coilbacille" [On a remarkable example of antagonism between two strains of coilbacille]. Compt. Rend. Soc. Biol. (in French). 93: 1040–2. NAID 10027104803.
  3. ↑ Gratia JP (October 2000). "André Gratia: a forerunner in microbial and viral genetics". Genetics. 156 (2): 471–6. doi:10.1093/genetics/156.2.471. PMC 1461273. PMID 11014798.
  4. 1 2 Cascales E, Buchanan SK, Duché D, Kleanthous C, Lloubès R, Postle K, et al. (March 2007). "Colicin biology". Microbiology and Molecular Biology Reviews. 71 (1): 158–229. doi:10.1128/MMBR.00036-06. PMC 1847374. PMID 17347522.
  5. ↑ Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, et al. (January 2013). "Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature". Natural Product Reports. 30 (1): 108–60. doi:10.1039/c2np20085f. PMC 3954855. PMID 23165928.
  6. ↑ Behrens HM, Six A, Walker D, Kleanthous C (April 2017). Walker D (ed.). "The therapeutic potential of bacteriocins as protein antibiotics". Emerging Topics in Life Sciences. 1 (1): 65–74. doi:10.1042/ETLS20160016. PMC 7243282. PMID 33525816.
  7. ↑ Michel-Briand Y, Baysse C (May 2002). "The pyocins of Pseudomonas aeruginosa". Biochimie. 84 (5–6): 499–510. doi:10.1016/S0300-9084(02)01422-0. PMID 12423794.
  8. ↑ Ghequire MG, De Mot R (July 2014). "Ribosomally encoded antibacterial proteins and peptides from Pseudomonas". FEMS Microbiology Reviews. 38 (4): 523–68. doi:10.1111/1574-6976.12079. PMID 24923764.
  9. ↑ Vacheron J, Heiman CM, Keel C (January 2021). "Live cell dynamics of production, explosive release and killing activity of phage tail-like weapons for Pseudomonas kin exclusion". Communications Biology. 87 (4): 87. doi:10.1038/s42003-020-01581-1. PMC 7815802. PMID 33469108.
  10. ↑ Cotter PD, Hill C, Ross RP (February 2006). "What's in a name? Class distinction for bacteriocins". Nature Reviews Microbiology. 4 (2): 160. doi:10.1038/nrmicro1273-c2. S2CID 29421506. is author reply to comment on article :Cotter PD, Hill C, Ross RP (October 2005). "Bacteriocins: developing innate immunity for food". Nature Reviews. Microbiology. 3 (10): 777–88. doi:10.1038/nrmicro1273. PMID 16205711. S2CID 19040535.
  11. ↑ Zhu, Liyan; Zeng, Jianwei; Wang, Chang; Wang, Jiawei (2022-02-08). "Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1". Applied and Environmental Microbiology. 88 (3): e0199221. doi:10.1128/AEM.01992-21. ISSN 1098-5336. PMC 8824269. PMID 34851716.
  12. ↑ Zhu, Liyan; Zeng, Jianwei; Wang, Jiawei (2022-06-15). "Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins". Applied and Environmental Microbiology. 88 (13): e0048122. doi:10.1128/aem.00481-22. ISSN 1098-5336. PMC 9275228. PMID 35703550.
  13. ↑ Heng NC, Wescombe PA, Burton JP, Jack RW, Tagg JR (2007). "The Diversity of Bacteriocins in Gram-Positive Bacteria". Bacteriocins. pp. 45–92. doi:10.1007/978-3-540-36604-1_4. ISBN 978-3-540-36603-4.
  14. ↑ Nissen-Meyer J, Rogne P, Oppegård C, Haugen HS, Kristiansen PE (January 2009). "Structure-function relationships of the non-lanthionine-containing peptide (class II) bacteriocins produced by gram-positive bacteria". Current Pharmaceutical Biotechnology. 10 (1): 19–37. doi:10.2174/138920109787048661. PMID 19149588.
  15. ↑ Netz DJ, Pohl R, Beck-Sickinger AG, Selmer T, Pierik AJ, Bastos M, Sahl HG (June 2002). "Biochemical characterisation and genetic analysis of aureocin A53, a new, atypical bacteriocin from Staphylococcus aureus". Journal of Molecular Biology. 319 (3): 745–56. doi:10.1016/S0022-2836(02)00368-6. PMID 12054867.
  16. ↑ Netz DJ, Sahl HG, Marcelino R, dos Santos Nascimento J, de Oliveira SS, Soares MB, et al. (August 2001). "Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus". Journal of Molecular Biology. 311 (5): 939–49. doi:10.1006/jmbi.2001.4885. PMID 11531330.
  17. ↑ Bastos MD, Coutinho BG, Coelho ML (April 2010). "Lysostaphin: A Staphylococcal Bacteriolysin with Potential Clinical Applications". Pharmaceuticals. 3 (4): 1139–1161. doi:10.3390/ph3041139. PMC 4034026. PMID 27713293.
  18. ↑ Oman TJ, Boettcher JM, Wang H, Okalibe XN, van der Donk WA (February 2011). "Sublancin is not a lantibiotic but an S-linked glycopeptide". Nature Chemical Biology. 7 (2): 78–80. doi:10.1038/nchembio.509. PMC 3060661. PMID 21196935.
  19. ↑ Stepper J, Shastri S, Loo TS, Preston JC, Novak P, Man P, et al. (February 2011). "Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins". FEBS Letters. 585 (4): 645–50. doi:10.1016/j.febslet.2011.01.023. PMID 21251913. S2CID 29992601.
  20. ↑ de Jong A, van Hijum SA, Bijlsma JJ, Kok J, Kuipers OP (July 2006). "BAGEL: a web-based bacteriocin genome mining tool". Nucleic Acids Research. 34 (Web Server issue): W273-9. doi:10.1093/nar/gkl237. PMC 1538908. PMID 16845009.
  21. ↑ Hammami R, Zouhir A, Ben Hamida J, Fliss I (October 2007). "BACTIBASE: a new web-accessible database for bacteriocin characterization". BMC Microbiology. 7 (1): 89. doi:10.1186/1471-2180-7-89. PMC 2211298. PMID 17941971.
  22. ↑ Hammami R, Zouhir A, Le Lay C, Ben Hamida J, Fliss I (January 2010). "BACTIBASE second release: a database and tool platform for bacteriocin characterization". BMC Microbiology. 10 (1): 22. doi:10.1186/1471-2180-10-22. PMC 2824694. PMID 20105292.
  23. 1 2 Fahim HA, Khairalla AS, El-Gendy AO (16 September 2016). "Nanotechnology: A Valuable Strategy to Improve Bacteriocin Formulations". Frontiers in Microbiology. 7: 1385. doi:10.3389/fmicb.2016.01385. PMC 5026012. PMID 27695440.
  24. 1 2 Schulz S, Stephan A, Hahn S, Bortesi L, Jarczowski F, Bettmann U, et al. (October 2015). "Broad and efficient control of major foodborne pathogenic strains of Escherichia coli by mixtures of plant-produced colicins". Proceedings of the National Academy of Sciences of the United States of America. 112 (40): E5454-60. Bibcode:2015PNAS..112E5454S. doi:10.1073/pnas.1513311112. PMC 4603501. PMID 26351689.
  25. ↑ Schneider T, Hahn-Löbmann S, Stephan A, Schulz S, Giritch A, Naumann M, et al. (March 2018). "Plant-made Salmonella bacteriocins salmocins for control of Salmonella pathovars". Scientific Reports. 8 (1): 4078. Bibcode:2018NatSR...8.4078S. doi:10.1038/s41598-018-22465-9. PMC 5840360. PMID 29511259.
  26. ↑ Paškevičius Š, Starkevič U, Misiūnas A, Vitkauskienė A, Gleba Y, Ražanskienė A (3 October 2017). "Plant-expressed pyocins for control of Pseudomonas aeruginosa". PLOS ONE. 12 (10): e0185782. Bibcode:2017PLoSO..1285782P. doi:10.1371/journal.pone.0185782. PMC 5626474. PMID 28973027.
  27. ↑ Rooney WM, Grinter RW, Correia A, Parkhill J, Walker DC, Milner JJ (May 2020). "Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae". Plant Biotechnology Journal. 18 (5): 1296–1306. doi:10.1111/pbi.13294. PMC 7152609. PMID 31705720.
  28. ↑ Nardis C, Mosca L, Mastromarino P (Sep–Oct 2013). "Vaginal microbiota and viral sexually transmitted diseases". Annali di Igiene. 25 (5): 443–56. doi:10.7416/ai.2013.1946. PMID 24048183.
  29. ↑ Rezaei Javan R, van Tonder AJ, King JP, Harrold CL, Brueggemann AB (August 2018). "Genome Sequencing Reveals a Large and Diverse Repertoire of Antimicrobial Peptides". Frontiers in Microbiology. 9 (9): 2012. doi:10.3389/fmicb.2018.02012. PMC 6120550. PMID 30210481.
  30. ↑ 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 (3–4): 177–85. doi:10.1007/s12602-014-9162-6. PMID 24880436. S2CID 43785241.
  31. ↑ Huang K, Zeng J, Liu X, Jiang T, Wang J (April 2021). "Structure of the mannose phosphotransferase system (man-PTS) complexed with microcin E492, a pore-forming bacteriocin". Cell Discovery. 7 (1): 20. doi:10.1038/s41421-021-00253-6. PMC 8021565. PMID 33820910.
  32. ↑ Lagos R, Tello M, Mercado G, García V, Monasterio O (January 2009). "Antibacterial and antitumorigenic properties of microcin E492, a pore-forming bacteriocin". Current Pharmaceutical Biotechnology. 10 (1): 74–85. doi:10.2174/138920109787048643. hdl:10533/142500. PMID 19149591.
  33. ↑ Naclerio G, Ricca E, Sacco M, De Felice M (December 1993). "Antimicrobial activity of a newly identified bacteriocin of Bacillus cereus". Applied and Environmental Microbiology. 59 (12): 4313–6. Bibcode:1993ApEnM..59.4313N. doi:10.1128/AEM.59.12.4313-4316.1993. PMC 195902. PMID 8285719.
  34. ↑ Kawai Y, Kemperman R, Kok J, Saito T (October 2004). "The circular bacteriocins gassericin A and circularin A" (PDF). Current Protein & Peptide Science. 5 (5): 393–8. doi:10.2174/1389203043379549. PMID 15544534. S2CID 25735597.
  35. ↑ Pandey N, Malik RK, Kaushik JK, Singroha G (November 2013). "Gassericin A: a circular bacteriocin produced by lactic acid bacteria Lactobacillus gasseri". World Journal of Microbiology & Biotechnology. 29 (11): 1977–87. doi:10.1007/s11274-013-1368-3. PMID 23712477. S2CID 30931536.
  36. ↑ Mørtvedt CI, Nissen-Meyer J, Sletten K, Nes IF (June 1991). "Purification and amino acid sequence of lactocin S, a bacteriocin produced by Lactobacillus sake L45". Applied and Environmental Microbiology. 57 (6): 1829–34. Bibcode:1991ApEnM..57.1829M. doi:10.1128/AEM.57.6.1829-1834.1991. PMC 183476. PMID 1872611.
  37. ↑ Bogaardt C, van Tonder AJ, Brueggemann AB (July 2015). "Genomic analyses of pneumococci reveal a wide diversity of bacteriocins - including pneumocyclicin, a novel circular bacteriocin". BMC Genomics. 16 (1): 554. doi:10.1186/s12864-015-1729-4. PMC 4517551. PMID 26215050.
  38. ↑ Michel-Briand Y, Baysse C (2002). "The pyocins of Pseudomonas aeruginosa". Biochimie. 84 (5–6): 499–510. doi:10.1016/s0300-9084(02)01422-0. PMID 12423794.
  39. ↑ Kabuki T, Saito T, Kawai Y, Uemura J, Itoh T (February 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): 145–56. doi:10.1016/s0168-1605(96)01180-4. PMID 9039561.
  40. ↑ Wescombe PA, Upton M, Dierksen KP, Ragland NL, Sivabalan S, Wirawan RE, et al. (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): 1459–66. Bibcode:2006ApEnM..72.1459W. doi:10.1128/aem.72.2.1459-1466.2006. PMC 1392966. PMID 16461700.
  41. ↑ Müller I, Lurz R, Geider K (July 2012). "Tasmancin and lysogenic bacteriophages induced from Erwinia tasmaniensis strains". Microbiological Research. 167 (7): 381–7. doi:10.1016/j.micres.2012.01.005. PMID 22381912.
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