A New Structure-based Classification of Gram-positive Bacteriocins

Abstract

Bacteriocins are ribosomally-synthesized peptides or proteins produced by a wide range of bacteria. The antimicrobial activity of this group of natural substances against foodborne pathogenic and spoilage bacteria has raised considerable interest for their application in food preservation. Classifying these bacteriocins in well defined classes according to their biochemical properties is a major step towards characterizing these anti-infective peptides and understanding their mode of action. Actually, the chosen criteria for bacteriocins' classification lack consistency and coherence. So, various classification schemes of bacteriocins resulted various levels of contradiction and sorting inefficiencies leading to bacteriocins belonging to more than one class at the same time and to a general lack of classification of many bacteriocins. Establishing a coherent and adequate classification scheme for these bacteriocins is sought after by several researchers in the field. It is not straightforward to formulate an efficient classification scheme that encompasses all of the existing bacteriocins. In the light of the structural data, here we revisit the previously proposed contradictory classification and we define new structure-based sequence fingerprints that support a subdivision of the bacteriocins into 12 groups. The paper lays down a resourceful and consistent classification approach that resulted in classifying more than 70% of bacteriocins known to date and with potential to identify distinct classes for the remaining unclassified bacteriocins. Identified groups are characterized by the presence of highly conserved short amino acid motifs. Furthermore, unclassified bacteriocins are expected to form an identified group when there will be sufficient sequences.

Antimicrobial activity and safety of use of Enterococcus faecium PC4.1 isolated from Mongol yogurt

“…First, Klaenhammer, 1993, then Franz, Belkum, Holzapfel, Abriouel, andGálvez (2007) with some modifications subdivide bacteriocins into four classes according to their biochemical properties: Class I, which corresponds to bacteriocins known as lantibiotics, Class II corresponds to low molecular mass < 10 kDa, heat stable and membrane-active peptides without modified amino acid residues, Class III cyclic antibacterial peptides; and Class IV, large proteins. Recently, Zouhir, Hammami, Fliss, and Hamida (2010) proposed a new structure based classification that regroups bacteriocins into 12 classes.…”

Genetic characterisation and heterologous expression of leucocin C, a class IIa bacteriocin from Leuconostoc carnosum 4010

“…The bacteriocins from LAB have been sorted based on their producers, molecular sizes, structures and/or mode of actions, etc. (Klaenhammer 1993;Jack et al 1995;Cotter et al 2005b;Zouhir et al 2010). Klaenhammer (1993) divided LAB bacteriocins into four classes which are now commonly accepted.…”

“…Recently, a new structure-based classification was proposed. G + bacteriocins were classified into 12 groups based on their amino acid sequences (Zouhir et al 2010).…”

“…Since there is no agreement on the classification of LAB bacteriocins, common structural characteristics have been usually accepted to be the basis for sorting these AMPs (Klaenhammer 1993;Cotter et al 2005b;Zouhir et al 2010;Belguesmia et al 2011). LAB bacteriocins which have been thoroughly studied and abundantly reported are those in class I (lantibiotics) and class II (unmodified bacteriocins).…”

The Two Faces ofLeuconostoc mesenteroidesin Food Systems

“…In addition, the resistance to high temperatures, low pH, and organic solvents, together with the fact that they are easily digested by human proteolytic enzymes, make them an interesting tool for application in food preservation. (19)(20)(21) However, since the discovery of nisin, which is the only bacteriocin approved by Food and Agriculture Organization/World Health Organization (FAO/WHO), US Food and Drug Agency (FDA) and EU Directive (22) , the search for new successful bacteriocins, produced by LAB, is still labor intensive.Generally, bacteriocins are small cationic and amphipathic molecules, presenting α-helix and/or β-sheet protein structure, which can aggregate when present in liquid media or in high concentrations. (23) Bacteriocin production is common for LAB.…”