Establishing a reference array for the CS-αβ superfamily of defensive peptides

Abstract

Background“Invertebrate defensins” belong to the cysteine-stabilized alpha-beta (CS-αβ), also known as the scorpion toxin-like, superfamily. Some other peptides belonging to this superfamily of defensive peptides are indistinguishable from “defensins,” but have been assigned other names, making it unclear what, if any, criteria must be met to qualify as an “invertebrate defensin.” In addition, there are other groups of defensins in invertebrates and vertebrates that are considered to be evolutionarily unrelated to those in the CS-αβ superfamily. This complicates analyses and discussions of this peptide group. This paper investigates the criteria for classifying a peptide as an invertebrate defensin, suggests a reference cysteine array that may be helpful in discussing peptides in this superfamily, and proposes that the superfamily (rather than the name “defensin”) is the appropriate context for studying the evolution of invertebrate defensins with the CS-αβ fold.MethodsCS-αβ superfamily sequences were identified from previous literature and BLAST searches of public databases. Sequences were retrieved from databases, and the relevant motifs were identified and used to create a conceptual alignment to a ten-cysteine reference array. Amino acid sequences were aligned in MEGA6 with manual adjustments to ensure accurate alignment of cysteines. Phylogenetic analyses were performed in MEGA6 (maximum likelihood) and MrBayes (Bayesian).ResultsAcross invertebrate taxa, the term “defensin” is not consistently applied based on number of cysteines, cysteine spacing pattern, spectrum of antimicrobial activity, or phylogenetic relationship. The analyses failed to reveal any criteria that unify “invertebrate defensins” and differentiate them from other defensive peptides in the CS-αβ superfamily. Sequences from various groups within the CS-αβ superfamily of defensive peptides can be described by a ten-cysteine reference array that aligns their defining structural motifs.ConclusionsThe proposed ten-cysteine reference array can be used in addition to current nomenclature to compare sequences in the CS-αβ superfamily and clarify their features relative to one another. This will facilitate analysis and discussion of “invertebrate defensins” in an appropriate evolutionary context, rather than relying on nomenclature.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2291-0) contains supplementary material, which is available to authorized users.

Molecular Diversity of Mytilin-Like Defense Peptides in Mytilidae (Mollusca, Bivalvia)

“…Since our investigation has been restricted to the very few genera out of the 63 currently included in the family Mytilidae (i.e., only those with available -omic information), our observations suggest that, along with the discovery of novel AMPs in Mytilidae, the nomenclature scheme of these molecules might require some modification, consistently with the previously reported widespread inconsistencies that affect the nomenclature of CS-αβ peptides in scientific literature [60]. As a matter of fact, the current distinction between mytilins, myticins and defensins is likely to become more and more unclear and AMPs with mixed features are likely to be uncovered.…”

Screening, large-scale production and structure-based classification of cystine-dense peptides

“…5e ). These results echo previous studies identifying knotted CDP sub-type structural clusters, eg., the Möbius and Bracelet clusters of the type 1–4, 2–5, [3–6] cyclotides 6 , and, more broadly, the “ cysteine-stabilized αβ defensins ” 29 . These results also validated our proposed classification focused on core cystines, by revealing hitchin structural homologies despite variable accessory cystines.…”

Functional Insights From the Evolutionary Diversification of Big Defensins

“…Cis-defensins contain two parallel disulfide bonds that stabilize the final β-strand to an α-helix (6). This folding is a key element in a 3D structure known as cysteine-stabilized α-helix/β-sheet (CSαβ) motif, which is shared by all cis-defensins as well as by plant trypsin inhibitors and scorpion neurotoxins (7). In trans-defensins, two disulfide bonds point in opposite directions from the final β-strand and stabilize different secondary structure elements (6).…”