New fungal defensin-like peptides provide evidence for fold change of proteins in evolution

Abstract

Defensins containing a consensus cystine framework, Cys[1]…Cys[2]X3Cys[3]…Cys[4]… Cys[5]X1Cys[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus – Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds.

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

“…Therefore, it was not possible to prospectively generate a complete CDP catalogue based solely on sequence. Previous proposed structural classification schemes 28 – 30 , sometimes also relying on inconsistent functional annotations, were too narrow to be applied globally, also precluding a unified classification based solely on structure.…”

Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria

“…Since CPP2 and Copsin are functionally redundant regarding their antibacterial activity, this special regulation pattern implies a mechanism where a Csαβ-defensin-mediated, constitutive defense of C. cinerea against bacteria is fortified in response to bacterial challenge. Genes coding for Csαβ defensins (of different classes) have recently been identified in a wide range of fungal genomes and, based on characterized antibacterial activities thus far, might be part of a general defense of fungi against bacteria [61, 62, 76–78]. Accordingly, structural modeling predicts additional defensin-like proteins among our set of bacteria-induced, non-annotated C. cinerea proteins.…”

Recombinant AfusinC, an anionic fungal CSαβ defensin from Aspergillus fumigatus, exhibits antimicrobial activity against gram-positive bacteria

“…However, more than 60% of the putative fungal CSαβ defensins are anionic [ 11 ]. Probably not all of them are involved in the defence response because, despite their CSαβ motif, some of them have been found to lack antibacterial activity [ 34 ]. Moreover, CSαβ defensins exhibit a variety of biological functions alternative to antimicrobial activity [ 6 ].…”