Functional Insights From the Evolutionary Diversification of Big Defensins

Abstract

Big defensins are antimicrobial polypeptides believed to be the ancestors of β-defensins, the most evolutionary conserved family of host defense peptides (HDPs) in vertebrates. Nevertheless, big defensins underwent several independent gene loss events during animal evolution, being only retained in a limited number of phylogenetically distant invertebrates. Here, we explore the evolutionary history of this fascinating HDP family and investigate its patchy distribution in extant metazoans. We highlight the presence of big defensins in various classes of lophotrochozoans, as well as in a few arthropods and basal chordates (amphioxus), mostly adapted to life in marine environments. Bivalve mollusks often display an expanded repertoire of big defensin sequences, which appear to be the product of independent lineage-specific gene tandem duplications, followed by a rapid molecular diversification of newly acquired gene copies. This ongoing evolutionary process could underpin the simultaneous presence of canonical big defensins and non-canonical (β-defensin-like) sequences in some species. The big defensin genes of mussels and oysters, two species target of in-depth studies, are subjected to gene presence/absence variation (PAV), i.e., they can be present or absent in the genomes of different individuals. Moreover, big defensins follow different patterns of gene expression within a given species and respond differently to microbial challenges, suggesting functional divergence. Consistently, current structural data show that big defensin sequence diversity affects the 3D structure and biophysical properties of these polypeptides. We discuss here the role of the N-terminal hydrophobic domain, lost during evolution toward β-defensins, in the big defensin stability to high salt concentrations and its mechanism of action. Finally, we discuss the potential of big defensins as markers for animal health and for the nature-based design of novel therapeutics active at high salt concentrations.

Comparative Genomics Reveals 13 Different Isoforms of Mytimycins (A-M) in Mytilus galloprovincialis

“…The comparative analysis of 16 individual genomes confirmed that PAV plays a major role in shaping the exceptional level of inter-individual sequence diversity in this AMP family (Figure 3), whereas RNA editing processes are likely not involved. Some of the isoforms described in this study (i.e., 18 out of 106) incorporated in-frame STOP codons, which is in line with the tendency of some recently duplicated AMP gene copies to undergo pseudogenization [20]. Cluster H, which mostly comprises sequences including STOP codons, with poor conservation of regulatory elements in the promoter region ( Figure 6) and lack of expression ( Figure 7), is a major candidate as a non-functional evolutionary relict.…”

“…Some of the isoforms described in this study (i.e., 18 out of 106) incorporated in-frame STOP codons, which is in line with the tendency of some recently duplicated AMP gene copies to undergo pseudogenization [ 20 ]. Cluster H, which mostly comprises sequences including STOP codons, with poor conservation of regulatory elements in the promoter region ( Figure 6 ) and lack of expression ( Figure 7 ), is a major candidate as a non-functional evolutionary relict.…”

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

“…Moreover, while just 240 genes (i.e., 1.17% of the total) are presumably dispensable in humans [38], we show that 25% of mussel genes are subject to PAV and that each of the individual mussels resequenced in this study lacked on average 8141 dispensable genes identified in the pan-genome, pointing out that the fraction of protein-coding genes affected by this phenomenon in mussel is 20 times higher than in humans (Additional file 1: Data Note 22). To the best of our knowledge, PAV has been only marginally explored in bivalves as a phenomenon linked to a few gene families involved in immune functions, such as big defensins in Crassostrea gigas [22,24] and myticins and myticalins in M. galloprovincialis [23,25]. Therefore, this is the first study to report the widespread occurrence of gene PAV at a whole-genome scale in the animal kingdom.…”

“…The remarkable level of intraspecific sequence diversity which characterizes several bivalve immune gene families [21], together with the recent implication of high standing genetic variation within natural populations in the extraordinary capability of environmental adaptation of M. galloprovincialis [7], stimulate further investigation about the role played by the genomic complexity of this species in explaining its invasiveness and resilience [18]. While a small but growing number of studies connected gene presence-absence variation (PAV) to the generation of this molecular diversity in a few gene families encoding antimicrobial peptides (AMPs) [22][23][24][25], it is presently unclear whether and to what extent this phenomenon is widespread in bivalve genomes.…”

A Chimeric Cationic Peptide Composed of Human β-Defensin 3 and Human β-Defensin 4 Exhibits Improved Antibacterial Activity and Salt Resistance

“…Research on the modification of defensins is therefore particularly important (Gerdol et al, 2020). It has been previously reported that the common methods for the modification of defensins are as follows (Papo et al, 2002;Zelezetsky and Tossi, 2006): (a) different antimicrobial peptides are spliced to form a new type of active antimicrobial peptides; (b) unnecessary amino acid sequences are cut off or specific amino acids are mutated to cause higher activity in antimicrobial peptides; and (c) according to the bactericidal characteristics of antimicrobial peptides, antimicrobial peptides are designed from scratch.…”