Molecular diversity and evolution of defensins in the manila clam  Ruditapes philippinarum

Abstract

a b s t r a c tFour types of defensins were identified in Manila clam and designated as Rpdef1, Rpdef2, Rpdef3 and Rpdef4, which encoded a polypeptide of 49, 46, 45 and 42 amino acids, respectively. Sequence alignments indicated that Rpdef1 shared 46.9% identity with Rpdef2, 40.8% with Rpdef3, and 34.7% with Rpdef4. Analysis of transcript polymorphism showed that Rpdef3 accounted for about 60% frequency of Rpdefs occurrence in clams from three geographic origins (Dalian, Qingdao and Hangzhou). By quantitative real-time RT-PCR (qRT-PCR) analysis, the transcripts of Rpdefs were mainly detected in hemocytes and they responded sensitively to bacterial challenge in hemocytes. Evolutionary analysis indicated that all Rpdefs were under positive selection with positively selected basic amino acid residues detected in the C-terminal regions, which perhaps have a functional relevance by modifying the charge distribution of Rpdefs. The results also showed some lineages with dN/dS > 1, suggesting positive selection pressures existed in some lineages of phylogeny tree constructed by mollusk defensins. Overall, our results suggest that Rpdefs perhaps played important roles in host defense and positive selection is the major driving force in generating high diversity of defensins in the Manila clam.

Immunity in Molluscs: Recognition and Effector Mechanisms, with a Focus on Bivalvia

“…This high level of polymorphisms has been also observed in other (but curiously not in all) mussel AMPs with targeted massive parallel sequencing (Rosani et al 2011). Similar considerations are also valid for oyster and clams defensins, whose sequence variability can be linked to relevant directional selection pressures (Schmitt et al 2010;Wang et al 2015c). It is still not entirely clear whether this remarkable sequence diversity is due to a high number of paralogous genes, high allelic variability, RNA editing, or all of these factors combined.…”

“…For example, a foot-specific defensin-like peptide has been linked to byssogenesis in zebra mussels (Xu and Faisal 2010), whereas a gill-specific peptide with marked activity against Gram-positive bacteria has been isolated from gills extracts of C. virginica (Seo et al 2005). Clam and freshwater mussel defensins display a spectrum of activity and tissue specificity similar to those of Mytilus AMPs, but they are reportedly upregulated following bacterial challenges (Peng et al 2012;Wang et al 2015c). These reports suggest that different cysteine-rich peptides currently classified with the same label could have slightly different biological properties depending on the species of origin.…”

High dietary lipid level decreases the immunity and disease resistance of abalone Haliotis discus hannai and affects the perilipin‐2/TLR4, JNK and Keap1/Nrf2 pathways

“…LZ and ACP are also important components of innate immune responses (Ivanina et al, 2014; Uribe et al, 2011). Besides, antibacterial peptides, such as β‐defensin and mytimacin 6, are all important components of innate immune responses which is essential in defending against bacteria, fungi and enveloped viruses (Hoar et al, 1997; Suzuki & Iida, 1992; Wang, Zhang, et al, 2015). In the present study, compared with the 38.25 g/kg of dietary lipid level, the higher dietary lipid level (67.19 g/kg) decreased the activities of LZ and ACP in serum and down‐regulated the mRNA levels of β ‐ defensin and mytimacin 6 in the hepatopancreas of abalone.…”

Antibacterial activities and mechanisms of action of a defensin from manila clam Ruditapes philippinarum

“…Rpdef1 (AFP49990), whereas it had only 15.15% identity with RpdefB (KX45449). From an evolutionary perspective, defensins exhibit an extraordinary diversity in their molecular, structure and functions, which contributes to confer with altered/new pathogens successfully [39]. Tissue distribution of Rpdef1α transcripts and peptide was determined by using qRT-PCR and immunohistochemical technique.…”

“…An EST homologous to defensin was identified through large scale EST sequencing of the constructed cDNA library [39]. Forward primers P1 and forward primers P2 were used to clone the full-length cDNA of Rpdef1α with primer oligo (d T ) as the reverse primer (Table 1).…”