Characterization of the β-defensin genes in giant panda

Abstract

β-Defensins are small antimicrobial proteins expressed in various organisms and have great potential for improving animal health and selective breeding programs. Giant pandas have a distinctive lineage in Carnivora, and it is unclear whether β-defensin genes have experienced different selective pressures during giant panda evolution. We therefore characterized the giant panda (Ailuropoda melanoleuca) β-defensin gene family through gap filling, TBLASTN, and HMM searches. Among 36 β-defensins identified, gastrointestinal disease may induce the expression of the DEFB1 and DEFB139 genes in the digestive system. Moreover, for DEFB139, a significant positive selection different from that of its homologs was revealed through branch model comparisons. A Pro-to-Arg mutation in the giant panda DEFB139 mature peptide may have enhanced the peptide’s antimicrobial potency by increasing its stability, isoelectric point, surface charge and surface hydrophobicity, and by stabilizing its second β-sheet. Broth microdilution tests showed that the increase in net charge caused by the Pro-to-Arg mutation has enhanced the peptide’s potency against Staphylococcus aureus, although the increase was minor. We expect that additional gene function and expression studies of the giant panda DEFB139 gene could improve the existing conservation strategies for the giant panda.

Antimicrobial activity and structure of a consensus human β‐defensin and its comparison to a novel putative hBD10

“…Also, the proportion of hydrophobic groups in the surface is quite similar in most defensins, ranging from 45% to 65%. Thus, the ability of β‐defensins to interact with microbial membranes is determined more by the ratio of polar to hydrophobic residues on the peptide surface or by the total positive charge, rather than by their individual primary structures or three‐dimensional structures, with the β‐defensin fold or disulfide pattern not being mandatory for antimicrobial activity . Even though these common features are required for antimicrobial activity, structure analyses have failed to detect a common pattern of amino acidic residues for the distribution of polar and hydrophobic residues on the surface of β‐defensins .…”

“…Thus, the ability of β-defensins to interact with microbial membranes is determined more by the ratio of polar to hydrophobic residues on the peptide surface or by the total positive charge, rather than by their individual primary structures or three-dimensional structures, with the β-defensin fold or disulfide pattern not being mandatory for antimicrobial activity. 41,48,49,51,53,54 Even though these common features are required for antimicrobial activity, structure analyses have failed to detect a common pattern of amino acidic residues for the distribution of polar and hydrophobic residues on the surface of β-defensins. 41 However, minor differences in β-defensin structural features may be responsible for their specificity toward certain types of bacteria, fungi or protozoa.…”

Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis)

“…Selection pressure characterization of the CA-BD genes revealed ample evidence of episodic diversifying selection in the ruminants, including the buffalo. Many immune-related genes have revealed evidence of directional or diversifying selection as they have to counter a variety of pathogenic fauna and gut flora which are evolving at high rates of genetic drift and shift [7, 69–71], and [72]. Afferent molecules, which are involved in sensing and recognizing the pathogens, are required to distinguish and thus help to eliminate a variety of pathogens.…”

Genomic evidence of adaptive evolution in the reptilian SOCS gene family

“…We speculate that the positive selection sites in Crocodilia might be linked with their semiaquatic habitat, which contains more environmental pathogens compared to that of their terrestrial relatives. However, the branch-site model analysis did not find any significant positive selection evidence for the remaining seven SOCS genes, which might be due strong purifying selection's masking effect (Zhi-Yi et al, 2018). Differences in SOCS genes across reptiles may also reflect differences in selection pressure.…”