Proteases of Dermatophagoides pteronyssinus

Abstract

Since the discovery that Der p 1 is a cysteine protease, the role of proteolytic activity in allergic sensitization has been explored. There are many allergens with proteolytic activity; however, exposure from dust mites is not limited to allergens. In this paper, genomic, transcriptomic and proteomic data on Dermatophagoides pteronyssinus (DP) was mined for information regarding the complete degradome of this house dust mite. D. pteronyssinus has more proteases than the closely related Acari, Dermatophagoides farinae (DF) and Sarcoptes scabiei (SS). The group of proteases in D. pteronyssinus is found to be more highly transcribed than the norm for this species. The distribution of protease types is dominated by the cysteine proteases like Der p 1 that account for about half of protease transcription by abundance, and Der p 1 in particular accounts for 22% of the total protease transcripts. In an analysis of protease stability, the group of allergens (Der p 1, Der p 3, Der p 6, and Der p 9) is found to be more stable than the mean. It is also statistically demonstrated that the protease allergens are simultaneously more highly expressed and more stable than the group of D. pteronyssinus proteases being examined, consistent with common assumptions about allergens in general. There are several significant non-allergen outliers from the normal group of proteases with high expression and high stability that should be examined for IgE binding. This paper compiles the first holistic picture of the D. pteronyssinus degradome to which humans may be exposed.

Keywords: allergen source-derived proteases; allergens; allergic sensitization; exposure; proteases.

Figure 1

Venn diagram and statistics of proteases from three Acari. (A) Venn diagram of orthologous clusters of proteases from D. pteronyssinus, D. farinae, and Sarcoptes scabiei; (B) Total numbers of clusters in each species; and (C) Number of shared elements by number of groups.

Figure 2

Statistical analyses of protease expression in D. pteronyssinus. (A) Histogram and boxplot of log₁₀ fragments per kilobase per million reads (FPKM) (relative expression) of proteases in DP (plus signs indicate outliers from the quartile analysis); (B) Histogram and boxplot of log₁₀ FPKM of all transcripts in DP; (C) Histogram of protease relative expression subdivided by protease type; (D) Boxplot of protease relative expression subdivided by type; and (E) Bar graph and inset pie chart of FPKM relative expression (not scaled by log₁₀) colored according to protease type with scaled insets for Der p 1 and DEPT_09745.

Figure 3

Alignment of catalytic residues of Der p 1 with two new C1 proteases. A multi-sequence alignment is shown for DEPT_09745, DEPT_09537 and Der p 1 over the region containing the Cys/His/Asn catalytic triad residues of Der p 1 in red (Cys34, His170, Asn190). “*”—Identity; “:”—strong similarity; “.”—similarity.

Figure 4

Stability and expression of DP proteases. Panels (A,B) are the same stability and expression data grouped differently. The colors in (A) refer to: green, aspartyl; yellow, cysteine; black, metallo; blue, serine; red, threonine proteases. The colors in (B) refer to: light blue, non-allergens, and purple, allergens. Dotted lines are the mean for the axis measurement of all proteases; x, GND½; y, log₁₀ FPKM. Ellipses are centered at the mean in x and y of each group and the radii are determined by the standard deviations in x and y of each group.

Figure 5

Phylogenetic tree of cysteine- and trypsin-related proteases within the Astigmata mites. A circular tree is depicted. 100 bootstrap iterations of the data were performed to estimate significance. All nodes with bootstrapping values >50 are shown. The branch lengths do not reflect the distances between the proteins in the tree but are drawn for visual clarity. The cysteine proteases are highlighted with a blue ball while all of the allergens are highlighted with red balls. The S. scabiei gene family expansion is noted by the branches highlighted in red. All of the proteases fitting the PFAM peptidase_C1 model are prefixed “C1”.