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Comparative Study
. 2012 Jul 11:13:307.
doi: 10.1186/1471-2164-13-307.

Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach

María Estrella Santamaría  1 , Pedro Hernández-Crespo, Félix Ortego, Vojislava Grbic, Miodrag Grbic, Isabel Diaz, Manuel Martinez
Affiliations
Comparative Study

Cysteine peptidases and their inhibitors in Tetranychus urticae: a comparative genomic approach

María Estrella Santamaría et al. BMC Genomics. .

Abstract

Background: Cysteine peptidases in the two-spotted spider mite Tetranychus urticae are involved in essential physiological processes, including proteolytic digestion. Cystatins and thyropins are inhibitors of cysteine peptidases that modulate their activity, although their function in this species has yet to be investigated. Comparative genomic analyses are powerful tools to obtain advanced knowledge into the presence and evolution of both, peptidases and their inhibitors, and could aid to elucidate issues concerning the function of these proteins.

Results: We have performed a genomic comparative analysis of cysteine peptidases and their inhibitors in T. urticae and representative species of different arthropod taxonomic groups. The results indicate: i) clade-specific proliferations are common to C1A papain-like peptidases and for the I25B cystatin family of inhibitors, whereas the C1A inhibitors thyropins are evolutionarily more conserved among arthropod clades; ii) an unprecedented extensive expansion for C13 legumain-like peptidases is found in T. urticae; iii) a sequence-structure analysis of the spider mite cystatins suggests that diversification may be related to an expansion of their inhibitory range; and iv) an in silico transcriptomic analysis shows that most cathepsin B and L cysteine peptidases, legumains and several members of the cystatin family are expressed at a higher rate in T. urticae feeding stages than in embryos.

Conclusion: Comparative genomics has provided valuable insights on the spider mite cysteine peptidases and their inhibitors. Mite-specific proliferations of C1A and C13 peptidase and I25 cystatin families and their over-expression in feeding stages of mites fit with a putative role in mite's feeding and could have a key role in its broad host feeding range.

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Figures

Figure 1
Figure 1
Number of cysteine peptidases and their inhibitors in selected arthropod species. Schematic evolutionary tree of fully sequenced arthropods including for each species the number of inhibitory cystatin (I25CPI) and thyropin (I31Thy) domains and the C1A (papain-like, C1APap) and C13 (legumain-like, C13Leg and GPI:protein transamidases, C13GPI) cysteine peptidases, putative targets of both inhibitors. MYA, million years ago.
Figure 2
Figure 2
Evolutionary features of cystatins in arthropods. (A) Number of cystatin domains in each species distributed in base of their protein architecture. In brackets the number of repeats in multicystatin domains. CPI, single cystatin domain; MultiCPI, multicystatin domains. (B) Phylogenetic tree using the selected cystatin sequences from the different arthropod species. Coloured triangles show species-specific gene proliferations. In brackets the number of proteins in each subtree.
Figure 3
Figure 3
Evolutionary features of thyropins in arthropods. (A) Phylogenetic tree using the selected thyropin sequences from the different arthropod species. Coloured triangles show thyropin gene proliferations associated to other protein domains. In brackets the number of proteins in each subtree. (B) Presence (+) or absence (−) of thyropins members of each subtree in the different arthropod species. WAP, whey acidic protein; ATN, antistasin; SPARC, secreted protein acidic and rich in cysteine.
Figure 4
Figure 4
Evolutionary features of cystatins inT. urticae. (A) Phylogram of T. urticae cystatin sequences showing the presence of functional conserved residues in the four cystatin groups deduced from the phylogenetic tree. Amino acid sequences responsible of the inhibitor-C1A enzyme interaction are shaded in green. Putative sequences involved in C13 legumain inhibition are coloured in purple. Cysteine residues involved in disulphide bridges are in blue. (B) Homology models of T. urticae cystatins created using SWISS-MODEL. The residues in the region that interacts with C1A peptidases are coloured in green. The residues that could be involved in legumain inhibition are coloured in purple. Cysteines are coloured in blue. Red, α-helix; yellow, β-sheets.
Figure 5
Figure 5
Expression profiling of cysteine peptidases and their inhibitors inT. urticae. (A) Number of genes for the different cysteine peptidase and inhibitor groups assigned to the developmental stage (embryo, larvae, nymph and adult) in which their highest expression was detected. (B) Number of genes for the different cysteine peptidase and inhibitor groups assigned to the intervals of normalized expression values (0–10, 10–100, 100–1000, >1000) in which their highest expression was detected, independently of the mite developmental stage analysed. (C) Number of genes for the different cystatin groups (Groups 1 to 4, see Figure 4) assigned to the developmental stage in which their highest expression was detected. (D) Number of genes for the different cystatin groups assigned to the intervals of expression values in which their highest expression was detected, independently of the mite developmental stage analysed.
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