Genome-wide identification and comprehensive analyses of the kinomes in four pathogenic microsporidia species

Abstract

Microsporidia have attracted considerable attention because they infect a wide range of hosts, from invertebrates to vertebrates, and cause serious human diseases and major economic losses in the livestock industry. There are no prospective drugs to counteract this pathogen. Eukaryotic protein kinases (ePKs) play a central role in regulating many essential cellular processes and are therefore potential drug targets. In this study, a comprehensive summary and comparative analysis of the protein kinases in four microsporidia—Enterocytozoon bieneusi, Encephalitozoon cuniculi, Nosema bombycis and Nosema ceranae—was performed. The results show that there are 34 ePKs and 4 atypical protein kinases (aPKs) in E. bieneusi, 29 ePKs and 6 aPKs in E. cuniculi, 41 ePKs and 5 aPKs in N. bombycis, and 27 ePKs and 4 aPKs in N. ceranae. These data support the previous conclusion that the microsporidian kinome is the smallest eukaryotic kinome. Microsporidian kinomes contain only serine-threonine kinases and do not contain receptor-like and tyrosine kinases. Many of the kinases related to nutrient and energy signaling and the stress response have been lost in microsporidian kinomes. However, cell cycle-, development- and growth-related kinases, which are important to parasites, are well conserved. This reduction of the microsporidian kinome is in good agreement with genome compaction, but kinome density is negatively correlated with proteome size. Furthermore, the protein kinases in each microsporidian genome are under strong purifying selection pressure. No remarkable differences in kinase family classification, domain features, gain and/or loss, and selective pressure were observed in these four species. Although microsporidia adapt to different host types, the coevolution of microsporidia and their hosts was not clearly reflected in the protein kinases. Overall, this study enriches and updates the microsporidian protein kinase database and may provide valuable information and candidate targets for the design of treatments for pathogenic diseases.

Figure 1. Composition of the Kinomes by Group Level.

The kinome compositions are colored by group level. For comparison, the data from the model organisms Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, and Dictyostelium discoideum are shown in the figure. A: the number of protein kinases and the group distribution. The number of protein kinases within each group is numbered with Arabic numerals. B: the percentage of the kinome accounted for by the group. The microsporida are indicated as follows: EB, Enterocytozoon bieneusi; EC, Encephalitozoon cuniculi; NB, Nosema bombycis; NC, Nosema ceranae.

Figure 2. Correlation between Kinome Size, Density and Proteome Size.

The ePKinome represents the total number of ePKs in the kinome. Data from the model organisms, the microsporidia, Trypanosomatid, Plasmodium and Toxoplasma were used in the analysis. The scatter plot is colored according to species. The model organism Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Dictyostelium discoideum are respective showed as a black scatter plot.

Figure 3. Comparison of ePK Sequence Lengths in the Microsporidia.

A, B and C show a comparison of the sequence lengths of the domains, the sequence lengths of the full proteins, and the percentage of the domain overlaps with the full proteins, respectively. The microsporidia are abbreviated as follows: EB, Enterocytozoon bieneusi; EC, Encephalitozoon cuniculi; NB, Nosema bombycis; NC, Nosema ceranae.

Figure 4. Conservation of ePK Domains, Key Motifs, and Residues.

The overall height of a stack indicates the sequence conservation at that position. The height of the symbols within each stack indicates the relative frequency of the key amino acid at that position. The conservation of key residues is presented as a percentage and labeled at the bottom of each logo.

Figure 5. Unrooted Tree Representation of the Microsporidian Kinome.

An unrooted tree was constructed using the catalytic domain sequences. The classification of the protein kinase is colored by group level. The species names are abbreviated as follows: EB, Enterocytozoon bieneusi; EC, Encephalitozoon cuniculi; NB, Nosema bombycis; NC, Nosema ceranae.

Figure 6. Kinase Subfamily Gain and Loss.

A: Subfamily distributions in the microsporidia and model organisms. B: Subfamilies lost in the microsporidia.

Figure 7. Nonsynonymous (Ka), Synonymous (Ks) and Ka/Ks Ratio Calculations.

Gene sequence alignments were generated based on the best matches to the human kinase reference at the subfamily level. The Ka, Ks, and Ka/Ks ratios were analyzed to assess and compare the differences in selection pressure among the four species.