In silico analysis of the cyclophilin repertoire of apicomplexan parasites

Abstract

Background: Cyclophilins (Cyps) are peptidyl cis/trans isomerases implicated in diverse processes such as protein folding, signal transduction, and RNA processing. They are also candidate drug targets, in particular for the immunosuppressant cyclosporine A. In addition, cyclosporine is known to exhibit anti-parasitic effects on a wide range of organisms including several apicomplexa. In order to obtain new non-immunosuppressive drugs targeting apicomplexan cyclophilins, a profound knowledge of the cyclophilin repertoire of this phylum would be necessary.

Results: BLAST and maximum likelihood analyses identified 16 different cyclophilin subfamilies within the genomes of Cryptosporidium hominis, Toxoplasma gondii, Plasmodium falciparum, Theileria annulata, Theileria parva, and Babesia bovis. In addition to good statistical support from the phylogenetic analysis, these subfamilies are also confirmed by comparison of cyclophilin domain architecture. Within an individual genome, the number of different Cyp genes that could be deduced varies between 7-9 for Cryptosporidia and 14 for T. gondii. Many of the putative apicomplexan cyclophilins are predicted to be nuclear proteins, most of them presumably involved in RNA processing.

Conclusion: The genomes of apicomplexa harbor a cyclophilin repertoire that is at least as complex as that of most fungi. The identification of Cyp subfamilies that are specific for lower eukaryotes, apicomplexa, or even the genus Plasmodium is of particular interest since these subfamilies are not present in host cells and might therefore represent attractive drug targets.

Figure 1

Unrooted phylogram representing evolutionary relationship between apicomplexan Cyps. (A) Sequences of putative Cyp domains were aligned using ClustalW2 and an unrooted maximum likelihood tree was calculated using PhyML [34]. For comparison, the human and fission yeast Cyp repertoires were included in the analysis. Statistical support of nodes calculated as likelihood ratios is indicated for those nodes with at least 70% support. Cyp subfamilies as revealed by phylogenetic analysis and domain architecture are highlighted by different colors. The dark gray background in the lower part of the figures marks Cyp subfamilies containing Cyp_ABH type or related domains. (B) Subtree from phylogram presented only compressed in (A). The scale bars represent 0.5 substitutions per amino acid position. Ch, C. hominis; Tg, T. gondii; Pf, P. falciparum; Py, Plasmodium yoelii; Bb, B. bovis; Ta, T. annulata; Tp, T. parva; Hs, Homo sapiens; Sp, Schizosaccharomyces pombe. The identity of individual protein sequences used for analyses can be obtained from Tables 1–6 and Table S1 in Additional file 1.

Figure 2

Domain architecture and genomic organization of PPIA-like Cyps. (A) PPIA-like cytosolic Cyps. For each Cyp, proteins domains are shown in the upper and exon/intron structure in the lower panel. Proteins and genes are presented by lines, domains and exons are highlighted by boxes. Separate scale bars are given for protein and genome scemes. (B) Cyps with apicoplast localization signal. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); SP, signal peptide; AP, apicolast transit signal.

Figure 3

PPIA-like Cyps with signal peptide. Domain architecture and genomic organization of Cyps with signal peptide are shown. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); SP, signal peptide.

Figure 4

Mitochondrial Cyps. Domain architecture and genomic organization of mitochondrial Cyps. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); Mito, mitochondrial localization signal.

Figure 5

Cyps with SYF2 domain. Domain architecture and genomic organization of Cyps with SYF2 domain. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); SYF2, SYF2 splicing factor domain (PFAM accession-no.: [pfam08231]); NLS, nuclear localization signal.

Figure 6

Small apicomplexa-specific Cyps. Domain architecture and genomic organization of small apicomplexa-specific Cyps. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); Mito, mitochondrial localization signal.

Figure 7

PPIH-like Cyps. Domain architecture and genomic organization of PPIH-like Cyps. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); NR-rich, Asn-rich domain.

Figure 8

FCBP proteins. Domain architecture and genomic organization of FCBPs from apicomplexa. Species are abbreviated as in Fig. 1. Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); FKBP, FK506-binding domain (PFAM accession-no.: [pfam00254]); TPR, Tetratricopeptide repeat (InterProScan accession-no.: [IPR001440]).

Figure 9

Phylogram showing evolutionary relationships for Cyp and FKBP domains of FCBPs and CFBPs. Cyp domains (A) and FKBP domains (B) of FCBPs and CFBPs were aligned with related domains identified by BLAST analyses in archaebacteria, eubacteria and eukaryotes. Unrooted maximum likelihood phylograms were calculated using PhyML [34]. Statistical support for branches is given as approximate likelihood ratio at the nodes. Only likelihoods of at least 70% are presented. FCBPs of apicomplexa, ciliophora, oomyceta, chlorophyta, and archaebacteria are highlighted in red, orange, yellow, green, and purple, respectively. CFBP of spirochaetes and flavo-/proteobacteria are marked in different blue tones. Species abbreviations: Ta, Theileria annulata; Tp, Theileria parva; Tg, Toxoplasma gondii; Bb, Babesia bovis; Gj, Griffithsia japonica; Pt, Paramecium tetraurelia; Tt, Tetrahymena thermophila; Cw, Crocosphaera watsonii; Pca, Phytophora capsici; Mm, Mus musculus; Eh, Entamoeba histolytica; Ot, Ostreococcus tauri; Tc, Trypanosoma cruzi; Ss, Synechocystis spec.; Cl, Codonopsis lanceolata; Cb, Caenorhabditis briggsae; Bm, Blastupirellula marina; Sa, Stigmatella aurantiaca; Ar, uncultured archaeon GZfos18C8; Cbe, Clostridium beijerincki; Mb, Methanococcoides burtonii; Gf, Gramella forsetii; Ca, Croceibacter atlanticus; Fb, Flavobacteriales bacterium; Fba, Flavobacteria bacterium; Cs, Celluphaga spec. MED134; Lb, Leeuwenhoekiella blandensis; Dp, Desulfotalea psychrophilia; Td, Treponema denticulata; Bh, Borrelia hermsii; Hm, Haloarcula marismortui; Haloquadrantum walsbyi; Mg, Magnaporthe grisea; Pn, Phaeosphaeria nodorum; Aa, Aedes aegyptii; Lm, Leishmania major; Tn, Tetraodon nigroviridis; Py, Plasmodium yoelii; Pc, Plasmodium chabaudi; Pb, Plasmodium berghei; Pf, Plasmodium falciparum; Ec, Entodinium caudatum; Te, Trichodesmium erythraeum; No, Nitrosococcus oceani; Ps, Polaromonas spec. Js666; Yl, Yarrowia lipolytica; Gs, Geobacter spec. FRC-32; Mba, Methanosarcina barkeri; Mbu, Methanococcoides burtonii; Mt, Methanotherococcus thermolithotrophicus; Ma, Methanosarcina acetivorans; Mma, Methanoculleus marisnigri; Cf, Chlorobium ferrooxidans.

Figure 10

Cyps with WD40 repeats. Domain architecture and genomic organization of Cyps with WD40 repeats. Species are abbreviated as in Fig. 1. NLS, nuclear localization signal; WD40 repeat (CD accession-no.: [cl02567]), Cyp_ABH, ABH-type Cyp domain (CD accession-no.: [cd01926]); NR, Asp-rich region; KR, Lys-rich region.

Figure 11

PPIL3-like Cyps. Domain architecture and genomic organization of PPIL3-like Cyps. Species are abbreviated as in Fig. 1. Cyp_PPIL3, PPIL3-type Cyp domain (CD accession-no: [cd01928]).

Figure 12

PPIL2-like Cyps. Domain architecture and genomic organization of Cyps with RING finger domain. Species are abbreviated as in Fig. 1. RING, RING finger domain (Interpro accession-no.: IPR003613); Cyp_RING, RING-type Cyp domain (CD accession-no: [cl00197]); NLS, nuclear localization signal.

Figure 13

CeCyp16-like Cyps. Domain architecture and genomic organization of CeCyp16-like Cyps. Species are abbreviated as in Fig. 1. Cyp_CeCyp16, CeCyp16-type Cyp domain (CD accession-no: [cd01925]); NLS, nuclear localization signal; coiled-coil, coiled-coil protein interaction region; RR, Arg-rich region; KR, Lys-rich region.