Research article
Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes
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* Corresponding author: Vito Turk vito.turk@ijs.si
1 Department of Molecular and Biomedical Sciences, J. Stefan Institute, Ljubljana, Slovenia
2 Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
BMC Evolutionary Biology 2009, 9:266 doi:10.1186/1471-2148-9-266
Published: 18 November 2009Additional files
Additional file 1:
Supplementary Table 1. A list of eukaryotic representatives of the cystatin superfamily.
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Additional file 2:
Supplementary Table 2. A short list of representatives of cystatins C, E/M and F from vertebrates, CRP1 from rodents and vertebrate stefins (except the amniote stefins A and B).
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Additional file 3:
Supplementary Figure 1. Alignment of stefins and cystatins from the unicellular eukaryotes. The following protein sequences were used: Giardia lamblia (EAA37282) cystatin; Karlodinium micrum stefin (EC157232, Alveolata; Dinophyceae); Euglena gracilis stefin (EC675023); Bigelowiella natans stefin (DR038546, Rhizaria); Isochrysis galbana stefin (EC143415, Haptophyta); Euplotes vannus stefin (CAH04421, Chromalveolata; Ciliophora); Capsaspora owczarzaki stefin (EC736635, Ichthyosporea); 1Naegleria stefin (sc_81); Monosiga brevicollis stefin (estExt_fgenesh2_kg.C_20002 [Monbr1:35345]); 2Naegleria cystatin, (estExt_fgeneshNG_pg.C_180157 [Naegr1:79400]); Phytophthora infestans cystatin EPC2B (AAY21183); Trichomonas vaginalis cystatin (XP_001323421); Prototheca wickerhamii cystatin (EC178142, Chlorophyta); Cyanophora paradoxa cystatin (EG944090, Glaucophyta); Chlamydomonas cystatins estExt_fgenesh2_kg.C_150044 [Chlre3:183419]; Malawimonas californiana cystatin (EC715563); Reclinomonas americana cystatin (EC798377); 1 Homo sapiens stefin B (NP_000091) and 2 Homo sapiens cystatin C (CAA36497). Highly conserved QXVXG region is in bold.
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Additional file 4:
Supplementary Table 3. Distribution of the cystatin superfamily in the plant kingdom.
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Additional file 5:
Supplementary Table 4. Distribution of the cystatin superfamily in Holozoa (Metazoa plus Choanozoa).
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Additional file 6:
Supplementary Table 5. Loss of the cystatin superfamily representatives in Eukaryota.
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Additional file 7:
Supplementary Figure 2. Cystatin from Giardia resembles the most ancestral eukaryotic cystatin. The following protein sequences were used: Giardia lamblia (EAA37282) cystatin; Euglena gracilis stefin (EC675023); Naegleria cystatin, (estExt_fgeneshNG_pg.C_180157 [Naegr1:79400]); Phytophthora infestans cystatin EPC2B (AAY21183); Trichomonas vaginalis cystatin (XP_001323421); Reclinomonas americana cystatin (EC798377); and Homo sapiens cystatin C (CAA36497). Highly conserved QXVXG region is in bold.
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Additional file 8:
Supplementary Figure 3. Legumain binding motif in bifunctional cystatins is conserved in all land plants and in some green algae. The following protein sequences were used: Physcomitrella (estExt_gwp_gw1.C_2380025 [Phypa1_1:195387]); Oryza Oryzacystatin-12 (NP_001042702); Marchantia (BJ841987); Selaginella (BM402705); Zamia fischeri (DY036558); Pseudotsuga menziesii (CN639199); Ginkgo biloba (EX934790); Ceratopteris richardii (BE641752); Amborella trichopoda (CK755139) and green alga Scenedesmus obliquus cystatin (EC184546 + EC184713). Highly conserved QXVXG region and legumain binding motif (SNSL) are in bold.
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Additional file 9:
Supplemetary Figure 4. Gain of signal peptide in some eukaryotic stefins. The following protein sequences were used: Karlodinium micrum stefin (EC157232, Alveolata; Dinophyceae); Capsaspora owczarzaki stefin (EC736635, Ichthyosporea); Hyperamoeba dachnaya stefin (EC853881), Nannochloropsis oculata stefin (EE109499, stramenopiles; Eustigmatophyceae); Euglena gracilis stefin (EC675023); Monosiga stefin (estExt_fgenesh2_kg.C_20002 [Monbr1:35345]); Dictyostelium discoideum (XP_629960) stefin; Reclinomonas stefin (EC788759, Jakobidae); and Homo sapiens stefin B (NP_000091). Highly conserved G and QXVXG region are in bold. The names of the taxa where stefins gained signal peptide are in bold.
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Additional file 10:
Supplementary Table 6. Ancestral states for the cystatin superfamily in eukaryotic supergroups.
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Additional file 11:
Supplementary Figure 5. Functionally important structural motif of eukaryotic cystatins is conserved in the bacterial stefins and cystatins. Highly conserved QXVXG region is in bold. Eukaryotic cystatin (Giardia) and stefin (Euglena) have been included.
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