| Literature DB >> 18372053 |
Louise A Ryan1, Elizabeth Hoey, Alan Trudgett, Ian Fairweather, Marc Fuchs, Mark W Robinson, Emma Chambers, David J Timson, Eimear Ryan, Theresa Feltwell, Al Ivens, Geoffrey Bentley, David Johnston.
Abstract
We have identified five alpha-tubulin and six beta-tubulin isotypes that are expressed in adult Fasciola hepatica. Amino acid sequence identities ranged between 72 and 95% for fluke alpha-tubulin and between 65 and 97% for beta-tubulin isotypes. Nucleotide sequence identity ranged between 68-77% and 62-80%, respectively, for their coding sequences. Phylogenetic analysis indicated that two of the alpha-tubulins and two of the beta-tubulins were distinctly divergent from the other trematode and nematode tubulin sequences described in this study, whereas the other isotypes segregated within the trematode clades. With regard to the proposed benzimidazole binding site on beta-tubulin, three of the fluke isotypes had tyrosine at position 200 of beta-tubulin, two had phenylalanine and one had leucine. All had phenylalanine at position 167 and glutamic acid at position 198. When isotype RT-PCR fragment sequences were compared between six individual flukes from the susceptible Cullompton isolate and from seven individual flukes from the two resistant isolates, Sligo and Oberon, these residues were conserved.Entities:
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Year: 2008 PMID: 18372053 PMCID: PMC3820024 DOI: 10.1016/j.molbiopara.2008.02.001
Source DB: PubMed Journal: Mol Biochem Parasitol ISSN: 0166-6851 Impact factor: 1.759
Primers used for the determination of tubulin isotype sequences
| α-tubulin primers | |
| α-tub 44 | 5′ AAATGGGAAATGCTTGYT 3′ |
| α-tub 637 | 5′ AAATATCATAAATGGCCTCGTT 3′ |
| α-tub 397 | 5′ CARGGWTTYCTRATWTTCCAYTC 3′ |
| α-tub 1160 | 5′ GCTTCRGCNATNGCSCTNGT 3′ |
| A1 490r 5′RACE | 5′ GCTCAACCACGGCAGTGGAGATTTG 3′ |
| A4 718r 5′RACE | 5′ CGGCCGTGAGGGTACTGATCACTTG 3′ |
| A4 543f 3′RACE | 5′ CGGTTCCGGATTCACAGCACTACTG 3′ |
| β-tubulin primers | |
| β-tub 295f | 5′AAYAAYTGGGCYAARGGNCAYTA3′ |
| β-tub 1230r | 5′ TCRGTRAAYTCCATYTCRTCCAT 3′ |
| β-tub 1281r | 5′CTCCTGGTATTGCTGATATT |
| B2 737r 5′RACE | 5′ AGCTGACCAGGGAAACGCAACAGG 3′ |
| B2 712f 3′RACE | 5′ ACCTGTTTGCGTTTCCCTGGTCAGC 3′ |
| B3 519r 5′RACE | 5′ GGTCAGCTTCAAAGTGCGGAAGCAA 3′ |
| B3 361f 3′RACE | 5′ CTCCGTGGTTCCCTCACCCAAGGTA 3′ |
| B4 756r 5′RACE | 5′ TTCCGGAGATCGGCGTTCAGTTGAC 3′ |
| B6 714r 5′RACE | 5′ GTGGTCACACCGGACATTGTTGCACT 3′ |
| B6 506f 3′RACE | 5′ GCGTATCCGTCGCCCAAAGTATCTGA 3′ |
| Anchored primers used to amplify isotype coding sequences | |
| α-tub1Fcomp | 5′GACGACGACAAGATGCGCGAATGCATCAGTATTC3′ |
| α-tub1Rcomp | 5′GAGGAGAAGCCCGGTTTAATATTCTTCACCCAATTCCTGCCC3′ |
| α-tub2Fcomp | 5′GACGACGACAAGATGCGCGAATGTATCAGTGTTC3′ |
| α-tub2Rcomp | 5′GAGGAGAAGCCCGGTTTAGTATTCTTCACCCTCGCCTTC3′ |
| α-tub3Fcomp | 5′GACGACGACAAGATGCGTGAATGCATCAGCGTAC3′ |
| α-tub3Rcomp | 5′GAGGAGAAGCCCGGTTTAGTATTCCGCCTCTTCTTCCTC3′ |
| α-tub4Fcomp | 5′GACGACGACAAGATGAGGGAATGTATCAGTCTGC3′ |
| α-tub4Rcomp | 5′GAGGAGAAGCCCGGTTCAGTATTCCACTTTTTCGTCCAAAATG3′ |
| α-tub5Fcomp | 5′GACGACGACAAGATGACCAATAATCATTCACGCG3′ |
| α-tub5Rcomp | 5′GAGGAGAAGCCCGGTTCAGTCTAACTCCTTATCATCC3′ |
| β-tub1Fcomp | 5′GACGACGACAAGATGCGGGAAATAGTTCACC3′ |
| β-tub1Rcomp | 5′GAGGAGAAGCCCGGTTTAGACTTGTTCTCCTTCC3′ |
| β-tub2Fcomp | 5′GACGACGACAAGATGCGTGAAATCGTTCATATTC3′ |
| β-tub2Rcomp | 5′GAGGAGAAGCCCGGTTTAGGCTTCCTCAGCCTCTTCATC3′ |
| β-tub3Fcomp | 5′GACGACGACAAGATGCGTGAGATTGTCCACATTC3′ |
| β-tub3Rcomp | 5′GAGGAGAAGCCCGGTCTACGCTTCCTCATTCTCTTC3′ |
| β-tub4Fcomp | 5′GACGACGACAAGATGCGGGAAATCGTGCATATG3′ |
| β-tub4Rcomp | 5′GAGGAGAAGCCCGGTTTAAGCCTCCTCTTCCCCTTCCTC3′ |
| β-tub5Fcomp | 5′GACGACGACAAGATGCGGGAAATTGTTTTTCTACAAG3′ |
| β-tub5Rcomp | 5′GAGGAGAAGCCCGGTTCAAATATCAACCTTTGCGTCTTG3′ |
| β-tub6Fcomp | 5′GACGACGACAAGATGCGTGAAATTATCTACATTCAG3′ |
| β-tub6Rcomp | 5′GAGGAGAAGCCCGGTCTAATGTTCAACATCTTGAAATTG3′ |
Primers and PCR conditions taken from [13]. Y: pyrimidine; R: purine; S: C/G; W: A/T; N: any nucleotide.
Fig. 1Clustal W sequence alignments of Cullompton triclabendazole-susceptible isolate (A) α-tubulin isotypes, F.hep-α-tub1, 2, 3, 4 and 5 and (B) β-tubulin isotypes, F.hep-β-tub1, 2, 3, 4, 5 and 6 predicted from their coding sequences. The tubulin signal sequence motifs are underlined and the axonemal signal motif is in bold in the β-tubulin alignments. The secondary structures of porcine α- and β-tubulin are shown above the alignments (adapted from [14]). Gaps represent regions of low density in the crystal structure data. H: helix, S: β-strand. Initial full-length sequence was obtained using data from PCR-based experiments using Cullompton isolate cDNA and from adult Fasciola EST clones. Primer sequences are given in Table 1. When isotype coding sequences were complete, primers were developed that allowed full-length coding sequences to be cloned and sequenced from Cullompton isolate cDNA. These sequences are presented. The initial sequences were established as follows. (A) α-tubulin isotypes. F.hep-α-tub1: a cloned PCR fragment generated using degenerate primers α-tub 44 and α-tub 637 (Table 1) from Fasciola cDNA gave 600 bp of the coding sequence of F.hep-α-tub1. The 5′ end of the coding sequence was obtained from a RACE product using primer A1 490r 5′RACE. The EST clone 36h02 contained the 3′ end of this isotype. F.hep-α-tub2: the complete coding sequence was determined from EST clones 51d06 and 52e12. F.hep-α-tub3: the complete coding sequence was determined from EST clone 42e05. F.hep-α-tub4: an PCR fragment, generated using primers α-tub 397 and α-tub 1160, gave 760 bp of the F.hep-α-tub4 coding sequence and was completed using 5′ and 3′RACE products generated using primers A4 718r 5′RACE and A4 543f 3′RACE, respectively. F.hep-α-tub5: plasmid inserts in clones 09c01 and 39b11 contained the complete-coding sequence. (B) β-tubulin isotypes. F.hep-β-tub1: the EST clone 06g07 contained the 3′ end of the coding region of the coding sequence and completed the previously reported sequence of F.hep-β-tub1 [11]. F.hep-β-tub2 and 3: cloned fragments (approximately 1 kb), generated using degenerate primers β-tub 295f and β-tub 1230r and conditions given in [13], yielded two separate partial coding sequences for these isotypes. They were completed from 5′ and 3′RACE cDNA fragments generated using primers B2 737r 5′RACE and 712F 3′RACE for F.hep-β-tub2 and primers B3 519r 5′RACE and B3 361f 3′RACE for F.hep-β-tub3. F.hep-β-tub4: the plasmid insert of EST clone 28d07 contained from coding sequence nucleotides 1097 to the poly A tract. Further sequence was obtained following amplification of a cDNA fragment using primers β-tub 295 and 4 1281r. The 5′ end was obtained from a RACE fragment generated using primers B4 756r 5′RACE. F.hep-β-tub5: the EST clone 09h06 plasmid insert gave the full sequence of this isotype. F.hep-β-tub6: EST clone 18a05 contained from coding nucleotides 302–1286. The sequence was completed using 5′ and 3′RACE fragments generated using primers β-tub6 714r 5′RACE and β-tub6 506f 3′RACE, respectively.
Fig. 2Phylogenetic analyses of (A) Fasciola α-tubulin and (B) β-tubulin isotypes and those of selected nematode, cestode and protozoan species accessed from the GenBank protein database. The Neighbour–Joining method was used and the trees were drawn using MEGA 4.0. All positions containing gaps and missing data were eliminated from the datasets. Numbers on branches represent bootstrapping values as a percentage of 500 replicates. Databank accession numbers are in brackets. (A) α-tubulin isotypes. F.hepAT1 to F.hepAT5: Fasciola hepatica α-tubulin isotypes F.hep-α-tub1 to F.hep-α-tub5 (GenBank accession nos. –; S.manSat1: Schistosoma mansoni α-tubulin (GenBank accession no. ); S.manAT: S. mansoni α-tubulin (GenBank accession no. ); S.japAT1: Schistosoma japonicum α-tubulin (GenBank accession no. ); S.japAT2: S. japonicum α-tubulin (GenBank accession no. ); S.japAT3: S. japonicum α-tubulin (GenBank accession no. ); H.dimAT: Hymenolepis diminuta (GenBank accession no. ); S.erinAT: Spirometra erinaceieuropaei α-tubulin (GenBank accession no. ); B.malAT: Brugia malayi α-tubulin (GenBank accession no. ); C.brigAT: Caenorhabditis briggsae hypothetical protein CBG20310 (GenBank accession no. ); C.elegAT3: Caenorhabditis elegans α-tubulin3 (GenBank accession no. ); C.elegAT5: C. elegans tba5 (GenBank accession no. ); C.elegAT9: C. elegans α-tubulin9 (GenBank accession no. ); H.contAT1: Haemonchus contortus α-tubulin isotype (GenBank accession no. ); O.volvAT1: Onchocerca volvulus α-tubulin (GenBank accession no. ); O.volvAT2: O. volvulus α-tubulin (GenBank accession no. AAY27745); C.parvAT: Cryptosporidium parvum α-tubulin (GenBank accession no. ); P.falcAT1: Plasmodium falciparum α-tubulin (GenBank accession no. ); P.falcAT2: P. falciparum α-tubulin II (GenBank accession no. ). (B) β-tubulin isotypes. F.hepBT1 to F.hepBT6: F. hepatica isotypes F.hep-β-tub1 to F.hep-β-tub6 (–); S.haemBT: Schistosoma haematobium β-tubulin (GenBank accession no. ); S.japBT: S. japonicum β-tubulin (GenBank accession no. ); E.multBT1 to E.multBT3: Echinococcus multilocularis β-tubulin isotypes, 1 (GenBank accession no. ), 2 (GenBank accession no ) and 3 (GenBank accession no. ); B.malBT: B. malayi β-tubulin (GenBank accession no. ); C.catBT1: Cyathostomum catinatum β-tubulin1 (GenBank accession no. ); C.catBT2: C. catinatum β-tubulin2 (GenBank accession no. ); CnasBT1: Cylicocyclus nassatus β-tubulin1 (GenBank accession no. ); C.nasBT2: C. nassatus β-tubulin2 (GenBank accession no. AAT76619); C.oncBT1: Cooperia oncophora β-tubulin1 (GenBank accession no. AAP20434); C.oncBT2: C. oncophora β-tubulin2 (GenBank accession no. ); H.contBT1: H. contortus β-tubulin (Tub 8–9) (GenBank accession no. ); H.contBT2: H. contortus β-tubulin (Tub 12–16) (GenBank accession no. ); O.volvBT: O. volvulus β-tubulin (GenBank accession no. ); C.parvBT: C. parvum β-tubulin (GenBank accession no. AAN78304); L.majBT: Leishmania major β-tubulin (GenBank accession no. ); P.falcBT: P. falciparum β-tubulin (GenBank accession no. ); T.brucBT: Trypanosoma brucei (GenBank accession no. ).