Abstract
Evolutionary patterns of sequence divergence were analyzed in genes from the conifer genus Taxus (yew), encoding paclitaxel biosynthetic enzymes taxadiene synthase (TS) and 10-deacetylbaccatin III-10β-O-acetyltransferase (DBAT). N-terminal fragments of TS, full-length DBAT and internal transcribed spacer (ITS) were amplified from 15 closely related Taxus species and sequenced. Premature stop codons were not found in TS and DBAT sequences. Codon usage bias was not found, suggesting that synonymous mutations are selectively neutral. TS and DBAT gene trees are not consistent with the ITS tree, where species formed monophyletic clades. In fact, for both genes, alleles were sometimes shared across species and parallel amino acid substitutions were identified. While both TS and DBAT are, overall, under purifying selection, we identified a number of amino acids of TS under positive selection based on inference using maximum likelihood models. Positively selected amino acids in the N-terminal region of TS suggest that this region might be more important for enzyme function than previously thought. Moreover, we identify lineages with significantly elevated rates of amino acid substitution using a genetic algorithm. These findings demonstrate that the pattern of adaptive paclitaxel biosynthetic enzyme evolution can be documented between closely related Taxus species, where species-specific taxane metabolism has evolved recently.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anisimova M, Nielsen R, Yang Z (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229–1236
Bishop JG (2005) Directed mutagenesis confirms the functional importance of positively selected sites in polygalacturonase inhibitor protein. Mol Biol Evol 22:1531–1534
Cheng Y, Nicolson RG, Tripp K, Chaw SM (2000) Phylogeny of taxaceae and cephalotaxaceae genera inferred from chloroplast matK gene and nuclear rDNA ITS region. Mol Phylogenet Evol 14:353–365
Doron-Faigenboim A, Pupko TA (2007) Combined empirical and mechanistic codon model. Mol Biol Evol 24:388–397
Grantham R (1974) Amino-acid difference formula to help explain protein evolution. Science 185:862–864
Hartmann T, Kutchan TM, Strack D (2005) Evolution of metabolic diversity. Phytochemistry 66:1198–1199
Koepp E, Hezari M, Zajicek J et al (1995) Cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene is the committed step of Taxol biosynthesis in Pacific yew. J Biol Chem 270:8686–8690
Kosakovsky Pond SL, Frost SD (2005a) Not so different after All: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222
Kosakovsky Pond SL, Frost SD (2005b) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21:2531–2533
Kosakovsky Pond SL, Frost SD (2005c) A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol 22:478–485
Kress WJ, Wurdack KJ, Zimmer EA et al (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374
Li WH, Wu CI, Luo CC (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58–71
Li J, Davis CC, Tredici PD et al (2001) Phylogeny and biogeography of Taxus (Taxaceae) inferred from sequences of the internal transcribed spacer region of nuclear ribosomal DNA. Harvard Papers Bot 6:267–274
Liu Z, Bos JIB, Armstrong M et al (2005) Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans. Mol Biol Evol 22:659–672
Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the psbA locus based on tRNA availability. J Mol Evol 37:273–280
Nielsen R, Bustamante C, Clark AG et al (2005) A scan for positively selected genes in the genomes of Humans and Chimpanzees. PloS Biol 3:976–985
Posada D (2006) ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Res 34:W700–703
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574
Rozas J, Sa´nchez-DelBarrio JC, Messeguer X et al (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496–2497
Sharp PM (1991) Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol 33:23–33
Spjut RW (2007a) Taxonomy and nomenclature of Taxus. J Bot Res Inst Texas 23:203–289
Spjut RW (2007b) A phytogeographical analysis of Taxus (Taxaceae) based on leaf anatomical characters. J Bot Res Inst Texas 23:291–332
Swanson WJ, Yang Z, Wolfner MF et al (2001) Positive darwinian selection in the evolution of mammalian female reproductive proteins. Proc Natl Acad Sci USA 98:2509–2514
Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts
Trapp SC, Croteau RB (2001) Genomic organization of plant terpene synthases and molecular evolutionary implications. Genetics 158:811–832
van Rozendaal EL, Lelyveld GP, van Beek TA (2000) Screening of the needles of different yew species and cultivars for paclitaxel and related taxoids. Phytochemistry 53:383–389
Walker K, Croteau RB (2000) Molecular cloning of a 10-deacetylbaccatin III-10-O-acetyl transferase cDNA from Taxus and functional expression in Escherichia coli. Proc Natl Acad Sci USA 97:583–587
Walker K, Croteau RB (2001) Taxol biosynthetic genes. Phytochemistry 58:1–7
Wildung MR, Croteau RB (1996) A cDNA clone for taxadiene synthase, the diterpene cyclase that catalyzes the committed step of Taxol biosynthesis. J Biol Chem 271:9201–9204
Williams DC, Wildung MR, Jin AQ et al (2000) Heterologous expression and characterization of a “Pseudomature” form of taxadiene synthase involved in paclitaxel (Taxol) biosynthesis and evaluation of a potential intermediate and inhibitors of the multistep diterpene cyclization reaction. Arch Biochem Biophys 379:137–146
Wright F (1990) The “effective number of codons” used in a gene. Gene 87:23–29
Yang Z (2007) PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591
Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641–1650
Yang Z, Nielsen R, Goldman N et al (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449
Zhang J (2003) Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions. Mol Biol Evol 20:1310–1317
Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin
Acknowledgments
We thank the following experts for providing plant materials: YunFen Geng (YunNan Academy of Forestry, KunMing, China), YinKe Zhang (HangZhou Botanical Garden, China), Ron Determann (Atlanta Botanical Garden, GA, USA), Richard W. Spjut (World Botanical Associates, CA, USA), Robert G. Nicolson (Smith College, USA), Stephane Bailleul (Montreal Botanical Garden, Canada), Eric La Fountaine (University of British Columbia Botanical Garden, Canada), and James Stevenson (University of Oxford Botanic Garden, UK). We are grateful to Sergei L. Kosakovsky Pond and Leslie M. Turner (University of California, San Diego, USA) for suggestions in genetic algorithm and parallel amino acid substitutions, respectively, and to two anonymous reviewers for their critical comments. This study is supported by the National 973 Project (2007CB707802) of the Ministry of Science & Technology of China.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Hao, D.C., Yang, L. & Huang, B. Molecular evolution of paclitaxel biosynthetic genes TS and DBAT of Taxus species. Genetica 135, 123–135 (2009). https://doi.org/10.1007/s10709-008-9257-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10709-008-9257-7