Patterns of variation in the evolution of carotenoid biosynthetic pathway enzymes of higher plants

Journal of Heredity

Volumn 100, Issue 6, 2009, Pages 754-761

  Livingstone, Kevin ^a   Anderson, Stephanie ^a  

^a TRINITY UNIVERSITY   (United States)

Author keywords

Carotenoid; Evolution; Metabolic pathway

Indexed keywords

ANTHOCYANIN; CAROTENOID; LYCOPENE; LYCOPENE BETA CYCLASE; PHYTOENE SYNTHASE; UNCLASSIFIED DRUG; ZEAXANTHIN; ZEAXANTHIN EPOXIDASE; ZETA CAROTENE;

ARTICLE; BIOSYNTHESIS; CODON USAGE; CONTROLLED STUDY; GENE SEQUENCE; METABOLITE; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PLANT METABOLISM; PRIORITY JOURNAL; TOMATO;

ANGIOSPERMS; CAROTENOIDS; CODON; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENETIC VARIATION; INTRAMOLECULAR LYASES; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR STRUCTURE; OXIDOREDUCTASES; PHYLOGENY; SELECTION, GENETIC;

EMBRYOPHYTA;

EID: 71049169647     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esp026     Document Type: Article

References (44)

1. Bradshaw H, Schemske D. 2003. Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers. Nature. 426:176-178.
2. Bramley P. 2002. Regulation of carotenoid formation during tomato fruit ripening and development. J Exp Bot. 53:2107-2113.
3. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450:203-218. (Pubitemid 351972300)
4. Clegg M, Durbin M. 2003. Tracing floral adaptations from ecology to molecules. Nat Rev Genet. 4:206-215.
5. Copley S. 2003. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol. 7:265-272.
6. Cork JM, Purugganan MD. 2004. The evolution of molecular genetic pathways and networks. Bioessays. 26:479-484.
7. Cunningham FX. 2002. Regulation of carotenoid synthesis and accumulation in plants. Pure Appl Chem. 74:1409-1417.
8. Cuttriss A, Pogson B. 2004. Carotenoids. In: Davies KM, editor. Plant pigments and their manipulation. Oxford (UK): Blackwell Publishing. p. 57-91.
9. DellaPenna D, Pogson B. 2006. Vitamin synthesis in plants: tocopherols and carotenoids. Annu Rev Plant Biol. 57:711-738.
10. Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V. 2005. Comparative plant genomics resources at PlantGDB. Plant Physiol. 139:610-618.
11. Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
12. Emanuelsson O, Nielsen H, Von Hejine G. 1999. CHLOROP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8:978-984.
13. Felsenstein J. 2008. Phylip (phylogeny inference package). Version 3.6. Distributed by the author. Seattle (WA): Department of Genome Sciences, University of Washington.
14. Flowers J, Sezgin E, Kumagai S, Duvernell D, Matzkin L, Schmidt PS, Eanes WF. 2007. Adaptive evolution of metabolic pathways in Drosophila. Mol Biol Evol. 24:1347-1354.
15. Foxe J, Dar V, Zheng H, Nordborg M, Gaut B, Wright SI. 2008. Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol. 25:1375-1383.
16. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science. 296:750-752.
17. Galpaz N, Ronen G, Khalfa Z, Zamir D, Hirschberg J. 2006. A chromoplast-specific carotenoid biosynthesis pathway is revealed by cloning of the tomato white-flower locus. Plant Cell. 18:1947-1960.
18. Goodwin T. 1980. The biochemistry of the carotenoids. Volume 1: Plants. London: Chapman & Hall.
19. Greenberg AJ, Stockwell SR, Clark AG. 2008. Evolutionary constraint and adaptation in the metabolic network of Drosophila. Mol Biol Evol. 25:2537-2546.
20. Hahn M, Kern AD. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol. 22:803-806.
21. Hall B. 2004. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol. 22:792-802.
22. Hall TA. 1999. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 41:95-98.
23. Hirschberg J. 2001. Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol. 4:210-218.
24. Howitt C, Pogson B. 2006. Carotenoid accumulation and function in seeds and non-green tissues. Plant Cell Environ. 29:435-445.
25. Jordan IK, Wolf YI, Koonin E. 2003. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve more slowly. BMC Evol Biol. 3:1.
26. Just B, Santos C, Fonseca M, Boiteux L, Oloizia B, Simon PW. 2007. Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping. Theor Appl Genet. 114:693-704.
27. Kato M, Ikoma Y, Matsumoto H, Sugiura M, Hyodo H, Yano M. 2004. Accumulation of carotenoids and expression of carotenoid biosynthetic genes during maturation in citrus fruit. Plant Physiol. 134:824-837.
28. Kishimoto S, Ohmiya A. 2006. Regulation of carotenoid biosynthesis in petals and leaves of chrysanthemum (Chrysanthemum morifolium). Physiol Plant. 128:436-447.
29. Koes RWD, Verweij W, Quattrocchio F. 2005. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci. 10:236-242.
30. Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWillian H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. CLUSTALW and CLUSTALX version 2.0. Bioinformatics. 23:2947-2948.
31. Larracuente A, Sackton T, Greenberg A, Wong A, Singh N, Clark AG. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24:114-123.
32. Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J. 2004. The TIGR gene indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 33:D71-D74.
33. Lu Y, Rausher MD. 2003. Evolutionary rate variation in anthocyanin pathway genes. Mol Biol Evol. 20:1844-1853.
34. Pál C, Papp B, Lercher M. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
35. Rausher MD, Lu Y, Meyer K. 2008. Variation in constraint versus positive selection as an explanation for evolutionary rate variation among anthocyanin genes. J Mol Evol. 67:137-144.
36. Rausher MD, Miller R, Tiffin P. 1999. Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. Mol Biol Evol. 16:266-274.
37. Rozas J, Sánchez-Delbarrio JC, Messegyer X, Rozas R. 2003. DNASP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19:2496-2497.
38. Soltis P, Soltis D. 2004. The origin and diversification of angiosperms. Am J Bot. 91:1614-1626.
39. Streisfeld MA, Rausher MD. 2008. Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea. Mol Biol Evol. 24:2816-2826.
40. Winkel B. 2004. Metabolic channeling in plants. Annu Rev Plant Biol. 55:85-107.
41. Woitsch S, Römer S. 2003. Expression of xanthophyll biosynthetic genes during light-dependent chloroplast differentiation. Plant Physiol. 132:1508-1517.
42. Wright F. 1990. The "effective number of codons" used in a gene. Gene. 87:23-29.
43. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
44. Zufall R, Rausher MD. 2003. The genetic basis of a flower color polymorphism in the common morning glory (Ipomoea purpurea). J Hered. 94:442-448.