A single-base substitution suppresses flower color mutation caused by a novel miniature inverted-repeat transposable element in gentian

Molecular Genetics and Genomics

Volumn 286, Issue 5-6, 2011, Pages 371-382

  Nishihara, Masahiro ^a   Hikage, Takashi ^b   Yamada, Eri ^a   Nakatsuka, Takashi ^a  

^a IWATE BIOTECHNOLOGY RESEARCH CENTER   (Japan)

^b Hachimantai City Floricultural Research and Development Center   (Japan)

Author keywords

Flavonoid 3',5' hydroxylase; Gentian; Miniature inverted repeat transposable element (MITE); Single base substitution

Indexed keywords

3',5' HYDROXYLASE GENE; ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; CONTROLLED STUDY; DNA STRUCTURE; FLOWER COLOR; GENE EXPRESSION; GENE INSERTION; GENTIAN; MINIATURE INVERTED REPEAT TRANSPOSABLE ELEMENT; MOLECULAR PHYLOGENY; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT EVOLUTION; PLANT GENE; PLANT GENETICS; PRIORITY JOURNAL; RETROPOSON; RNA SPLICING; SEQUENCE ANALYSIS;

BASE SEQUENCE; BIOLOGICAL EVOLUTION; COLOR; DNA TRANSPOSABLE ELEMENTS; FLOWERS; GENES, PLANT; GENOME, PLANT; GENTIANA; INVERTED REPEAT SEQUENCES; MOLECULAR SEQUENCE DATA; POINT MUTATION;

GENTIANA;

EID: 84855713168     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-011-0652-x     Document Type: Article

References (61)

1. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, Debarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer KM, Bennetzen JL, Kruegger RR, Malek JA (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29:521-527
2. Behm-Ansmant I, Gatfield D, Rehwinkel J, Hilgers V, Izaurralde E (2007) A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J 26:1591-1601 (Pubitemid 46480926)
3. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251-269 (Pubitemid 30096120)
4. Britt AB (1999) Molecular genetics of DNA repair in higher plants. Trends Plant Sci 4:20-25 (Pubitemid 29130800)
5. Brown JW (1996) Arabidopsis intron mutations and pre-mRNA splicing. Plant J 10:771-780 (Pubitemid 27102993)
6. Brown JW, Smith P, Simpson CG (1996) Arabidopsis consensus intron sequences. Plant Mol Biol 32:531-535 (Pubitemid 27016986)
7. Bureau TE, Wessler SR (1992) Tourist: A large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4:1283-1294
8. Bureau TE, Wessler SR (1994a) Mobile inverted-repeat elements of the tourist family are associated with the genes of many cereal grasses. Proc Natl Acad Sci USA 91:1411-1415 (Pubitemid 24059021)
9. Bureau TE, Wessler SR (1994b) Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6:907-916
10. Casacuberta JM, Santiago N (2003) Plant LTR-retrotransposons and MITEs: Control of transposition and impact on the evolution of plant genes and genomes. Gene 311:1-11 (Pubitemid 36830797)
11. Charrier B, Foucher F, Kondorosi E, d'Aubenton-Carafa Y, Thermes C, Kondorosi A, Ratet P (1999) Bigfoot. A new family of MITEelements characterized from the Medicago genus. Plant J 18:431-441
12. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev 8:93-103 (Pubitemid 46122839)
13. Clegg MT, Durbin ML (2000) Flower color variation: A model for the experimental study of evolution. Proc Natl Acad Sci USA 97:7016-7023 (Pubitemid 30431410)
14. Doi H, Takahashi R, Hikage T, Takahata Y (2010) Embryogenesis and doubled haploid production from anther culture in gentian (Gentiana triflora). Plant Cell Tissue Organ Cult 102:27-33
15. Dooner HK, Robbins TP, Jorgensen RA (1991) Genetic and developmental control of anthocyanin biosynthesis. Annu Rev Genet 25:173-199 (Pubitemid 21903719)
16. Feschotte C, Zhang X, Wessler SR (2002) Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, DC, pp 1147-1158
17. Flowers JM, Purugganan MD (2008) The evolution of plant genomes: Scaling up from a population perspective. Curr Opin Genet Dev 18:565-570
18. Gerats AG, Huits H, Vrijlandt E, Marana C, Souer E, Beld M (1990) Molecular characterization of a nonautonomous transposable element (dTph1) of petunia. Plant Cell 2:1121-1128 (Pubitemid 120015463)
19. Goto T, Kondo T, Tamura H, Imagawa H, Iino H, Takeda K (1982) Structure of gentiodelphin, an acylated anthocyanin isolated from Gentiana makinori, that is stable in dilute aqueous solution. Tetrahedron Lett 23:3695-3698
20. Grzebelus D, Gladysz M, Macko-Podgorni A, Gambin T, Golis B, Rakoczy R, Gambin A (2009) Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula. Gene 448:214-220
21. Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Ann Rev Plant Biol 54:375-401 (Pubitemid 37399999)
22. Holton TA, Brugliera F, Lester DR, Tanaka Y, Hyland CD, Menting JG, Lu CY, Farcy E, Stevenson TW, Cornish EC (1993) Cloning and expression of cytochrome P450 genes controlling flower colour. Nature 366:276-279 (Pubitemid 23359712)
23. Hoshino A, Johzuka-Hisatomi Y, Iida S (2001) Gene duplication and mobile genetic elements in the morning glories. Gene 265:1-10 (Pubitemid 32209245)
24. Hosokawa K, Fukushi E, Kawabata J, Fujii C, Ito T, Yamamura S (1995) Three acylated cyaniding glucosides in pink flowers of Gentiana. Phytochemistry 40:941-944
25. Hosokawa K, Fukushi E, Kawabata J, Fujii C, Ito T, Yamamura S (1997) Seven acylated anthocyanins in blue flowers of Gentiana. Phytochemistry 45:167-171 (Pubitemid 27175482)
26. Isken O, Maquat LE (2007) Quality control of eukaryotic mRNA: Safeguarding cells from abnormal mRNA function. Genes Dev 21:1833-1856 (Pubitemid 47204924)
27. Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K (1998) A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 50 splice site of the first intron. Plant J 15:133-138
28. Jiang N, Bao Z, Zhang X, Hirochika H, Eddy SR, McCouch SR, Wessler SR (2003) An active DNA transposon family in rice. Nature 421:163-167 (Pubitemid 36090982)
29. Johzuka-Hisatomi Y, Hoshino A, Mori T, Habu Y, Iida S (1999) Characterization of the chalcone synthase genes expressed in flowers of the common and Japanese morning glories. Genes Genet Syst 74:141-147
30. Kakizaki Y, Nakatsuka T, Kawamura H, Abe Y, Yamamura S, Nishihara M (2009) Development of codominant DNA marker distinguishing pink from blue flowers in Gentiana scabra. Breed Res 11:9-14 (in Japanese)
31. Kaltenbach M, Schroder G, Schmelzer E, Lutz V, Schroder J (1999) Flavonoid hydroxylase from Catharanthus roseus: CDNA, heterologous expression, enzyme properties and cell-type specific expression in plants. Plant J 19:183-193
32. Kikuchi K, Terauchi K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421:167-170 (Pubitemid 36090983)
33. Kumekawa N, Ohtsubo H, Horiuchi T, Ohtsubo E (1999) Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol Gen Genomics 260:593-602 (Pubitemid 29046165)
34. Lal S, Choi JH, Shaw JR, Hannah LC (1999) A splice site mutant of maize activates cryptic splice sites, elicits intron inclusion and exon exclusion, and permits branch point elucidation. Plant Physiol 121:411-418 (Pubitemid 29498902)
35. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:7376-7381 (Pubitemid 30431471)
36. Levin HL (2002) Newly identified retrotransposons of the Ty3/gypsy class in fungi, plants and vertebrates. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, D. C
37. Luo D, Coen ES, Doyle S, Carpenter R (1991) Pigmentation mutants produced by transposon mutagenesis in Antirrhinum majus. Plant J 1:59-69 (Pubitemid 121001033)
38. Lyons M, Cardle L, Rostoks N, Waugh R, Flavell AJ (2008) Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome. Mol Gen Genomics 280:275-285
39. McGlincy NJ, Smith CW (2008) Alternative splicing resulting in nonsense-mediated mRNA decay: What is the meaning of nonsense? Trends Biochem Sci 33:385-393
40. Mishiba K, Yamane K, Nakatsuka T, Nakano Y, Yamamura S, Abe J, Kawamura H, Takahata Y, Nishihara M (2009) Genetic relationships in the genus Gentiana based on chloroplast DNA sequence data and nuclear DNA content. Breeding Sci 59:119-127
41. Momose M, Abe Y, Ozeki Y (2010) Miniature inverted-repeat transposable elements of Stowaway are active in potato. Genetics
42. Nakatsuka T, Nishihara M, Mishiba K, Yamamura S (2005) Two different mutations are involved in the formation of whiteflowerd gentian plants. Plant Sci 169:949-958 (Pubitemid 41225307)
43. Nakatsuka T, Nishihara M, Mishiba K, Hirano H, Yamamura S (2006) Two different transposable elements inserted in flavonoid 30, 50-hydroxylase gene contribute to pink flower coloration in Gentiana scabra. Mol Gen Genomics 275:231-241 (Pubitemid 43357660)
44. Nakatsuka T, Haruta KS, Pitaksutheepong C, Abe Y, Kakizaki Y, Yamamoto K, Shimada N, Yamamura S, Nishihara M (2008a) Identification and characterization of R2R3-MYB and bHLH transcription factors regulating anthocyanin biosynthesis in gentian flowers. Plant Cell Physiol 49:1818-1829
45. Nakatsuka T, Sato K, Takahashi H, Yamamura S, Nishihara M (2008b) Cloning and characterization of the UDP-glucose:anthocyanin 5-O-glucosyltransferase gene from blue-flowered gentian. J Exp Bot 59:1241-1252
46. Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M, Nishida H, Inoue H, Tanisaka T (2003) Mobilization of a transposon in the rice genome. Nature 421:170-172 (Pubitemid 36090984)
47. Nishihara M, Nakatsuka T, Mizutani-Fukuchi M, Tanaka Y, Yamamura S (2008) Gentians: From gene cloning to molecular breeding. In: Jaime A, da Silva T (eds) Floricultural and ornamental biotechnology V. Global Science Books, UK, pp 57-67
48. Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T (2008) A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice, Oryza sativa ssp. japonica. Genes Genet Syst 83:321-329
49. Sablowski RWM, Meyerowitz EM (1998) Temperature-sensitive splicing in the floral homeotic mutant apetala3-1. Plant Cell 10:1453-1463 (Pubitemid 28542150)
50. Sanmiguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annal Bot 82:37-44 (Pubitemid 29014739)
51. Santiago N, Herraiz C, Goni JR, Messeguer X, Casacuberta JM (2002) Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana. Mol Biol Evol 19:2285-2293 (Pubitemid 35440462)
52. Sato K, Hamada M, Asai K, Mituyama T (2009) CENTROIDFOLD: A web server for RNA secondary structure prediction. Nucleic Acids Res 37:W277-W280
53. Shimada N, Sasaki R, Sato S, Kaneko T, Tabata S, Aoki T, Ayabe S (2005) A comprehensive analysis of six dihydroflavonol 4-reductases encoded by a gene cluster of the Lotus japonicus genome. J Exp Bot 56:2573-2585 (Pubitemid 41191474)
54. Smyth DR, Kalitsis P, Joseph JL, Sentry JW (1989) Plant retrotransposon from Lilium henryi is related to Ty3 of yeast and the gypsy group of Drosophila. Proc Natl Acad Sci USA 86:5015-5019
55. Snowden KC, Napoli CA (1998) Psl: A novel Spm-like transposable element from Petunia hybrida. Plant J 14:43-54 (Pubitemid 28186914)
56. Tanaka Y, Yonekura K, Fukuchi-Mizutani M, Fukui Y, Fujiwara H, Ashikari T, Kusumi T (1996) Molecular and biochemical characterization of three anthocyanin synthetic enzymes from Gentiana triflora. Plant Cell Physiol 37:711-716 (Pubitemid 26383240)
57. Yang G, Zhang F, Hancock CN, Wessler SR (2007) Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci USA 104:10962-10967 (Pubitemid 47175209)
58. Yang G, Nagel DH, Feschotte C, Hancock CN, Wessler SR (2009) Tuned for transposition: Molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 325:1391-1394
59. Yi Y, Jack T (1998) An intragenic suppressor of the Arabidopsis floral organ identity mutant apetala3-1 functions by suppressing defects in splicing. Plant Cell 10:1465-1477 (Pubitemid 28542151)
60. Yuan YX, Wu J, Sun RF, Zhang XW, Xu DH, Bonnema G, Wang XW (2009) A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time. J Exp Bot 60:1299-1308
61. Zhang Q, Arbuckle J, Wessler SR (2000) Recent, extensive, and preferential insertion of members of the miniature invertedrepeat transposable element family Heartbreaker into genic regions of maize. Proc Natl Acad Sci USA 97:1160-1165 (Pubitemid 30080829)