Genomic characterization of Rim2 / Hipa elements reveals a CACTA-like transposon superfamily with unique features in the rice genome

Molecular Genetics and Genomics

Volumn 270, Issue 3, 2003, Pages 234-242

  Wang, G D ^a,c   Tian, P F ^b   Cheng, Z K ^d   Wu, G ^a   Jiang, J M ^d   Li, D B ^b   Li, Q ^a   He, Z H ^a,b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c EAST CHINA NORMAL UNIVERSITY   (China)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

CACTA like elements; CACTG TIRs; Genomic structure; Insertion preference; Rim2 Hipa family

Indexed keywords

COMPLEMENTARY DNA; GLYCOPROTEIN;

ARTICLE; CACTA LIKE ELEMENT; CACTG TERMINAL INVERTED REPEAT; DNA FLANKING REGION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE INSERTION SEQUENCE; GENOME; HIPA ELEMENT; INVERTED REPEAT; LONG TERMINAL REPEAT; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; PRIORITY JOURNAL; RICE; RIM2 ELEMENT; TRANSPOSON;

AMINO ACID SEQUENCE; BASE SEQUENCE; CARRIER PROTEINS; CLONING, MOLECULAR; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOME, PLANT; MOLECULAR SEQUENCE DATA; MUTAGENESIS, INSERTIONAL; NUCLEAR PROTEINS; ORYZA SATIVA; PHYLOGENY; PLANT PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSPOSASES;

EMBRYOPHYTA; INSERTION SEQUENCES; MAGNAPORTHE; MAGNAPORTHE GRISEA; ORYZA; TRANSPOSONS; UNIDENTIFIED INSERTION SEQUENCE;

EID: 0345548556     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-003-0918-z     Document Type: Article

References (49)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Arnault C, Dufournel I (1994) Genome and stresses: reactions against aggressions, behavior of transposable elements. Genetica 93:149-160
3. Bercury SD, Panvas T, Irenze K, Walker EL (2001) Molecular analysis of the Doppia transposable element of maize. Plant Mol Biol 47:341-351
4. Bureau TE, Ronald PC, Wessler SR (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci USA 93:8524-8529
5. Chopra S, Brendel V, Zhang J, Axtell JD, Peterson T (1999) Molecular characterization of a mutable pigmentation phenotype and isolation of the first active transposable element from Sorghum bicolor. Proc Natl Acad Sci USA 96:15330-15335
6. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet 3:329-341
7. Gierl A (1996) The En/Spm transposable element of maize. Curr Topics Microbiol Immunol 204:145-159
8. Goff SA, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100
9. Han CG, Frank MJ, Ohtsubo H, Ohtsubo E (2000) New transposable elements identified as insertions in rice transposon Tnr1. Genes Genet Syst 75:69-77
10. He ZH, Dong HT, Dong JX, Li DB, Ronald PC (2000) The rice Rim2 transcript accumulates in response to Magnaporthe grisea and its predicted protein product shares similarity with TNP2-like proteins encoded by CACTA transposons. Mol Gen Genet 264:2-10
11. Henikoff S, Henikoff JG (1993) Performance evaluation of amino acid substitution matrices. Proteins 17:49-61
12. Hirochika H (1993) Activation of tobacco retransposons during tissue culture. EMBO J 12:2521-2528
13. Hirochika H, Sugimito K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposon of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783-7788
14. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92:4487-4491
15. Jiang N, Wessler SR (2001) Insertion preference of maize and rice miniature inverted repeat transposable elements as revealed by the analysis of nested elements. Plant Cell 13:2553-2564
16. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR (2002) Dasheng. A recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161:1293-1305
17. Jiang N, Bao ZR, Zhang XY, Hirochika H, Eddy SR, McCouch S, Wessler S (2003) An active DNA transposon family in rice. Nature 421:163-167
18. Kapitonov VV, Jurka J (1999) Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107:27-37
19. Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704-7711
20. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479-532
21. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
22. Kunze R, Weil CF (2002) The hAT and CACTA superfamilies of plant transposons. In: Craig NL, Craigie R, Gellert M, Lambowitz AM (eds) Mobile DNA II. ASM Press, Washington, pp 565-609
23. Kunze R, Saedler H, Lönnig WE (1997) Plant transposable elements. Adv Bot Res 27:331-470
24. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proc Natl Acad Sci USA 97:7376-7381
25. Leprinc AS, Grandbastien MA, Christian M (2001) Retrotransposons of the Tnt1B family are mobile in Nicotiana plumbaginifolia and can induce alternative splicing of the host gene upon insertion. Plant Mol Biol 47:533-541
26. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinowski M, Presting G, Frisch D, Goff S, Dean RA, Wing RA (2000) Rice transposable elements: a survey of 73,000 sequence-tagged connectors. Genome Res 10:982-990
27. McClintock B (1984) The significance of responses of the genome to challenge. Science 226:792-801
28. McDonald JF (1995) Transposable elements:-possible catalysts of organismic evolution. Trends Ecol Evol 10:123-126
29. Melayah D, Bonnivard E, Chalhoub B, Audeon C, Grandbastien MA (2001) The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant J 28:159-168
30. Mhiri C, Morel JB, Vernhettes S, Casacuberta JM, Lucas H, Grandbastien MA (1997) The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress. Plant Mol Biol 33:257-266
31. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212-214
32. Motohashi R, Ohtsubo E, Ohtsubo H (1996) Identification of Tnr3, a Suppressor-Mutator/Enhancer -like transposable element from rice. Mol Gen Genet 250:148-152
33. Nacken WKF, Piotrowiak R, Saedler H, Sommer H (1991) The transposable element Tam1 from Antirrhinum majus shows structural homology to the maize transposon En/Spm and has no sequence specificity of insertion. Mol Gen Genet 228:201-208
34. Ohtsubo H, Kumekawa N, Ohtsubo E (1999) RIRE2, a novel gypsy-type retrotransposon from rice. Genes Genet Syst 74:83-91
35. Ozeki Y, Davies E, Takeda J (1997) Somatic variation during long-term subculturing of plant cells caused by insertion of a transposable element in a phenylalanine ammonia-lyase (PAL) gene. Mol Gen Genet 254:407-416
36. Panaud O, Vitte C, Hivert J, Muzlak S, Talag J, Brar D, Sarr A (2002) Characterization of transposable elements in the genome of rice (Oryza sativa L.) using representational difference analysis (RDA). Mol Genet Genomics 268:113-121
37. Panavas T, Weir J, Walker EL (1999) The structure and paramutagenicity of the R-marbled haplotype of Zea mays. Genetics 153:979-991
38. Pereira A, Cuyoers H, Gierl A, Schwarz-Sommer Z, Saedler H (1986) Molecular analysis of the En/Spm element system of Zea mays. EMBO J 5:835-841
39. Pouteau S, Boccara M, Grandbastien MA (1994) Microbial elicitors of plant defense responses activate transcription of a retrotransposon. Plant J 5:535-542
40. Rhodes PR, Vodkin LO (1988) Organization of the Tgm family of transposable elements in soybean. Genetics 120:597-604
41. Snowden KC, Napoli A (1998) PsI: a novel Spm -like transposable element from Petunia hybrida. Plant J 14:43-54
42. Song WY, Pi LY, Bureau TE, Ronald PC (1998) Identification and characterization of 14 transposon-like elements in the non-coding regions of the members of the Xa21 family of disease resistance genes in rice. Mol Gen Genet 258:449-456
43. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:381-391
44. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24:4876-4882
45. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169-179
46. Vernhettes S, Grandbastien MA, Casacuberta JM (1997) In vivo characterization of transcriptional regulatory sequences involved in the defence-associated expression of the tobacco retrotransposon Tnt1. Plant Mol Biol 35:673-679
47. Wessler SR (1996) Plant retrotransposons: turned on by stress. Curr Biol 6:959-961
48. Witte CP, Le QH, Bureau T, Kumar A (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA 98:13778-13783
49. Yu J, et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92