Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Molecular Genetics and Genomics

Volumn 279, Issue 4, 2008, Pages 385-401

  Lopes, Fabrício Ramon ^a   Carazzolle, Marcelo Falsarella ^b   Pereira, Gonçalo Amarante Guimarães ^b   Colombo, Carlos Augusto ^c   Carareto, Claudia Marcia Aparecida ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSITY OF CAMPINAS   (Brazil)

^c INSTITUTO AGRONÔMICO   (Brazil)

Author keywords

Coffea genome; Gene transduction; Molecular domestication; Protein diversity; Transposable elements

Indexed keywords

6 PHOSPHOFRUCTOKINASE; PYROPHOSPHATE;

ARABIDOPSIS; ARTICLE; ASPEN; COFFEE; EVOLUTION; EXON; FERTILITY; FLOWERING; GENE; GENE INSERTION SEQUENCE; GENETIC TRANSDUCTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN VARIANT; RICE; TRANSPOSON;

AMINO ACID SEQUENCE; ANGIOSPERMS; ARABIDOPSIS; BASE SEQUENCE; COFFEA; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; EVOLUTION, MOLECULAR; EXONS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PHOSPHOTRANSFERASES; PHYLOGENY; PLANT PROTEINS; PROTEOME; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION, GENETIC; VARIATION (GENETICS);

ARABIDOPSIS THALIANA; COFFEA; COFFEA ARABICA; COFFEA CANEPHORA; COFFEA RACEMOSA; GENTIANALES; MAGNOLIOPHYTA; ORYZA SATIVA; POPULUS TRICHOCARPA;

EID: 43349108310     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-008-0319-4     Document Type: Article

References (89)

1. Almeida LM, Silva IT, Silva WAS Jr, Castro JP, Riggs PK, Carareto CMA, Amaral MEJ (2007) The contribution of transposable elements to Bos taurus gene structure. Gene 390:180-189
2. Alves AMCR, Meijer WG, Vrijbloed JW, Dijkhuizen L (1996) Characterization and phylogeny of the pfp gene of Amycolatopsis methanolica encoding PPi-dependent phosphofructokinase. J Bacteriol 178:149-155
3. Andrés C, Lurin C, Small ID (2007) The multifarious roles of PPR proteins in plant mitochondrial gene expression. Physiol Plant 129:14-22
4. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
5. Arkhipova IR, Meselson M (2005) Diverse DNA transposons in rotifers of the class Bdelloidea. Proc Natl Acad Sci USA 102:11781-11786
6. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251-269
7. Bennetzen JL (2002) Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115:29-36
8. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621-627
9. Biemont C, Vieira C (2006) Genetics: junk DNA as an evolutionary force. Nature 443:521-524
10. Blakeley SD, Crews L, Todd JF, Dennis DT (1992) Expression of the genes for the α-and β-subunits of pyrophosphate-dependent phosphofructokinase in germinating and developing seeds from Ricinus communis. Plant Physiol 99:1245-1250
11. Britten RJ (2004) Coding sequence of functioning human genes derived entirely from mobile elements sequences. Proc Natl Acad Sci USA 101:16825-16830
12. Brosius J (2003) The contribution of RNAs and retroposition to evolutionary novelties. Genetica 118:99-116
13. Brosius J, Gould SJ (1992) On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. Proc Natl Acad Sci USA 89:10706-10710
14. Carlisle SM, Blakeley SD, Hemmingsen SM, Trevanion SJ, Hiyoshi T, Kruger NJ, Dennis DT (1990) Pyrophosphate-dependent phosphofructokinase. Conservation of protein sequence between the subunits and with the ATP-dependent phosphofructokinase. J Biol Chem 265:18366-18371
15. DeBarry JD, Ganko E, McDonald JF (2005) The contribution of LTR retrotransposon sequences to gene evolution in Mus musculus. Mol Biol Evol 23:479-481
16. Deng Z, Huang M, Singh K, Albach RA, Latshaw SP, Chang KP, Kemp RG (1998) Cloning and expression of the gene for the active PPi-dependent phosphofructokinase of Entamoeba histolytica. Biochem J 329:659-664
17. Deng Z, Roberts D, Wang X, Kemp RG (1999) Expression, characterization, and crystallization of the pyrophosphate dependent phosphofructo-1-kinase of Borrelia burgdorferi. Arch Biochem Biophys 371:326-331
18. Deininger PL, Batzer MA (1999) Alu repeats and human disease. Mol Genet Metab 67:183-193
19. Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603
20. Eickler EE, Sankoff D (2003) Structural dynamics and eukaryotic chromosomal evolution. Science 301:793-797
21. Fedoroff N (2000) Transposon and genome evolution in plants. Proc Natl Acad Sci USA 97:7002-7007
22. Ganko EW, Bhattacharjee V, Schliekelman P, McDonald JF (2003) Evidence for the contribution of LTR retrotransposon to C. elegans gene evolution. Mol Biol Evol 20:1925-1931
23. Ganko EW, Greene CS, Lewis JA, Bhattacharjee VM, McDonald JF (2006) LTR retrotransposon-gene associations in Drosophila melanogaster. J Mol Evol 62:111-120
24. Gerber A, O'Connell MA, Keller W (1997) Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA 3:453-463
25. Gotea V, Makalowski W (2006) Do transposable elements really contribute to proteomes? Trends Genet 22:260-267
26. Gupta S, Gallavotti A, Stryker GA, Schmidt RJ, Lal SK (2005) A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol 57:115-127
27. Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T (2003) Can an arbitrary sequence evolve towards acquiring a biological function? J Mol Evol 56:162-168
28. Hilgard P, Huang TM, Wolkoff AW, Stockert RJ (2002) Translated Alu sequence determines nuclear localization of a novel catalytic subunit of casein kinase 2. Am J Physiol Cell Physiol 283:C472-C483
29. Hoenicka J, Arrasate M, de Yebenes JG, Avila J (2002) A two-hybrid screening of human Tau protein: interactions with Alu-derived domain. Neuroreport 13:343-349
30. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868-77
31. International Human Genome Sequencing Consortium (2001) A physical map of the human genome. Nature 409:934-941
32. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800
33. Jordan IK, Rogozin IB, Glazko GV, Koonin EV (2003) Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 19:68-72
34. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-573
35. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) RepBase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462-467
36. Kapitonov VV, Jurka J (2000) Non autonomous DNA transposon ATDNA1T9A - a consensus sequence. Repbase Update. http://www.girinst.org
37. Kapitonov VV, Jurka J (2001a) ATMU6N1 is a non-autonomous DNA transposon - a consensus sequence. Repbase Update. http://www.girinst.org
38. Kapitonov VV, Jurka J (2001b) Rolling-circle transposon in eukaryotes. Proc Natl Acad Sci USA 98:8714-8719
39. Kapitonov VV, Jurka J (2003) Molecular paleontology of the transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA 100:6569-6574
40. Kapitonov VV, Jurka J (2005) Helitron4_OS: a new, possibly active helitron from rice. Repbase Rep 5:181-181
41. Kapitonov VV, Jurka J (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23:521-529
42. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115:49-63
43. Kidwell MG, Lish D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704-7711
44. Lal SK, Giroux MJ, Brendel V, Vallejos CE, Hannah LC (2003) The maize genome contains a Helitron insertion. Plant Cell 15:381-391
45. Li WH, Gu ZL, Wang HD, Nekrutenko A (2001) Evolutionary analyses of the human genome. Nature 409:847-849
46. Lin C, Mueller LA, Carthy JM, Crouzillat D, Pétiard V, Tanksley SD (2005) Coffee and tomato share common gene repertories as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 112:114-130
47. Lorenc A, Makalowski W (2003) Transposable elements and vertebrate protein diversity. Genetica 118:183-191
48. Makalowski W (2000) Genomic scrap yard: how genomes utilize all that junk. Gene 259:61-67
49. Makalowski W, Mitchel GA, Labuda D (1994) Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 10:188-193
50. Mao L, Wood TC, Yu Y, Budiman MA, Tomkins J, Woo S, Sasinonowski M, Presting G, Frish D, Goff S, Dean RA, Wing RA (2000) Rice transposable elements: a survey of 73,000 sequence-tagged-connectors. Genome Res 10:982-990
51. Mertens E, Ladror US, Lee JA, Miretsky A, Morris A, Rozario C, Kemp RG, Muller M (1998) The pyrophosphate-dependent phosphofructokinase of the protist, Trichomonas vaginalis, and the evolutionary relationships of protist phosphofructokinases. J Mol Evol 47:739-750
52. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei FS, Fuks G, Soderlund CA, Mayer KFX, Wing RA (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101:14349-14354
53. Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660-1676
54. Miller WJ, McDonald JF, Nouaud D, Anxolabéhère D (1999) Molecular domestication-more than a sporadic episode in evolution. Genetica 107:197-207
55. Mitchell GA et al (1991) Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation. Proc Natl Acad Sci USA 88:815-819
56. Möhlmann T, Tjaden J, Schwoppe C, Winkler HH, Kampfenkel K, Neuhaus HE (1998) Occurrence of two plastidic ATP/ADP transporters in Arabidopsis thaliana L-molecular characterisation and comparative structural analysis of similar ATP/ADP translocators from plastids and Rickettsia prowazekii. Eur J Biochem 252:353-359
57. Moore SA, Ronimus RS, Roberson RS, Morgan HW (2002) The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdoferi. Structure 10:659-671
58. Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A (2005) Gene duplication and exon shuffling by Helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997-1002
59. Mustroph A, Sonnewald U, Biemelt S (2007) Characterization of the ATP-dependent phosphofructokinase gene family from Arabidopsis thaliana. FEBS Lett 581:2401-2410
60. Nekrutenko A, Li WH (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17:619-621
61. Ohno S (1970) Evolution by gene duplication. Springer, Berlin
62. Orgel LE, Crick FH (1980) Selfish DNA: the ultimate parasite. Nature 284:604-607
63. Poulter RTM, Goodwin TJD, Butler MI (2003) Vertebrate helentrons and other novel Helitrons. Gene 313:201-212
64. Pritham EJ, Feschotte C (2007) Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA 104:1895-1900
65. Pruitt KD, Maglott DR (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res 29:137-140
66. Roberson RS, Ronimus RS, Gephart S, Morgan HW (2000) Biochemical characterization of an active pyrophosphate-dependent phosphofructokinase from Treponema pallidum. FEMS Microbiol Lett 9735:1-4
67. Sakai H, Tanaka T, Itoh T (2007) Birth and death of genes promoted by transposable elements in Oryza sativa. Gene 392:59-63
68. SanMiguel P, Tihkonov A, Jin YK, Motchoulskaia N, Zkharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL (1996) Nested retrotransposon in the intergenic regions of the maize genome. Science 274:765-768
69. Sarkar A, Sim C, Hong YS, Hogan JR, Fraser MJ, Robertson HM, Collins FH (2003) Molecular evolutionary analysis of widespread piggy-back transposon family and related domesticated sequences. Mol Genet Genomics 270:173-180
70. Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biol Rev 80:227-250
71. Siebers B, Klenk HP, Hensel R (1998) PPi-dependent phophofructokinase from Thermoproteus tenax, an archaeal descendant of an ancient line in phosphofructokinase evolution. J Bacteriol 180:2137-2143
72. Sigrell JA, Cameron AD, Jones TA, Mowbray SL (1998) Structure of the Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 Å resolution: insights into a new family of kinase structures. Structure 6:183-193
73. Sorek R, Ast G, Graur D (2002) Alu-containing exons are alternatively spliced. Genome Res 12:1060-1067
74. Stephens RS, Kalman S, Lammel C, Fan J, Marathe R, Arvind L, Mitchell W, Olinger L, Tatusov RL, Zhao Q (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282:754-759
75. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland
76. The Gene Ontology Consortium (2001) Creating the gene ontology resource: design and implementation. Genome Res 11:1425-1433
77. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
78. Thornburg BG, Gotea V, Makalowski W (2006) Transposable elements as source of transcription regulation signals. Gene 365:104-110
79. Tikhonov AP et al. (1999) Collinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409-7414
80. Tjaden J, Schwoppe C, Mohlmann T, Quick PW, Neuhaus HE (1998) Expression of a plastidic ATP/ADP transporter gene in Escherichia coli leads to a functional adenine nucleotide transport system in the bacterial cytoplasmic membrane. J Biol Chem 273:9630-9636
81. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. Plant J 25:169-179
82. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596-1604
83. van de Lagemaat LN, Landry JR, Mager DL, Medstrand P (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19:530-536
84. Vieira LGE, Andrade AC, Colombo CA et al (2006) Brazilian coffee genome project: an EST-based genomic resource. Braz J Plant Physiol 18:95-108
85. Volff JN (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukariotes. BioEssays 28:913-922
86. Wu LF, Reizer A, Reizer J, Cai B, Tomich JM, Saier MH (1991) Nucleotide sequence of the Rhodobacter capsulatus fruK gene, which encodes fructose-1-phosphate kinase: superfamily including both phosphofructokinases of E. coli. J Bacteriol 173:3117-3127
87. Xu JH, Messing J (2006) Maize haplotyple with a Helitron-amplified cytidine deaminase gene copy. BMC Genetics 9:7-52
88. Zhang J, Peterson T (1999) Genome rearrangements by nonlinear transposons in maize. Genetics 153:1403-1410
89. Zhou Q et al (2006) Helitron transposons on the sex chromosomes of the platyfish Xiphophorus maculatus and their evolution in animal genomes. Zebrafish 3:39-52