The alternative oxidase family of Vitis vinifera reveals an attractive model to study the importance of genomic design

Physiologia Plantarum

Volumn 137, Issue 4, 2009, Pages 553-565

  Costa, José Hélio ^a   De Melo, Dirce Fernandes ^a   Gouveia, Zélia ^b   Cardoso, Hélia Guerra ^b   Peixe, Augusto ^b   Arnholdt Schmitt, Birgit ^b  

^a FEDERAL UNIVERSITY OF CEARÁ   (Brazil)

^b UNIVERSITY OF ÉVORA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE OXIDASE; MESSENGER RNA; OXIDOREDUCTASE;

ARTICLE; BASE PAIRING; BIOLOGICAL MODEL; ENZYMOLOGY; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GRAPE; INTRON; METABOLISM; MULTIGENE FAMILY; PHYLOGENY; PLANT GENOME; RETROPOSON;

BASE PAIRING; DATABASES, GENETIC; EXONS; EXPRESSED SEQUENCE TAGS; GENOME, PLANT; INTRONS; MODELS, GENETIC; MULTIGENE FAMILY; MUTAGENESIS, INSERTIONAL; OXIDOREDUCTASES; PHYLOGENY; RETROELEMENTS; RNA, MESSENGER; VITIS;

VITACEAE; VITIS; VITIS VINIFERA;

EID: 70450286223     PISSN: 00319317     EISSN: 13993054     Source Type: Journal    
DOI: 10.1111/j.1399-3054.2009.01267.x     Document Type: Article

References (55)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
2. Arnholdt-Schmitt B (2004) Stress-induced cell reprogramming. A role for global genome regulation? Plant Physiol 136: 2579-2586
3. Arnholdt-Schmitt B (2005) Functional markers and a 'systemic strategy': convergency between plant breeding, plant nutrition and molecular biology. Plant Physiol Biochem 43: 817-820
4. Arnholdt-Schmitt B, Costa JH, Fernandes de Melo D (2006) AOX-a functional marker for efficient cell reprogramming under stress? Trends Plant Sci 11: 281-287
5. Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7: 1513-1523
6. Borecky J, Nogueira FT, de Oliveira KA, Maia IG, Vercesi AE, Arruda P (2006) The plant energy-dissipating itochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots. J Exp Bot 57: 849-864
7. Cardoso HG, Campos MD, Costa AR, Campos MC, Nothnagel T, Arnholdt-Schmitt B (2009) Carrot alternative oxidase gene AOX2a demonstrates allelic and genotypic polymorphisms in intron3. Physiol Plant 137: 592-608
8. Carlini DB, Chen Y, Stephan W (2001) The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the Drosophilid alcohol dehydrogenase genes Adh and Adhr . Genetics 159: 623-633
9. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31: 415-418
10. Chung BYW, Simons C, Firth AE, Brown CM, Hellens RP (2006) Effects of 5' UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7: 120
11. Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Mol Biol 58: 193-212
12. Collins NC, Tardieu F, Tuberosa R (2008) Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol 147: 469-486
13. Considine MJ, Daley DO, Whelan J (2001) The expression of alternative oxidase and uncoupling protein during fruit ripening in mango. Plant Physiol 126: 1619-1629
14. Considine MJ, Holtzapffel RC, Day DA, Whelan J, Millar AH (2002) Molecular distinction between alternative oxidase from monocots and dicots. Plant Physiol 129: 949-953
15. Costa JH, Cardoso HC, Campos MD, Zavattieri A, Frederico AM, Fernandes de Melo D, Arnholdt-Schmitt B (2009) Daucus carota L.-an old model for cell reprogramming gains new importance through a novel expansion pattern of alternative oxidase (Aox) genes. Plant Physiol Biochem doi:10.1016/j.plaphy. 2009.03.011
16. Costa JH, Hasenfratz-Sauder MP, Pham-Thi AT, Silva Lima MG, Dizengremel P, Jolivet Y, Fernandes de Melo D (2004) Identification in Vigna unguiculata (L.) Walp. of two cDNAs encoding mitochondrial alternative oxidase orthologous to soybean alternative oxidase genes 2a and 2b. Plant Sci 167: 233-239
17. Costa JH, Jolivet Y, Hasenfratz-Sauder MP, Orellano EG, Silva Lima MG, Dizengremel P, Fernandes de Melo D (2007) Alternative oxidase regulation in roots of Vigna unguiculata cultivars differing in drought/salt tolerance. J Plant Physiol 164: 718-727
18. Duester G, Jornvall H, Hatfield GW (1986) Intron-dependent evolution of the nucleotide-binding domains within alcohol dehydrogenase and related enzymes. Nucleic Acids Res 14: 1931-1941
19. Ferreira A, Cardoso HG, Macedo ES, Breviario D, Arnholdt-Schmitt B (2009) Intron polymorphism pattern in AOX1b of wild St John's Wort (Hypericum perforatum L.) allows discrimination between individual plants. Physiol Plant 137: 520-531
20. Finnegan PM, Whelan J, Millar AH, Zhang Q, Smith MK, Wiskich JT, Day DA (1997) Differential expression of the multigene family encoding the soybean mitochondrial alternative oxidase. Plant Physiol 114: 455-466
21. Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376-380
22. Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P (2005) Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 6: R67
23. Hammer GL, Sinclair TR, Chapman SC, van Oosterom E (2004) On systems thinking, systems biology, and the in silico plant. Plant Physiol 134: 909-911
24. Huang Y-F, Niu D-K (2008) Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evol Biol 8: 154
25. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pé E, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quétier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-468.
26. Karpova OV, Kuzmin EV, Elthon TE, Newton KJ (2002) Differential expression of alternative oxidase genes in maize mitochondrial mutants. Plant Cell 14: 3271-3284
27. Kertesz S, Kerenyi Z, Merai Z, Bartos I, Palfy T, Barta E, Silhavy D (2006) Both introns and long 3'-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 34: 6147-6157
28. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304: 982
29. Lima-Júnior A, Fernandes de Melo D, Costa JH, Orellano EG, Jolivet Y, Jarmuszkiewicz W, Sluse F, Dizengremel P, Silva Lima M (2000) Effect of pH on CN-resistant respiratory activity and regulation on Vigna unguiculata mitochondria. Plant Physiol Biochem 38: 765-771
30. Mattick JS, Gagen MJ (2001) The evolution of controlled multitasked gene network: the role of introns and other non-coding RNAs in the development of complex organisms. Mol Biol Evol 18: 1611-1630
31. Millenaar FF, Lambers H (2003) The alternative oxidase: in vivo regulation and function. Plant Biol 5: 2-15
32. Mount SM, Rubin GM (1985) Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol Cell Biol 5: 1630-1638
33. Nitsch JP, Nitsch C (1969) Haploid plants from pollen grains. Science 163: 85-87
34. Ohtsu K, Hirano HY, Tsutsumi N, Hirai A, Nakazono M (2005) Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution. Mol Genet Genomics 274: 606-615
35. Pelsy F, Merdinoglu D (2002) Complete sequence of Tvv1, a family of Ty1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking. Theor Appl Genet 105: 614-621
36. Pereira HS, Barão A, Delgado M, Morais-Cecílio L, Viegas W (2005) Genomic analysis of Garpevine Retrotransposon 1 (Gret1) in Vitis vinifera. Theor Appl Genet 111: 871-878
37. Ren XY, Vorst O, Fiers MWEJ, Stiekema WJ, Nap JP (2006) In plants, highly expressed genes are the least compact. Trends Genet 22: 528-532
38. Roy SW, Penny D, Neafsey DE (2007) Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol 24: 1140-1148
39. Saisho D, Nambara E, Naito S, Tsutsumi N, Hirai A, Nakazono M (1997) Characterization of the gene family for alternative oxidase from Arabidopsis thaliana. Plant Mol Biol 35: 585-596
40. Saitou N, Nei M (1987) The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425
41. Seoighe C, Gehring C, Hurst LD (2005) Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet 1: e13
42. Shabalina S, Spiridonov N (2004) The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol 5: 105
43. Stenoien HK (2007) Compact genes are highly expressed in the moss Physcomitrella patens. J Evol Biol 20: 1223-1229
44. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
45. Tanudji M, Sjöling S, Glaser E, Whelan J (1999) Signals required for the import and processing of the alternative oxidase into mitochondria. J Biol Chem 274: 1286-1293
46. Thirkettle-Watts D, McCabe TC, Clifton R, Moore C, Finnegan PM, Day DA, Whelan J (2003) Analysis of the alternative oxidase promoters from soybean. Plant Physiol 133: 1158-1169
47. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
48. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G-L, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé J-C, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai C-J, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604
49. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, Battilana J, Stormo K, Costa F, Tao Q, Si-Ammour A, Harkins T, Lackey A, Perbost C, Taillon B, Stella A, Solovyev V, Fawcett JA, Sterck L, Vandepoele K, Grando SM, Toppo S, Moser C, Lanchbury J, Bogden R, Skolnick M, Sgaramella V, Bhatnagar SK, Fontana P, Gutin A, Van de Peer Y, Salamini F, Viola R (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2: e1326
50. Vinogradov AE (2001) Intron length and codon usage. J Mol Evol 52: 2-5
51. Vinogradov AE (2004) Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet 20: 248-253
52. Vinogradov AE (2005) Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res 33: 559-563
53. Walker AR, Lee E, Bogs J, McDavid DAJ, Thomas MR, Robinson SP (2007) White grapes arose through the mutation of two similar and adjacent regulatory genes. Plant J 49: 772-785
54. Whelan J, Millar AH, Day DA (1996) The alternative oxidase is encoded in a multigene family in soybean. Planta 198: 197-201
55. Xu Z, Ramakrishna W (2008) Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene 412: 50-58