Endosperm-preferred expression of maize genes as revealed by transcriptome-wide analysis of expressed sequence tags

Plant Molecular Biology

Volumn 59, Issue 2, 2005, Pages 363-374

  Verza, Natalia C ^a   Rezende E Silva, Thaís ^a   Neto, Germano Cord ^a   Nogueira, Fábio T S ^a   Fisch, Paulo H ^a   De Rosa Jr , Vincente E ^a   Rebello, Marcelo M ^a   Vettore, André L ^b   Da Silva, Felipe Rodrigues ^c   Arruda, Paulo ^a  

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b LUDWIG INSTITUTE FOR CANCER RESEARCH   (Brazil)

^c EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

Author keywords

Endosperm; Endosperm specific genes; ESTs; Maize transcriptome

Indexed keywords

CROPS; DATABASE SYSTEMS; DNA; HARVESTING; METABOLISM; TISSUE;

ENDOSPERM-SPECIFIC GENES; ESTS; EXPRESSED SEQUENCE TAGS (EST); MAIZE TRANSCRIPTOME;

GENES;

VEGETABLE PROTEIN;

ARTICLE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; MAIZE; METABOLISM; PLANT ROOT; PLANT SEED; SEEDLING;

EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; PLANT PROTEINS; PLANT ROOTS; SEEDLING; SEEDS; TRANSCRIPTION, GENETIC; ZEA MAYS;

CORN; ENDOSPERM; GENES; PLANT TISSUES; POLLINATION;

ZEA MAYS;

EID: 27144458860     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-005-8924-7     Document Type: Article

References (46)

1. S.F. Altschul T.L. Madden A.A. Schäffer J. Zhang Z. Zhang W. Miller D.J. Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 3389 3402
2. P. Arruda E.L. Kemper F. Papes A. Leite 2000 Regulation of lysine catabolism in higher plants Trends Plant Sci. 5 324 330
3. S. Audic J.M. Claverie 1997 The significance of digital gene expression profiles Genome Res 7 986 995
4. H.W. Bass C. Webster G.R. Obrian J.K.M. Roberts R.S. Boston 1992 A maize ribosome-inactivating protein is controlled by the transcriptional activator Opaque2 Plant Cell 4 225 234
5. D.A. Benson I. Karsch-Mizrachi D.J. Lipman J. Ostell B.A. Rapp D.L. Wheeler 2000 GenBank Nucleic Acids Res. 28 15 18
6. F. Berger 1999 Endosperm development Curr. Opin. Plant. Biol. 2 28 32
7. B. Boeckmann A. Bairoch R. Apweiler M.-C. Blatter A. Estreicher E. Gasteiger M.J. Martin K. Michoud C. O'Donovan I. Phan S. Pilbout M. Schneider 2003 The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 31 365 370
8. G. Cord Neto J.A. Yunes A.L. Vettore M.J. Da Silva P. Arruda A. Leite 1995 The involvement of Opaque2 on β-prolamin gene regulation in maize and Coix suggests a more general role for this transcriptional activator Plant Mol. Biol 27 1015 1029
9. Q. Dong L. Roy M. Freeling V. Walbot V. Brendel 2003 ZmDB, an integrated database for maize genome research Nucleic Acids Res 31 244 247
10. B. Ewing L.A. Hillier M.C. Wendl P. Green 1998 Base-calling of automated sequencer traces using Phred. I. Accuracy assessment Genome Res. 8 175 185
11. J. Fernandes V. Brendel X. Gai S. Lal V.L. Chandler R.P. Elumalai D.W. Galbraith E.A. Pierson V. Walbot 2002 Comparison of RNA expression profiles based on maize-expressed sequence tag frequency analysis and micro-array hybridization Plant Physiol 128 896 910
12. X. Gai S. Lal L. Xing V. Brendel V. Walbot 2000 Gene discovery using the maize genome database ZmDB Nucleic Acids Res 28 94 96
13. P. Gallusci S. Varott M. Matsuoko M. Maddaloni R.D. Thompson 1996 Regulation of cytosolic pyruvate, orthophosphate dikinase expression in developing maize endosperm Plant Mol. Biol. 31 45 55
14. M.J. Giroux C. Boyer G. Feix L.C. Hannah 1994 Coordinated transcriptional regulation of storage product genes in the maize endosperm Plant Physiol. 106 713 722
15. M. Guo M.A. Rupe O.N. Danilevskaya X. Yang Z. Hu 2003 Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm Plant J. 36 30 44
16. J.E. Habben A.W. Kirleis B.A. Larkins 1993 The origin of lysine-containing proteins in the opaque-2 maize endosperm Plant Mol. Biol. 23 825 838
17. X. Huang A. Madan 1999 CAP3: a DNA sequence assembly program Genome Res. 9 868 877
18. B.G. Hunter M.K. Beatty G.W. Singletary B.R. Hamaker B.P. Dilkes B.A. Larkins R. Jung 2002 Maize opaque endosperm mutations create extensive changes in patterns of gene expression Plant Cell. 14 2591 2612
19. International Human Genome Sequencing Consortium 2004 Finishing the euchromatic sequence of the human genome Nature 431 931 945
20. D. Job 2002 Génoplante: the French national network in plant genomics GenomXPress 4 13 17
21. E.L. Kemper G. Cord Neto F. Papes K.C.M. Moraes A. Leite P. Arruda 1999 The role of Opaque2 in the control of lysine-degrading activities in developing maize endosperm Plant Cell 11 1981 1993
22. J. Lai N. Dey C.S. Kim A.K. Bharti S. Rudd K.F. Mayer B.A. Larkins P. Becraft J. Messing 2004 Characterization of the maize endosperm transcriptome and its comparison to the rice genome Genome Res. 14 1932 1937
23. S. Lohmer M. Maddaloni M. Motto N. Di Fonzo H. Hartings F. Salamini R.D. Thompson 1991 The maize regulatory locus Opaque-2 encodes a DNA-binding protein which activates the transcription of the b-32 gene EMBO J. 10 617 624
24. M.A. Lopes B.A. Larkins 1993 Endosperm origin, development, and function Plant Cell 5 1383 1399
25. A. Maizel D. Weigel 2004 Temporally and spatially controlled induction of gene expression in Arabidopsis thaliana Plant J. 38 164 171
26. K. Manning 1991 Isolation of nucleic acids from plants by differential solvent precipitation Anal. Biochem. 195 45 50
27. M. Muller G. Dues C. Balconi F. Salamini R.D. Thompson 1997 Nitrogen and hormonal responsiveness of the 22 kDa alpha-zein and b-32 genes in maize endosperm is displayed in the absence of the transcriptional regulator Opaque-2 Plant J. 12 281 291
28. M.G. Neuffer W.F. Sheridan 1980 Defective kernel mutants of maize I Genetic and lethality studies Genetics 95 929 944
29. F.T.S. Nogueira V.E. De Rosa Jr M. Menossi E.C. Ulian P. Arruda 2003 RNA expression profiles and data mining of sugarcane response to low temperature Plant Physiol. 132 1811 1824
30. O-A. Olsen 2004 Nuclear endosperm development in cereals and Arabidopsis thaliana Plant Cell 16 S214 S227
31. D. Samson F. Legeai E. Karsenty S. Reboux J-B. Veyrieras J. Just E. Barillot 2003 GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics Nucleic Acids Res 31 179 182
32. M.J. Scanlon PS. Stinard M.G. James A.M. Myers D.S. Robertson 1994 Genetic analysis of 63 mutations affecting maize kernel development isolated from Mutator stocks Genetics 136 281 294
33. M.J. Scanlon A.M. Myers 1998 Phenotypic analysis and molecular cloning of discolored-1 (dsc1), a maize gene required for early kernel development Plant Mol. Biol. 37 483 493
34. M. Schmid T.S. Davison S.R. Henz U.J. Pape M. Demar M. Vingron B. Scholkopf D. Weigel J.U. Lohmann 2005 A gene expression map of Arabidopsis thaliana development Nat. Gen. 37 5 501 6
35. R.J. Schmidt M. Ketudat M.J. Aukerman G. Hoschek 1992 Opaque2 is a transcriptional activator that recognizes a specific target site in 22 kDa zein gene Plant Cell 4 689 700
36. V. Stolc Z. Gauhar C. Mason G. Halasz M.F. van Batenburg S.A. Rifkin S. Hua T. Herreman W. Tongprasit P.E. Barbano H.J. Bussemaker K.P. White 2004 A gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 655 660
37. G.P. Telles M.D.V. Braga Z. Dias T-L. Lin J.A.A. Quitzau F.R. da Silva J. Meidanis 2001 Bioinformatics of the sugarcane EST project Genet Mol. Biol. 24 9 15
38. G.P. Telles F.R. da Silva 2001 Trimming and clustering sugarcane ESTs Genet. Mol. Biol. 24 17 23
39. J.H. Tuteja S.J. Clough W.C. Chan L.O. Vodkin 2004 Tissue-specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max Plant Cell 16 819 835
40. V.E. Velculescu S.L. Madden L. Zhang A.E. Lash J. Yu C. Rago A. Lal C.J. Wang G.A. Beaudry K.M. Ciriello B.P. Cook M.R. Dufault A.T. Ferguson Y. Gao T.C. He H. Hermeking S.K. Hiraldo P.M. Hwang M.A. Lopez H.F. Luderer B. Mathews J.M. Petroziello K. Polyak L. Zawel K.W. Kinzler 1999 Analysis of human transcriptomes Nat. Genet. 23 387 388
41. A.L. Vettore F.R. da Silva E.L. Kemper P. Arruda 2001 The libraries that made SUCEST Genet. Mol. Biol. 24 1 7
42. A.L. Vettore F.R. da Silva E.L. Kemper G.M. Souza A.M. da Silva M.I. Ferro F. Henrique-Silva E.A. Giglioti M.V. Lemos L.L. Coutinho 2003 Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane Genome Res. 13 2725 2735
43. C.W. Whitfield M.R. Band M.F. Bonaldo C.G. Kumar L. Liu J.R. Pardinas H.M. Robertson M.B. Soares G.E. Robinson 2002 Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee Genome Res. 12 555 566
44. Y.M. Woo D.W.N. Hu B.A. Larkins R. Jung 2001 Genomics analysis of genes expressed in maize endosperm identifies novel seed proteins and clarifies patterns of zein gene expression Plant Cell 13 2297 2317
45. J. Yu S. Hu J. Wang G.K. Wong S. Li B. Liu Y. Deng L. Dai Y. Zhou X. Zhang 2002 A draft sequence of the rice genome (Oryza sativa L ssp. indica) Science 296 79 92
46. L. Yu T.L. Setter 2003 Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit Plant physio 131 568 582