BMC Plant Biology

Background: Accurate computational identification of cis -regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis -regulatory motifs. Results: We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis ( Arabidopsis thaliana (L.) Heynh.), soybean ( Glycine max (L.) Merr.) and rice ( Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis -regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis,

[1]  Mathieu Blanchette,et al.  Seeder: discriminative seeding DNA motif discovery , 2008, Bioinform..

[2]  Sébastien Baud,et al.  Storage Reserve Accumulation in Arabidopsis: Metabolic and Developmental Control of Seed Filling , 2008, The arabidopsis book.

[3]  François Parcy,et al.  Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. , 2008, The Plant journal : for cell and molecular biology.

[4]  F. Parcy,et al.  FUSCA3 from barley unveils a common transcriptional regulation of seed-specific genes between cereals and Arabidopsis. , 2007, The Plant journal : for cell and molecular biology.

[5]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[6]  S. Chen,et al.  The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. , 2007, The Plant journal : for cell and molecular biology.

[7]  O. Van Wuytswinkel,et al.  Combined networks regulating seed maturation. , 2007, Trends in plant science.

[8]  Panayiotis V. Benos,et al.  STAMP: a web tool for exploring DNA-binding motif similarities , 2007, Nucleic Acids Res..

[9]  M. Venter,et al.  Synthetic promoters: genetic control through cis engineering. , 2007, Trends in plant science.

[10]  Steven J. M. Jones,et al.  Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. , 2006, Genome research.

[11]  Dirk Inzé,et al.  Cell cycle regulation in plant development. , 2006, Annual review of genetics.

[12]  D. Guhathakurta,et al.  Computational identification of transcriptional regulatory elements in DNA sequence , 2006, Nucleic acids research.

[13]  K. Tsutsumi,et al.  The regulatory function of the upstream sequence of the beta-conglycinin alpha subunit gene in seed-specific transcription is associated with the presence of the RY sequence. , 2006, Genes & genetic systems.

[14]  Z. Zheng,et al.  Up-regulation of OsBIHD1, a rice gene encoding BELL homeodomain transcriptional factor, in disease resistance responses. , 2005, Plant biology.

[15]  A. Sandelin,et al.  Applied bioinformatics for the identification of regulatory elements , 2004, Nature Reviews Genetics.

[16]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[17]  K. Harada,et al.  Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene expression. , 2000, The Plant journal : for cell and molecular biology.

[18]  I. Ezcurra,et al.  Interaction between composite elements in the napA promoter: both the B-box ABA-responsive complex and the RY/G complex are necessary for seed-specific expression , 1999, Plant Molecular Biology.

[19]  Kyuya Harada,et al.  Identification of cis-regulatory elements required for endosperm expression of the rice storage protein glutelin gene GluB-1 , 1999, Plant Molecular Biology.

[20]  M. Mena,et al.  An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. , 1998, The Plant journal : for cell and molecular biology.

[21]  G. Vriend,et al.  ACGT and vicilin core sequences in a promoter domain required for seed-specific expression of a 2S storage protein gene are recognized by the opaque-2 regulatory protein , 1997, Plant Molecular Biology.

[22]  U. Yamanouchi,et al.  Characterization of common cis-regulatory elements responsible for the endosperm-specific expression of members of the rice glutelin multigene family , 1996, Plant Molecular Biology.

[23]  H. Hirano,et al.  Nucleotide Sequence of the Basic 7S Globulin Gene from Soybean , 1994, Plant physiology.

[24]  Y. Itoh,et al.  The glycinin box: a soybean embryo factor binding motif within the quantitative regulatory region of the 11S seed storage globulin promoter , 1994, Molecular and General Genetics MGG.

[25]  M. Müller,et al.  The nitrogen response of a barley C-hordein promoter is controlled by positive and negative regulation of the GCN4 and endosperm box. , 1993, The Plant journal : for cell and molecular biology.

[26]  Y. Itoh,et al.  Cis-acting regulatory regions of the soybean seed storage 11S globulin gene and their interactions with seed embryo factors , 1993, Plant Molecular Biology.

[27]  M. Delseny,et al.  The cruciferin gene family in radish , 1992, Plant Molecular Biology.

[28]  L. Josefsson,et al.  Characterization of a Brassica napus gene encoding a cruciferin subunit: estimation of sizes of cruciferin gene families , 1992, Plant Molecular Biology.

[29]  N. Daigle,et al.  The legumin boxes and the 3′ part of a soybean β-conglycinin promoter are involved in seed gene expression in transgenic tobacco plants , 1992, Plant Molecular Biology.

[30]  D. Inzé,et al.  Cis-analysis of a seed protein gene promoter: the conservative RY repeat CATGCATG within the legumin box is essential for tissue-specific expression of a legumin gene. , 1992, The Plant journal : for cell and molecular biology.

[31]  B. Larkins,et al.  Binding of an endosperm-specific nuclear protein to a maize beta-zein gene correlates with zein transcriptional activity , 1991, Plant Molecular Biology.

[32]  L. Josefsson,et al.  Analysis of the promoter region of napin genes from Brassica napus demonstrates binding of nuclear protein in vitro to a conserved sequence motif. , 1991, European journal of biochemistry.

[33]  T. Fujiwara,et al.  Multiple nuclear factors interact with upstream sequences of differentially regulated β-conglycinin genes , 1991, Plant Molecular Biology.

[34]  R. Flavell,et al.  Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin. , 1990, The Plant cell.

[35]  Y. Itoh,et al.  The complete nucleotide sequence of soybean glycinin A2B1a gene spanning to another glycinin gene A1aB1b. , 1990, Nucleic acids research.

[36]  A. Gould,et al.  Pea convicilin: structure and primary sequence of the protein and expression of a gene in the seeds of transgenic tobacco , 1990, Planta.

[37]  T. Higgins,et al.  Nucleotide sequence of an A-type legumin gene from pea. , 1990, Nucleic acids research.

[38]  Thomas L. Sims,et al.  The glycinin Gy1 gene from soybean. , 1989, Nucleic acids research.

[39]  Y. Takei,et al.  Nucleotide sequence of the canavalin gene from Canavalia gladiata seeds. , 1989, Nucleic acids research.

[40]  R. Allen,et al.  Nuclear factors interact with a soybean beta-conglycinin enhancer. , 1989, The Plant cell.

[41]  Anderson J. Ryan,et al.  Genomic sequence of a 12S seed storage protein from oilseed rape (Brassica napus c.v. jet neuf). , 1989, Nucleic acids research.

[42]  S. Barker,et al.  Soybean beta-conglycinin genes are clustered in several DNA regions and are regulated by transcriptional and posttranscriptional processes. , 1989, The Plant cell.

[43]  S. Hasnain,et al.  Characterization of the kafirin gene family from sorghum reveals extensive homology with zein from maize , 1989, Plant Molecular Biology.

[44]  B. Scallon,et al.  Characterization of the glycinin gene family in soybean. , 1989, The Plant cell.

[45]  J. Gatehouse,et al.  The sequence of a gene encoding convicilin from pea (Pisum sativum L.) shows that convicilin differs from vicilin by an insertion near the N-terminus. , 1988, The Biochemical journal.

[46]  J. Gatehouse,et al.  Two genes encoding 'minor' legumin polypeptides in pea (Pisum sativum L.). Characterization and complete sequence of the LegJ gene. , 1988, The Biochemical journal.

[47]  R. Beachy,et al.  A DNA sequence element that confers seed‐specific enhancement to a constitutive promoter , 1988, The EMBO journal.

[48]  C. D. Dickinson,et al.  RY repeats are conserved in the 5'-flanking regions of legume seed- protein genes , 1988, Nucleic Acids Res..

[49]  U. Wobus,et al.  Nucleotide sequence of a field bean (Vicia faba L.var.minor) vicilin gene. , 1987, Nucleic acids research.

[50]  L. Josefsson,et al.  Structure of a gene encoding the 1.7 S storage protein, napin, from Brassica napus. , 1987, The Journal of biological chemistry.

[51]  M. Schuler,et al.  Functional analysis of regulatory elements in a plant embryo-specific gene. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[52]  J. Doyle,et al.  The glycosylated seed storage proteins of Glycine max and Phaseolus vulgaris. Structural homologies of genes and proteins. , 1986, The Journal of biological chemistry.

[53]  U. Wobus,et al.  The legumin gene family: structure of a B type gene of Vicia faba and a possible legumin gene specific regulatory element. , 1986, Nucleic acids research.

[54]  J. Pywell,et al.  Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize. , 1985, Nucleic acids research.

[55]  A. Cornish-Bowden.  Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. , 1985, Nucleic acids research.

[56]  B. Larkins,et al.  Cloning and sequence analysis reveal structural variation among related zein genes in maize , 1982, Cell.

[57]  D. Meinke,et al.  Expression of storage-protein genes during soybean seed development , 1981, Planta.

[58]  A. Krishnamachari,et al.  Computational analysis of plant RNA Pol-II promoters. , 2006, Bio Systems.

[59]  Jesús Vicente-Carbajosa,et al.  Seed maturation: developing an intrusive phase to accomplish a quiescent state. , 2005, The International journal of developmental biology.

[60]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[61]  Roger N. Beachy,et al.  Tissue-specific and temporal regulation of a β-conglycinin gene: roles of the RY repeat and other cis-acting elements , 2004, Plant Molecular Biology.

[62]  D. Boulter,et al.  Sequences responsible for the tissue specific promoter activity of a pea legumin gene in tobacco , 2004, Molecular and General Genetics MGG.

[63]  I. Ezcurra,et al.  Disruption of an overlapping E-box/ABRE motif abolished high transcription of the napA storage-protein promoter in transgenic Brassica napus seeds , 2004, Planta.

[64]  T. Hall,et al.  Module-specific regulation of the beta-phaseolin promoter during embryogenesis. , 2003, The Plant journal : for cell and molecular biology.

[65]  T. D. Schneider,et al.  Consensus sequence Zen. , 2002, Applied bioinformatics.

[66]  K. Tsutsumi,et al.  Structure and characterization of the gene encoding alpha subunit of soybean beta-conglycinin. , 2001, Genes & genetic systems.

[67]  S. Yanagisawa,et al.  Diversity and similarity among recognition sequences of Dof transcription factors. , 1999, The Plant journal : for cell and molecular biology.

[68]  Kenichi Higo,et al.  PLACE: a database of plant cis-acting regulatory DNA elements , 1998, Nucleic Acids Res..

[69]  T. Guilfoyle.  The Structure of Plant Gene Promoters , 1997 .

[70]  Rob J Hyndman,et al.  Sample Quantiles in Statistical Packages , 1996 .

[71]  T. Fujiwara,et al.  Upstream regulatory sequences from two beta-conglycinin genes. , 1993, Plant molecular biology.

[72]  N. Nielsen,et al.  5'CATGCAT-3' Elements Modulate the Expression of Glycinin Genes. , 1992, Plant physiology.

[73]  L. Vodkin,et al.  Expression of soybean lectin gene deletions in tobacco. , 1990, Developmental genetics.

[74]  J. Rafalski,et al.  Structure of wheat gamma-gliadin genes. , 1986, Gene.

[75]  D. Söll,et al.  Conservation and variability of wheat alpha/beta-gliadin genes. , 1985, Nucleic acids research.