Structure and Expression of Maize Phytochrome Family Homeologs Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY234825, AY234826, AY234827, AY234828, AY234829, AY234830.

To begin the study of phytochrome signaling in maize, we have cloned and characterized the phytochrome gene family from the inbred B73. Through DNA gel blot analysis of maize genomic DNA and BAC library screens, we show that the PhyA, PhyB, and PhyC genes are each duplicated once in the genome of maize. Each gene pair was positioned to homeologous regions of the genome using recombinant inbred mapping populations. These results strongly suggest that the duplication of the phytochrome gene family in maize arose as a consequence of an ancient tetraploidization in the maize ancestral lineage. Furthermore, sequencing of Phy genes directly from BAC clones indicates that there are six functional phytochrome genes in maize. Through Northern gel blot analysis and a semiquantitative reverse transcriptase polymerase chain reaction assay, we determined that all six phytochrome genes are transcribed in several seedling tissues. However, expression from PhyA1, PhyB1, and PhyC1 predominate in all seedling tissues examined. Dark-grown seedlings express higher levels of PhyA and PhyB than do light-grown plants but PhyC genes are expressed at similar levels under light and dark growth conditions. These results are discussed in relation to phytochrome gene regulation in model eudicots and monocots and in light of current genome sequencing efforts in maize.

[1]  R. Sharrock,et al.  Differential activities of the Arabidopsis phyB/D/E phytochromes in complementing phyB mutant phenotypes , 2003, Plant Molecular Biology.

[2]  D. Grant,et al.  Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population , 2002, Plant Molecular Biology.

[3]  D. Basu,et al.  Rice PHYC gene: structure, expression, map position and evolution , 2000, Plant Molecular Biology.

[4]  S. Mathews,et al.  The phytochrome apoprotein family inArabidopsis is encoded by five genes: the sequences and expression ofPHYD andPHYE , 1994, Plant Molecular Biology.

[5]  C. Gatz,et al.  Isolation and characterization of a cDNA-clone coding for potato type A phytochrome , 1992, Plant Molecular Biology.

[6]  P. Quail,et al.  phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots , 1991, Molecular and General Genetics MGG.

[7]  P. Quail,et al.  Phytochrome regulation of phytochrome mRNA abundance , 2004, Plant Molecular Biology.

[8]  T. Brutnell,et al.  Photomorphogenic Responses in Maize Seedling Development1[w] , 2003, Plant Physiology.

[9]  E. Schäfer,et al.  Light perception and signalling in higher plants. , 2003, Current opinion in plant biology.

[10]  The Phytochrome Gene Family in the Stellaria longipes Complex , 2003, International Journal of Plant Sciences.

[11]  E. Huq,et al.  Nuclear translocation of the photoreceptor phytochrome B is necessary for its biological function in seedling photomorphogenesis. , 2003, The Plant journal : for cell and molecular biology.

[12]  J. Ecker,et al.  Isolation and Characterization of phyC Mutants in Arabidopsis Reveals Complex Crosstalk between Phytochrome Signaling Pathways Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012971. , 2003, The Plant Cell Online.

[13]  R. Vierstra,et al.  Mutant Analyses Define Multiple Roles for Phytochrome C in Arabidopsis Photomorphogenesis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.015164. , 2003, The Plant Cell Online.

[14]  N. Mochizuki,et al.  Dimers of the N-terminal domain of phytochrome B are functional in the nucleus , 2003, Nature.

[15]  J. Casal,et al.  Light, phytochrome signalling and photomorphogenesis in Arabidopsis , 2003, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[16]  R. Sharrock,et al.  Signaling activities among the Arabidopsis phyB/D/E-type phytochromes: a major role for the central region of the apoprotein. , 2003, The Plant journal : for cell and molecular biology.

[17]  W. McCombie,et al.  Gene enrichment in plant genomic shotgun libraries. , 2003, Current opinion in plant biology.

[18]  42nd Annual Meeting of the American Society for Cell Biology, San Francisco, California, USA, 14–18 December 2002 , 2003, Breast Cancer Research.

[19]  J. Mullet,et al.  Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing1 , 2002, Plant Physiology.

[20]  T. Brutnell,et al.  elongated mesocotyl1, a Phytochrome-Deficient Mutant of Maize1 , 2002, Plant Physiology.

[21]  J. Bennetzen,et al.  Methylation-spanning linker libraries link gene-rich regions and identify epigenetic boundaries in Zea mays. , 2002, Genome research.

[22]  R. Sharrock,et al.  Patterns of Expression and Normalized Levels of the Five Arabidopsis Phytochromes1 , 2002, Plant Physiology.

[23]  E. Schäfer,et al.  Nucleocytoplasmic Partitioning of the Plant Photoreceptors Phytochrome A, B, C, D, and E Is Regulated Differentially by Light and Exhibits a Diurnal Rhythm Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001156. , 2002, The Plant Cell Online.

[24]  E. Huq,et al.  PIF4, a phytochrome‐interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis , 2002, The EMBO journal.

[25]  Ngozi A. Duru,et al.  Construction and characterization of a deep-coverage bacterial artificial chromosome library for maize , 2002 .

[26]  P. Quail.  Photosensory perception and signalling in plant cells: new paradigms? , 2002, Current opinion in cell biology.

[27]  B. Gaut.  Patterns of chromosomal duplication in maize and their implications for comparative maps of the grasses. , 2001, Genome research.

[28]  J. Hurley,et al.  Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor , 2000, The EMBO journal.

[29]  J. Reed,et al.  The histidine kinase-related domain participates in phytochrome B function but is dispensable. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[30]  C. Ballaré,et al.  Light signals perceived by crop and weed plants. , 2000 .

[31]  R. Alba,et al.  The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. , 2000, Molecular biology and evolution.

[32]  J. Chory,et al.  Light: an indicator of time and place. , 2000, Genes & development.

[33]  K. Shimamoto,et al.  Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant). , 1999, The Plant journal : for cell and molecular biology.

[34]  Robert A. Martienssen,et al.  Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome , 1999, Nature Genetics.

[35]  S. Mccouch,et al.  Inferences on the genome structure of progenitor maize through comparative analysis of rice, maize and the domesticated panicoids. , 1999, Genetics.

[36]  K. Harter,et al.  Light Quality–Dependent Nuclear Import of the Plant Photoreceptors Phytochrome A and B , 1999, Plant Cell.

[37]  Kirschner Ls,et al.  Large-scale preparation of sequence-ready bacterial artificial chromosome DNA using QIAGEN columns. , 1999 .

[38]  S. Kay,et al.  Light-dependent Translocation of a Phytochrome B-GFP Fusion Protein to the Nucleus in Transgenic Arabidopsis , 1999, The Journal of cell biology.

[39]  Pratt,et al.  A photoperiod-insensitive barley line contains a light-labile phytochrome B , 1999, Plant physiology.

[40]  R. Sharrock,et al.  Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. , 1999, Plant physiology.

[41]  Mahmoudkhani,et al.  Structure of , 1999, Acta crystallographica. Section B, Structural science.

[42]  K. Yeh,et al.  Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  P. Sassone-Corsi,et al.  PASting together the mammalian clock , 1998, Current Opinion in Neurobiology.

[44]  G. Whitelam,et al.  Phytochrome E Influences Internode Elongation and Flowering Time in Arabidopsis , 1998, Plant Cell.

[45]  S. Kay,et al.  Photoactive yellow protein: a structural prototype for the three-dimensional fold of the PAS domain superfamily. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[46]  B. Hauser,et al.  Temporal and photoregulated expression of five tomato phytochrome genes. , 1998, The Plant journal : for cell and molecular biology.

[47]  G. Howe,et al.  Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies. , 1998, Molecular biology and evolution.

[48]  C. Ponting,et al.  The GAF domain: an evolutionary link between diverse phototransducing proteins. , 1997, Trends in biochemical sciences.

[49]  R. Sharrock,et al.  Differential Patterns of Expression of the Arabidopsis PHYB, PHYD, and PHYE Phytochrome Genes , 1997, Plant physiology.

[50]  C. Ponting,et al.  PAS: a multifunctional domain family comes to light , 1997, Current Biology.

[51]  R. Amasino,et al.  A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing. , 1997, The Plant cell.

[52]  B. Gaut,et al.  DNA sequence evidence for the segmental allotetraploid origin of maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[53]  S. Mathews,et al.  Phytochrome gene diversity , 1997 .

[54]  P. Quail.  An emerging molecular map of the phytochromes , 1997 .

[55]  J. Mullet,et al.  The Sorghum Photoperiod Sensitivity Gene, Ma3, Encodes a Phytochrome B , 1997, Plant physiology.

[56]  A. Nagatani,et al.  Nuclear localization activity of phytochrome B. , 1996, The Plant journal : for cell and molecular biology.

[57]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[58]  S. Mathews,et al.  The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. , 1996, Molecular biology and evolution.

[59]  L. Kozma-Bognár,et al.  The Tissue-Specific Expression of a Tobacco Phytochrome B Gene , 1996, Plant physiology.

[60]  P. Quail,et al.  Mutational analysis of phytochrome B identifies a small COOH-terminal-domain region critical for regulatory activity. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[61]  P. Quail,et al.  Missense mutations define a restricted segment in the C-terminal domain of phytochrome A critical to its regulatory activity. , 1995, The Plant cell.

[62]  P. Quail,et al.  Phytochromes: photosensory perception and signal transduction , 1995, Science.

[63]  D. E. Somers,et al.  Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. , 1995, The Plant journal : for cell and molecular biology.

[64]  D. E. Somers,et al.  Phytochrome-Mediated Light Regulation of PHYA- and PHYB-GUS Transgenes in Arabidopsis thaliana Seedlings , 1995, Plant physiology.

[65]  Harry Smith.  Physiological and Ecological Function within the Phytochrome Family , 1995 .

[66]  S. Mathews,et al.  Evolution of the Phytochrome Gene Family and Its Utility for Phylogenetic Analyses of Angiosperms , 1995 .

[67]  J. Chory,et al.  Phytochrome A and Phytochrome B Have Overlapping but Distinct Functions in Arabidopsis Development , 1994, Plant physiology.

[68]  M. J. Terry,et al.  Biosynthesis of the plant photoreceptor phytochrome. , 1993, Archives of biochemistry and biophysics.

[69]  P. Quail,et al.  Arabidopsis HY8 locus encodes phytochrome A. , 1993, The Plant cell.

[70]  M. L. Anderson,et al.  Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white light. , 1993, The Plant cell.

[71]  J. Chory,et al.  Isolation and Initial Characterization of Arabidopsis Mutants That Are Deficient in Phytochrome A , 1993, Plant physiology.

[72]  J. Chory,et al.  Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. , 1993, The Plant cell.

[73]  P. Quail,et al.  hy8, a new class of arabidopsis long hypocotyl mutants deficient in functional phytochrome A. , 1993, The Plant cell.

[74]  P. Quail,et al.  A negatively acting DNA sequence element mediates phytochrome‐directed repression of phyA gene transcription. , 1991, The EMBO journal.

[75]  P. Quail,et al.  cis-acting elements involved in photoregulation of an oat phytochrome promoter in rice. , 1990, The Plant cell.

[76]  P. Quail,et al.  Structure and expression of a maize phytochrome-encoding gene. , 1989, Gene.

[77]  P. Quail,et al.  Photoregulation of a phytochrome gene promoter from oat transferred into rice by particle bombardment. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[78]  S. Kay,et al.  The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5' upstream region. , 1989, The Plant cell.

[79]  P. Quail,et al.  Rapid transcriptional regulation by phytochrome of the genes for phytochrome and chlorophyll a/b-binding protein in Avena sativa , 1988, Molecular and cellular biology.

[80]  J. Mol,et al.  Cloning of the two chalcone flavanone isomerase genes from Petunia hybrida: coordinate, light‐regulated and differential expression of flavonoid genes. , 1988, The EMBO journal.

[81]  Alan M. Jones,et al.  Quaternary structure of 124-kilodalton phytochrome from Avena sativa L. , 1986 .

[82]  P. Quail,et al.  Nucleotide and amino acid sequence of a Cucurbita phytochrome cDNA clone: identification of conserved features by comparison with Avena phytochrome. , 1986, Gene.

[83]  P. Quail,et al.  Molecular cloning of cDNA for Avena phytochrome. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[84]  G. Church,et al.  Genomic sequencing. , 1993, Methods in molecular biology.

[85]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[86]  P. Quail,et al.  Autoregulatory control of translatable phytochrome mRNA levels. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[87]  J. Miller,et al.  Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. , 1978, Journal of molecular biology.