The Rice COLEOPTILE PHOTOTROPISM1 gene encoding an ortholog of Arabidopsis NPH3 is required for phototropism of coleoptiles and lateral translocation of auxin

We isolated a mutant, named coleoptile phototropism1 (cpt1), from gamma-ray-mutagenized japonica-type rice (Oryza sativa). This mutant showed no coleoptile phototropism and severely reduced root phototropism after continuous stimulation. A map-based cloning strategy and transgenic complementation test were applied to demonstrate that a NPH3-like gene deleted in the mutant corresponds to CPT1. Phylogenetic analysis of putative CPT1 homologs of rice and related proteins indicated that CPT1 has an orthologous relationship with Arabidopsis thaliana NPH3. These results, along with those for Arabidopsis, demonstrate that NPH3/CPT1 is a key signal transduction component of higher plant phototropism. In an extended study with the cpt1 mutant, it was found that phototropic differential growth is accompanied by a CPT1-independent inhibition of net growth. Kinetic investigation further indicated that a small phototropism occurs in cpt1 coleoptiles. This response, induced only transiently, was thought to be caused by the CPT1-independent growth inhibition. The 3H-indole-3-acetic acid applied to the coleoptile tip was asymmetrically distributed between the two sides of phototropically responding coleoptiles. However, no asymmetry was induced in cpt1 coleoptiles, indicating that lateral translocation of auxin occurs downstream of CPT1. It is concluded that the CPT1-dependent major phototropism of coleoptiles is achieved by lateral auxin translocation and subsequent growth redistribution.     

Differential expression of two barley XET-related genes during coleoptile growth

Plant cell elongation depends on the physical properties of the primary cell wall. Because xyloglucan endotransglycosylases (XETs) are enzymes that mediate cleavage and rejoining of the beta(1-4)-XG backbone of primary cell wall, they are potentially involved in cell elongation. In this paper, the growth of the barley coleoptile was related to the expression patterns of two genes from this family (hvEXT, hvXEB) in experiments where coleoptile elongation varied according to light/dark treatments in order to assess the potential role of these genes in cell elongation. In dark-grown and light-grown coleoptiles, growth rate variations were associated with altered levels of expression of hvEXT and hvXEB: they were higher in dark-grown than in light-grown seedlings, and decreased after 5 d in darkness, and after 4 d in continuous light. In 4-d-old seedlings, coleoptile elongation decreased significantly 4 h after the onset of a continuous white- light irradiation, and hvXEB and hvEXT mRNA levels decreased, respectively, 2 h and 4 h after the onset of white-light irradiation. Moreover, the distribution of hvXEB and hvEXT along the coleoptiles of 4-d-old dark-grown seedlings were different. Altogether, these results suggest a complex pattern of temporal and positional expression for the different genes of the XET-related family.     

Photochemical properties of the flavin mononucleotide-binding domains of the phototropins from Arabidopsis,rice, and Chlamydomonas reinhardtii

Phototropins (phot1 and phot2, formerly designated nph1 and npl1) are blue-light receptors that mediate phototropism, blue light-induced chloroplast relocation, and blue light-induced stomatal opening in Arabidopsis. Phototropins contain two light, oxygen, or voltage (LOV) domains at their N termini (LOV1 and LOV2), each a binding site for the chromophore flavin mononucleotide (FMN). Their C termini contain a serine/threonine protein kinase domain. Here, we examine the kinetic properties of the LOV domains of Arabidopsis phot1 and phot2, rice (Oryza sativa) phot1 and phot2, and Chlamydomonas reinhardtii phot. When expressed in Escherichia coli, purified LOV domains from all phototropins examined bind FMN tightly and undergo a self-contained photocycle, characterized by fluorescence and absorption changes induced by blue light (T. Sakai, T. Kagawa, M. Kasahara, T.E. Swartz, J.M. Christie, W.R. Briggs, M. Wada, K. Okada [2001] Proc Natl Acad Sci USA 98: 6969-6974; M. Salomon, J.M. Christie, E. Knieb, U. Lempert, W.R. Briggs [2000] Biochemistry 39: 9401-9410). The photocycle involves the light-induced formation of a cysteinyl adduct to the C(4a) carbon of the FMN chromophore, which subsequently breaks down in darkness. In each case, the relative quantum efficiencies for the photoreaction and the rate constants for dark recovery of LOV1, LOV2, and peptides containing both LOV domains are presented. Moreover, the data obtained from full-length Arabidopsis phot1 and phot2 expressed in insect cells closely resemble those obtained for the tandem LOV-domain fusion proteins expressed in E. coli. For both Arabidopsis and rice phototropins, the LOV domains of phot1 differ from those of phot2 in their reaction kinetic properties and relative quantum efficiencies. Thus, in addition to differing in amino acid sequence, the phototropins can be distinguished on the basis of the photochemical cycles of their LOV domains. The LOV domains of C. reinhardtii phot also undergo light-activated spectral changes consistent with cysteinyl adduct formation. Thus, the phototropin family extends over a wide evolutionary range from unicellular algae to higher plants.     

Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35

Catalysing the hydrolysis of terminal beta-galactosyl residues from carbohydrates, galactolipids, and glycoproteins, glycoside hydrolase family 35 (beta-galactosidases; BGALs) are widely distributed in plants and believed to play many key roles, including modification of cell wall components. Completion of the Arabidopsis thaliana genome sequencing project has, for the first time, allowed an examination of the total number, gene structure, and evolutionary patterns of all Family 35 members in a representative (model) angiosperm. Reiterative database searches established a multigene family of 17 members (designated BGAL1-BGAL17). Using these genes as query sequences, BLAST and Hidden Markov Model searches identified BGAL genes among 22 other eukaryotes, whose genomic sequences are known. The Arabidopsis (n=17) and rice (n=15) BGAL families were much larger than those of Chlamydomonas, fungi, and animals (n=0-4), and a lineage-specific expansion of BGAL genes apparently occurred after divergence of the Arabidopsis and rice lineages. All plant BGAL genes, with the exception of Arabidopsis BGAL17 and rice Os 9633.m04334, form a monophyletic group. Arabidopsis BGAL expression levels are much higher in mature leaves, roots, flowers, and siliques but are lower in young seedlings. BGAL8, BGAL11, BGAL13, BGAL14, and BGAL16 are expressed only in flowers. Catalytically active BGAL4 was produced in the E. coli and baculoviral expression systems, purified to electrophoretic homogeneity, and partially characterized. The purified enzyme hydrolyzed p- and o-nitrophenyl-beta-d-galactosides. It also cleaved beta-(1,3)-, beta-(1,4)-, and beta-(1,6)-linked galactobiosides and galactotriosides, showing a marked preference for beta-(1,3)- and beta-(1,4)-linkages.     

Isolation and characterization of disease resistance gene homologues from rice cultivar IR64

We initiated a search for disease resistance (R) gene homologues in rice cultivar IR64, one of the most agronomically important rice varieties in the world, with the assumption that some of these homologues would correspond to previously identified disease resistance loci. A family of rice R gene homologues was identified using the Arabidopsis NBS-LRR disease resistance gene RPS2 as a hybridization probe. Because member genes of this rice R gene family exhibit features characteristic of the NBS-LRR class of resistance genes, the family was given the name NRH (for NBS-LRR resistance gene homologues). Three members of the NRH family, NRH1, NRH2, and NRH3, were cloned and studied in detail. In IR64, NRH1 and NRH2 appear to encode full-length polypeptides, whereas NRH3 is prematurely truncated with a stop codon generated by a frameshift. NRH1 maps on chromosome 5, and NRH2 and NRH3 are less than 48kb apart on chromosome 11. Although NRH1, NRH2, and NRH3 map to regions of the rice genome where disease resistance loci to Xanthomonas oryzae pv. oryzae (Xoo) have been identified, susceptible rice varieties transformed with either NRH1 or NRH2 failed to exhibit increased resistance to a set of well-characterized Xoo strains.     

Distinctive expression patterns and roles of the miRNA393/TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa)

? MicroRNA (miRNA)-mediated regulation of auxin signaling components plays a critical role in plant development. miRNA expression and functional diversity contribute to the complexity of regulatory networks of miRNA/target modules. ? This study functionally characterizes two members of the rice (Oryza sativa) miR393 family and their target genes, OsTIR1 and OsAFB2 (AUXIN SIGNALING F-BOX), the two closest homologs of Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 (TIR1). ? We found that the miR393 family members possess distinctive expression patterns, with miR393a expressed mainly in the crown and lateral root primordia, as well as the coleoptile tip, and miR393b expressed in the shoot apical meristem. Transgenic plants overexpressing miR393a/b displayed a severe phenotype with hallmarks of altered auxin signaling, mainly including enlarged flag leaf inclination and altered primary and crown root growth. Furthermore, OsAFB2- and OsTIR1-suppressed lines exhibited increased inclination of flag leaves at the booting stage, resembling miR393-overexpressing plants. Moreover, yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsTIR1 and OsAFB2 interact with OsIAA1. ? Expression diversification of miRNA393 implies the potential role of miRNA regulation during species evolution. The conserved mechanisms of the miR393/target module indicate the fundamental importance of the miR393-mediated regulation of auxin signal transduction in rice.     

Expression of α-expansin genes in young seedlings of rice (Oryza sativa L.)

 Rice is the only cereal in which germination and coleoptile elongation occur in hypoxia or anoxia. Little is known of the molecular basis directly underlying coleoptile cell extension. In this paper, we describe the expression of α-expansin genes in embryos during seed development and young seedlings grown under various oxygen concentrations. The genes Os-EXP2 and Os-EXP1 were predominantly expressed in the developing seeds, mainly in newly developed leaves, coleoptiles, and seminal roots. These expansins expressed in the developing seeds may give cells the potential to expand after seed imbibition begins. In coleoptiles, Os-EXP4 and Os-EXP2 mRNAs were greatly induced by submergence, while they were weakly detected in aerobic or anoxic conditions. Under submerged soil conditions, the signals hybridized with probes Os-EXP4 and Os-EXP2 in coleoptiles were strongest when coleoptiles elongated in the water layer. These data show that expansin gene expression is highly correlated with coleoptile elongation in response to oxygen concentrations. The Os-EXP4 gene was also expressed in leaves, mesocotyls, and coleorhizas of young seedlings. The growth of these tissues was also correlated with the presence of expansins. Therefore, the evidence derived from this study clearly demonstrates that expansins are indispensable for the growing tissues of rice seedlings. Received: 23 December 1999 / Accepted: 24 February 2000