Cloning and characterization of two genes encoding sulfate transporters from rice (Oryza sativa L.)*

Two genes were isolated from a rice genomic library and the coding region of their corresponding cDNAs generated by RT-PCR. These single copy genes, designated ORYsa;Sultr1;1 and ORYsa;Sultr4;1, encode putative sulfate transporters. Both genes encode proteins with predicted topologies and signature sequences of the H⁺/SO₄^2- symporter family of transporters and exhibit a high degree of homology to other plant sulfate transporters. ORYsa;Sultr1;1 is expressed in roots with levels of expression being strongly enhanced by sulfate starvation. In situ hybridization experiments revealed that ORYsa;Sultr1;1 expression is localized to the main absorptive region of roots. This gene probably encodes a transporter that is responsible for uptake of sulfate from the soil solution. In contrast, ORYsa;Sultr4;1 was expressed in both roots and shoots and was unresponsive to the sulfur status of the plant. The sequence of ORYsa;Sultr4;1 contains a possible plastid-targeting transit peptide which may indicate a role in transport of sulfate to sites of sulfate reduction in plastids. The role of the transporter encoded by ORYsa;Sultr4;1 is likely to be significantly different fromORYsa;Sultr1;1. These are the first reports of isolation of genes encoding sulfate transporters from rice and provide a basis for further studies involving sulfate transport.     

Comparative analysis of genes encoding methyl coenzyme M reductase in methanogenic bacteria

Summary The sequence of the gene cluster encoding the methyl coenzyme M reductase (MCR) in Methanococcus voltae was determined. It contains five open reading frames (ORF), three of which encode the known enzyme subunits. Putative ribosome binding sites were found in front of all ORFs. They differ in their degrees of complementarity to the 3 end of the 16 S rRNA, which is discussed in terms of different translation efficiencies of the respective genes. The codon usage bias is different in the subunit encoding genes compared with the two other ORFs in the cluster and two other known genes of Mc. voltae. This is interpreted in terms of increased translational accuracy of the highly expressed MCR subunit genes. The derived polypeptide sequences encoded by the five ORFs of the MCR cluster were compared to those of the respective genes in Methanobacterium thermoautotrophicum Marburg and Methanosarcina barkeri. Conserved regions were detected in the enzyme subunits, which are candidates for factor binding domains. Conserved hydrophobic sequences found in the and subunits are discussed with respect to the membrane association of the enzyme.     

Genetic analysis of fertility-restorer genes in rice

Wild-abortive (WA), Honglian (HL) and Baro-II (BT) are three important cytoplasmic male sterility (CMS) types in rice. It is essential to investigate genetic mode and allelism of fertility restorer (Rf) genes and the relationship between Rf and CMS. Fertility of the all test-cross F₁ plants shows that the restorer-maintainer relationship is similar for HL-CMS and BT-CMS, while that is variance for WA-CMS and HL-CMS (or BT-CMS), respectively. Genetic analysis of Rf genes indicates that HL-or BT-CMS are controlled by single dominant Rf gene and WA-CMS is controlled by one or two pairs of dominant Rf genes, which reflects the characters of the gametophytic and sporophytic restoration CMS type. It is concluded that there are at least three Rf loci in different accessions with Rf genes for each CMS type.     

Evaluation of phosphorus starvation inducible genes relating to efficient phosphorus utilization in rice

Plants develop strategies to recycle phosphorus so that all organs receive adequate amounts of phosphorus, especially new growing organs. To evaluate the metabolic adaptation of rice plants under phosphorus deficient conditions, we selected several genes related to phosphorus utilization efficiency in the cell. Phosphoenolpyruvate carboxylase, triose phosphate translocator, phosphoenolpyruvate/phosphate translocator (PPT), pyruvate kinase, NAD dependent glyceraldehyde-3-phosphate dehydrogenase, and NADP dependent glyceraldehyde-3-phosphate dehydrogenase were selected because of their important roles in phosphorus utilization by the cell, and because they are part of the proposed bypass pathways by which the cells save phosphate. The most dramatic change was observed in the expression level of PPT (which transports phosphoenolpyruvate (PEP) from the cytosol into the chloroplast); thus we believe that PEP may play an important role in maintaining carbon metabolism under phosphate deficient conditions.     

Comparative studies of isozymes in Oryza sativa,O. minuta,and their interspecific derivatives: evidence for homoeology and recombination

Enzyme electrophoresis was used to compare the isozyme phenotypes of Oryza sativa, IR31917 (AA genome), and two O. minuta accessions (Om 101089 and Om101141; BBCC genome) for ten enzyme systems. Between the two species, two systems were monomorphic (isocitrate dehydrogenase and alcohol dehydrogenase) and eight were polymorphic (shikimate dehydrogenase, phosphogluconate dehydrogenase, phosphoglucose isomerase, malate dehydrogenase, glutamate oxaloacetate transaminase, esterase, aminopeptidase, and endopeptidase). Polymorphism between O. minuta accessions was detected for shikimate dehydrogenase and glutamate oxaloacetate. As expected, the quaternary structure of the O. minuta isozymes was comparable to that of O. sativa. Possible allelic relationships with known O. sativa alleles and their genomic designation are discussed. Combined with chromosome data, the interspecific variation was exploited to monitor the relative genetic contribution of the two parents in the IR31917/Om101141 F₁ hybrids and recurrent (IR31917) backcross progenies. The isozyme content of F₁ hybrid reflected its triploid nature (ABC genome composition), while that of the backcross progenies paralleled the duplication of the A genome and the gradual loss of O. minuta chromosomes during the backcrossing process. Evidence is provided for a degree of homoeology between the A, B, and C genomes, and for introgression from O. minuta into O. sativa.     

Drought tolerance genes in rice

Quantitative trait loci (QTLs) for drought tolerance (DT) can be readily identified in available databases and in this paper, these QTLs were summarized in the form of a consensus map. An in silico strategy was then deployed to mine for candidate genes associated with DT QTLs using rice dbEST and rice genome databases. DT QTLs on rice chromosomes 1, 2, 4, 8, and 9 were selected to test the method. The result showed candidate genes associated with DT could be readily identified.     

RAPD analysis of blast resistant somaclones from upland rice cultivar IAC 47 for genetic divergence

Seventeen somaclones of upland rice cultivar IAC 47 showing different plant types, and either resistance or susceptibility to leaf blast, were utilized for random amplified polymorphic DNA (RAPD) analysis. Somaclones exhibited differences in reaction to isolates of Pyricularia grisea. Two somaclones (SC02 and SC04) were resistant to all three field isolates of somaclones, while the cultivar IAC 47 was susceptible. The inheritance study of two distinct plant types, one with erect bright green leaves and the other with droopy yellow green leaves, showed that a single possibly different, dominant gene governs each plant type. Of 32 random decamer primers utilized, OPA02 and OPD02 detected polymorphisms between somaclones showing erect bright green leaves and droopy yellow green leaves. Reliable grouping exhibiting 80% similarity was achieved with 17 primers. Leaf blast resistance to race IC-2 of P. grisea was associated with the plant type of erect bright green leaves.     

Sequence and expression analysis of the thioredoxin protein gene family in rice

Thioredoxin (Trx) proteins play important biological functions in cells by changing redox via thioldisulfied exchange. This system is especially widespread in plants. Through database search, we identified 30 potential Trx protein-encoding genes (OsTrx) in rice (Oryza sativa L.). An analysis of the complete set of OsTrx proteins is presented here, including chromosomal location, conserved motifs, domain duplication, and phylogenetic relationships. Our findings suggest that the expansion of the Trx gene family in rice, in large part, occurred due to gene duplication. A comprehensive expression profile of Trx genes family was investigated by analyzing the signal data of this family extracted from the whole genome microarray analysis of Minghui 63 and Zhenshan 97, two indica parents, and their hybrid Shanyou 63, using 27 different tissues representing the entire life cycle of rice. Results revealed specific expression of some members at germination transition as well as the 3-leaf stage during the vegetative growth phase of rice. OsTrx genes were also found to be differentially up- or down-regulated in rice seedlings subjected to treatments of phytohormones and light/dark conditions. The expression levels of the OsTrx genes in the different tissues and under different treatments were also checked by RT-PCR analysis. The identification of OsTrx genes showing differential expression in specific tissues among different genotypes or in response to different environmental cues could provide a new avenue for functional analyses in rice.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.     

A genome-wide gain-of-function analysis of rice genes using the FOX-hunting system

The latest report has estimated the number of rice genes to be approximately 32,000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13,980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12,000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene,confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.     

Identification of a high-affinity binding protein for N-acetylchitooligosaccharide elicitor in theplasma membrane from rice leaf and root cells

Presence of a high-affinity binding protein for N-acetylchitooligosaccharide (fragments of chitin) elicitor in the plasma membrane from rice leaf and root cells was shown by affinity labeling experiments with an ¹²⁵I-labeled N-acetylchitooligosaccharide derivative. Binding studies also showed that binding site in the leaf cells has a high affinity to highly elicitor-active, larger chitin fragments but much lower or no affinity to less elicitor-active or elicitor-inactive oligosaccharides. The amount of the binding protein in the leaf cells was slightly smaller than that in the suspension-cultured cells but much larger compared to that in the root cells. These results indicate the possible- involvement of the elicitor binding protein in the perception of the elicitor signal in intact rice plant.     

Allantoin involved in species interactions with rice and other organisms in paddy soil

Allantoin (5-ureidohydantoin) plays an essential role in the assimilation, metabolism, transport, and storage of nitrogen in numerous higher plants, but its ecological implications are largely unknown. In this study allantoin was found in tissues of 11 rice (Oryza sativa) varieties tested, and its structure was characterised by X-ray diffraction analysis to confirm the fact that allantoin was actually obtained from the rice plants. Furthermore, the endogenous allantoin was exuded from the rice roots into the rhizosphere soils and had a great diversity of biological effects on associated weeds and microbes by soil interactions once released. However, allantoin levels in tissues or soils could not be distinguished between the allelopathic and non-allelopathic rice varieties. Field experiments showed that levels of allantoin released from rice varieties varied with their growth stages and reached the maximal levels at the stem elongation or panicle initiation to booting stages and then decreased dramatically. Allantoin could significantly stimulate the germination and growth of Echinochloa crus-galli and populations of soil bacteria and actinomycetes at selected test concentrations (30–500 μg/g), but had no effect on soil fungi. The half-life (t _1/2 ) of allantoin in autoclaved soil (20.2 ± 2.5 h, r ² = 0.95) was almost three-times longer than in non-autoclaved soil (7.3 ± 1.9 h, r ² = 0.92), indicating that rapid biodegradation or transformation of allantoin occurs in paddy soil. The results suggest that not only may allantoin play a role in the transport and storage of nitrogen in rice tissues but it may also participate in species interactions between rice and other organisms in paddy soil.     

NaCl-Induced Changes in Putrescine Content and Diamine Oxidase Activity in Roots of Rice Seedlings

The effects of NaCl on putrescine (Put) content and diamine oxidase (DAO) activity in roots of rice seedlings were examined. NaCl treatment lowered the content of Put and increased the activity of DAO in roots. Our current results indicate that Cl^– is not required for NaCl-induced decline in Put content and increase in DAO activity in roots. Put content in roots of rice seedlings exposed to NaCl is possibly regulated by DAO activity.     

Increased expression of OsPT1, a high-affinity phosphate transporter, enhances phosphate acquisition in rice

Most high-affinity phosphate transporter genes (OsPTs) in rice were highly induced in roots when phosphate was depleted. OsPT1, however, was highly expressed in primary roots and leaves regardless of external phosphate concentrations. This finding was confirmed histochemically using transgenic rice plants that express the GUS reporter gene under the control of the OsPT1 promoter, which exhibited high GUS activity even in the phosphate sufficient condition. Furthermore, transgenic rice plants overexpressing the OsPT1 gene accumulated almost twice as much phosphate in the shoots as did wild-type plants. As a result, transgenic plants had more tillers than did wild-type plants, which is a typical physiological indicator for phosphate status in rice.     

Comparative membrane proteome analysis of three Borrelia species

The versatility of the surface of Borrelia, the causative agent of Lyme borreliosis, is very important in host-pathogen interactions allowing bacteria to survive in ticks and to persist in a mammalian environment. To identify the surface proteome of Borrelia, we have performed a large comparative proteomic analysis on the three most important pathogenic Borrelia species, namely B. burgdorferi (strain B31), B. afzelii (strain K78), and B. garinii (strain PBi). Isolation of membrane proteins was performed by using three different approaches: (i) a detergent-based fractionation of outer membrane proteins; (ii) a trypsin-based partial shedding of outer cell surface proteins; (iii) biotinylation of membrane proteins and preparation of the biotin-labelled fraction using streptavidin. Proteins derived from the detergent-based fractionation were further sub-fractionated by heparin affinity chromatography since heparin-like molecules play an important role for microbial entry into human cells. All isolated proteins were analysed using either a gel-based liquid chromatography (LC)-MS/MS technique or by two-dimensional (2D)-LC-MS/MS resulting in the identification of 286 unique proteins. Ninety seven of these were found in all three Borrelia species, representing potential targets for a broad coverage vaccine for the prevention of Lyme borreliosis caused by the different Borrelia species.