Massively parallel single-cell genomics of microbiomes in rice paddies.

Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution.

Effects of improved sodium uptake ability on grain yields of rice plants under low potassium supply.

Sodium uptake is a factor that determines potassium use efficiency in plants as sodium can partially replace potassium in plant cells. Rice () roots usually exclude sodium but actively take it up when the plant is deficient in potassium. In rice roots, a sodium transporter OsHKT2;1 mediates active sodium uptake.

Overexpression of exogenous in rice plants confers tolerance to biuret toxicity.

Biuret, a common impurity in urea fertilizers, is toxic to plants, but little is known about the physiological mechanisms underlying its toxicity. Here, we analyzed biuret toxicity in rice () plants. We carried out uptake experiments using N-labelled biuret and demonstrated that biuret could reach sub millimolar concentrations in rice plants.

Rice plants have three homologs of glutathione synthetase genes, one of which, , codes for hydroxymethyl-glutathione synthetase.

Glutathione is a ubiquitous thiol tripeptide in land plants, and glutathione-like tripeptides can also be found in some plant species. Rice () plants synthesize hydroxymethyl-glutathione, in which the terminal glycine residue of glutathione is replaced by a serine residue; however, the biosynthetic pathway of hydroxymethyl-glutathione has not been identified. We isolated three rice glutathione synthetase homologs, designated OsGS1, OsGS2, and OsGS3, and found that knockdown of via RNA interference markedly decreased hydroxymethyl-glutathione concentration in rice plants.

A new monoclonal antibody against rhamnogalacturonan II and its application to immunocytochemical detection of rhamnogalacturonan II in Arabidopsis roots.

Unlabelled: Rhamnogalacturonan II (RG-II) is a region of pectin macromolecules that is present in plant primary cell walls. RG-II can be solubilized from cell walls as a borate-RG-II complex (B-RG-II), where two RG-II fragments are cross-linked via a borate diester linkage. Here, a rabbit monoclonal antibody against B-RG-II was prepared, which recognized both B-RG-II and RG-II monomers without borate ester-crosslinking.

Rice phytochelatin synthases OsPCS1 and OsPCS2 make different contributions to cadmium and arsenic tolerance.

Cadmium (Cd) and arsenic (As) pollution in paddy soil and their accumulation in rice () pose serious threats to human health. Rice internally detoxifies these toxic metal and metalloid to some extent, resulting in their accumulation within the edible parts. However, the mechanisms of Cd and As detoxification in rice have been poorly elucidated.

Immunocytochemical detection of rhamnogalacturonan II on forming cell plates in cultured tobacco cells.

Rhamnogalacturonan II (RG-II) is a region of pectin macromolecules that is present in plant primary cell walls. The RG-II region serves as the site of borate cross-linking within pectin, via which pectin macromolecules link together to form a gel. In this study, we examined whether RG-II is present in the cell plate, the precursor of primary cell walls that forms during cytokinesis.

Genetic diversity of the flanking region in rice landraces in northern Laos.

A glutinous texture of endosperm is one of the important traits of rice ( L.). Northern Laos is known as a center of glutinous rice diversity.

Proton-dependent coniferin transport, a common major transport event in differentiating xylem tissue of woody plants.

Lignin biosynthesis is an essential physiological activity of vascular plants if they are to survive under various environmental stresses on land. The biosynthesis of lignin proceeds in the cell wall by polymerization of precursors; the initial step of lignin polymerization is the transportation of lignin monomers from the cytosol to the cell wall, which is critical for lignin formation. There has been much debate on the transported form of the lignin precursor, either as free monolignols or their glucosides.

Pathogenic diversity of Phytophthora sojae and breeding strategies to develop Phytophthora-resistant soybeans.

Phytophthora stem and root rot, caused by Phytophthora sojae, is one of the most destructive diseases of soybean [Glycine max (L.) Merr.], and the incidence of this disease has been increasing in several soybean-producing areas around the world.

Characterization of Arabidopsis CTP:3-deoxy-D-manno-2-octulosonate cytidylyltransferase (CMP-KDO synthetase), the enzyme that activates KDO during rhamnogalacturonan II biosynthesis.

In plant cells, boron (B) occurs predominantly as a borate ester associated with rhamnogalacturonan II (RG-II), but the function of this B-RG-II complex has yet to be investigated. 3-Deoxy-D-manno-2-octulosonic acid (KDO) is a specific component monosaccharide of RG-II. Mutant plants defective in KDO biosynthesis are expected to have altered RG-II structure, and would be useful for studying the physiological function of the B-RG-II complex.

Suppression of a NAC-like transcription factor gene improves boron-toxicity tolerance in rice.

We identified a gene responsible for tolerance to boron (B) toxicity in rice (Oryza sativa), named BORON EXCESS TOLERANT1. Using recombinant inbred lines derived from the B-toxicity-sensitive indica-ecotype cultivar IR36 and the tolerant japonica-ecotype cultivar Nekken 1, the region responsible for tolerance to B toxicity was narrowed to 49 kb on chromosome 4. Eight genes are annotated in this region.

Boron nutrition of cultured tobacco BY-2 cells. VI. Calcium is involved in early responses to boron deprivation.

Boron (B) deprivation induces various responses in plant cells, some of which can be observed very early. However, it has been unknown what kind of signal is generated by the stress. We found that B deprivation induced the expression of stress-responsive genes within 1 h in suspension-cultured tobacco BY-2 cells.

Boron deficiency: how does the defect in cell wall damage the cells?

Boron (B) is an essential micronutrient for vascular plants. Boron plays a structural role in cell walls through binding to pectic polysaccharides. It still remains unclear how B deficiency, and hence probably alterations in cell wall structure, leads to various metabolic disorders and cell death.

Boron nutrition of tobacco BY-2 cells. V. oxidative damage is the major cause of cell death induced by boron deprivation.

Boron (B) is an essential micronutrient for vascular plants. However, it remains unclear how B deficiency leads to various metabolic disorders and cell death. To understand this mechanism, we analyzed the physiological changes in suspension-cultured tobacco (Nicotiana tabacum) BY-2 cells upon B deprivation.

Boron nutrition of cultured tobacco BY-2 cells. IV. Genes induced under low boron supply.

Genes whose expression was up-regulated in low boron (B)-acclimated tobacco BY-2 (Nicotiana tabacum L. cv. Bright Yellow 2) cells, which had been selected under a low supply of B, were screened by the cDNA differential subtraction method.

Arabidopsis 3-deoxy-D-manno-oct-2-ulosonate-8-phosphate synthase: cDNA cloning and expression analyses.

The molecular characterization of two isoforms of 3-deoxy-d-manno-oct-2-ulosonate (KDO) -8-phosphate synthase (AtkdsA1 and AtkdsA2) from Arabidopsis is reported here. First, by isolating a full-length cDNA for AtkdsA1, it was confirmed that the deduced primary structures of AtkdsA1 and AtkdsA2 proteins were 93% identical. Functional expression and purification studies demonstrated the efficient catalytic activity of the AtkdsA1 enzyme to produce KDO-8-phosphate from phosphoenolpyruvate and d-arabinose-5-phosphate.

Purification and cDNA cloning of UDP-D-glucuronate carboxy-lyase (UDP-D-xylose synthase) from pea seedlings.

Uridine diphospho-D-glucuronate carboxy-lyase (UDP-D-xylose synthase; EC 4.1.1.

F-actin-dependent endocytosis of cell wall pectins in meristematic root cells. Insights from brefeldin A-induced compartments.

Brefeldin A (BFA) inhibits exocytosis but allows endocytosis, making it a valuable agent to identify molecules that recycle at cell peripheries. In plants, formation of large intracellular compartments in response to BFA treatment is a unique feature of some, but not all, cells. Here, we have analyzed assembly and distribution of BFA compartments in development- and tissue-specific contexts of growing maize (Zea mays) root apices.

Short-term boron deprivation inhibits endocytosis of cell wall pectins in meristematic cells of maize and wheat root apices.

By using immunofluorescence microscopy, we observed rapidly altered distribution patterns of cell wall pectins in meristematic cells of maize (Zea mays) and wheat (Triticum aestivum) root apices. This response was shown for homogalacturonan pectins characterized by a low level (up to 40%) of methylesterification and for rhamnogalacturonan II pectins cross-linked by a borate diol diester. Under boron deprivation, abundance of these pectins rapidly increased in cell walls, whereas their internalization was inhibited, as evidenced by a reduced and even blocked accumulation of these cell wall pectins within brefeldin A-induced compartments.