Hirofumi Ishihara

• Dr
• University Researcher at University of Helsinki

Studies have uncovered delicate mechanisms that enable plant acclimation to fluctuating light. Translating the knowledge to controlled environment agriculture could advance the development of cost-effective dynamic lighting strategies, but the effects of varying light intensities on vegetable crops remain poorly understood. Here we recorded chlorop...

The effects of transient increases in UVB radiation on plants are not well known; whether cumulative damage dominates or, alternately, an increase in photoprotection and recovery periods ameliorates any negative effects. We investigated photosynthetic capacity and metabolite accumulation of grapevines (Vitis vinifera Cabernet Sauvignon) in response...

Kales (Brassica oleracea convar acephala) are fast-growing, nutritious leafy vegetables ideal for year-round indoor farming. However, selection of best cultivars for growth under artificial lighting necessitates a deeper understanding of leaf metabolism in different kale types. Here we examined a curly leaved cultivar Half Tall and a lacinato type...

C4 photosynthesis allows faster photosynthetic rates and higher water and nitrogen use efficiency than C3 photosynthesis, but at the cost of lower quantum yield due to the energy requirement of its biochemical carbon concentration mechanism. It has also been suspected that its operation may be impaired in low irradiance. To investigate fluxes under...

Aromatic compounds having unusual stability provide high-value chemicals and considerable promise for carbon storage. Terrestrial plants can convert atmospheric CO 2 into diverse and abundant aromatic compounds. However, it is unclear how plants control the shikimate pathway that connects the photosynthetic carbon fixation with the biosynthesis of...

Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that A...

Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the light and remobilize it to support maintenance and growth at night. Starch synthesis and degradation are usually viewed as temporally separate processes. Recently, we reported that starch is also degraded in the light. Degradation rates are generally low early in th...

Plants continually synthesize and degrade proteins, for example, to adjust protein content during development or during adaptation to new environments. In order to estimate global protein synthesis and degradation rates in plants, we developed a relatively simple and inexpensive method using a combination of ¹³ CO 2 labeling and mass spectrometry–b...

Phytochrome (phy) photoreceptors are known to regulate plastic growth responses to vegetation shade. However, recent reports also suggest an important role for phys in carbon resource management, metabolism, and growth. Here, we use 13CO2 labelling patterns in multi-allele phy mutants to investigate the role of phy in the control of metabolic fluxe...

Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that A...

Introduction of a C4 photosynthetic mechanism into C3 crops offers an opportunity to improve photosynthetic efficiency, biomass and yield in addition to potentially improving nitrogen and water use efficiency. To create a two‐cell metabolic prototype for an NADP‐malic enzyme type C4 rice, we transformed Oryza sativa spp.japonica cultivar Kitaake wi...

The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD‐box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this stud...

The phytochromes (phys) photoreceptors are known to be major regulators of plastic growth responses to vegetation shade. Recent reports have begun to uncover an important role for phys in carbon resource management. Our earlier work showed that phy mutants had a distinct metabolic profile with elevated levels of metabolites including TCA intermedia...

We investigated whether starch degradation occurs at the same time as starch synthesis in Arabidopsis (Arabidopsis thaliana) leaves in the light. Starch accumulated in a linear fashion for about 12 h after dawn, then accumulation slowed and content plateaued. Following decreases in light intensity, the rate of accumulation of starch declined in pro...

Previous studies with Arabidopsis accessions revealed biomass correlates negatively to dusk starch content and total protein, and positively to the maximum activities of enzymes in photosynthesis. We hypothesised that large accessions have lower ribosome abundance and lower rates of protein synthesis, and that this is compensated by lower rates of...

Incidence of natural light stress renders it important to enhance our understanding of the mechanisms by which plants protect themselves from harmful effects of UV-B irradiation, as this is critical for fitness of land plant species. Here we describe natural variation of a class of phenylacylated-flavonols (saiginols), which accumulate to high leve...

Identification of syntenic genes located in the intrasyntenic genomic region of AtFPT/SCPL genomic region in the Brassicaceae species. Syntenic genes of intrasyntenic block, Arabidopsis thaliana chromosome 4 (AtChr.4)(defined as Block II) of AtFPT/SCPL genomic region, were found in 2) Arabidopsis lyrata chromosome 7 (AlChr.7), 3) Capsella rubella c...

Identification of syntenic genes located in the Brassicaceae syntenic block of AtFPT/SCPL genomic region. Syntenic block (defined as Block I) of AtFPT/SCPL genomic region, 1) Arabidopsis thaliana chromosome 2 (AtChr.2), were found in 2) Arabidopsis lyrata chromosome 4 (AlChr.4), 3) Capsella rubella chromosome 4 (CrChr.4), 4) Thellungiella parvula c...

Supplementary Figures 1 - 17, Supplementary Tables 1 - 3 and Supplementary Note 1

Secondary metabolite profiling of Arabidopsis thaliana accession flower

Saiginol profiling of near-isogenic line (NIL) Arabidopsis thaliana lines mQTL. Samples obtained from 45 M lines (C24 background) and 69 N lines (Col-0 background) were evaluated with three independent biological replications (n=3).

Improving carbon fixation in order to enhance crop yield is a major goal in plant sciences. By quantitative trait locus (QTL) mapping, it has been demonstrated that a vacuolar invertase (vac-Inv) plays a key role in determining the radical length in Arabidopsis. In this model, variation in vac-Inv activity was detected in a near isogenic line (NIL)...

The Plant Journal

Flavonols are colourless secondary metabolites, primarily regarded as UV-protection pigments that are deposited in plants in their glycosylated forms. The glycosylation of flavonols is mainly catalysed by UDP-sugar-dependent glycosyltransferases (UGTs). Although the structures of flavonol glycosides accumulating in Arabidopsis thaliana are known, m...

Trehalose 6-phosphate (Tre6P) is an essential signal metabolite in plants, linking growth and development to carbon metabolism. The sucrose-Tre6P nexus model postulates that Tre6P acts as both a signal and negative feedback regulator of sucrose levels. To test this model, short-term metabolic responses to induced increases in Tre6P levels were inve...

Protein synthesis and degradation represent substantial costs during plant growth. To obtain a quantitative measure of the rate of protein synthesis and degradation, we supplied 13CO2 to intact Arabidopsis thaliana Col-0 plants and analyzed enrichment in free amino acids and in amino acid residues in protein during a 24 hour pulse and 4 day chase....

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Proteaceae species in south-western Australia occur on phosphorus- (P) impoverished soils. Their leaves contain very low P levels, but have relatively high rates of photosynthesis. We measured ribosomal RNA (rRNA) abundance, soluble protein, activities of several enzymes, and glucose 6-phosphate (Glc6P) levels in expanding and mature leaves of six...

Rates of expansion of Arabidopsis thaliana rosette leaves; plants were grown in short days (8 h/16 h light/dark). Table S1. Recovery of enzyme activities. Powdered samples were prepared from a standard greenhouse-grown Arabidopsis (‘Arabidopsis’) and from a mix in equal parts of Banksia attenuata, B. menziesii and B. candolleana (‘Banksia-mix’). Th...

Growth is driven by newly fixed carbon in the light, but depends at night on reserves, like starch, that are laid down in the light. Unless plants coordinate their growth with diurnal changes in the carbon supply, they will experience acute carbon starvation during the night. Protein synthesis represents a major component of cellular growth. Polyso...

Natural genetic diversity provides a powerful tool to study the complex interrelationship between metabolism and growth. Profiling of metabolic traits combined with network-based and statistical analyses allow the comparison of conditions and identification of sets of traits that predict biomass. However, it often remains unclear why a particular s...

Diurnal cycles provide a tractable system to study the response of metabolism and growth to fluctuating temperatures. We reasoned that the response to daytime and night temperature may vary; while daytime temperature affects photosynthesis, night temperature affects use of carbon that was accumulated in the light. Three Arabidopsis thaliana accessi...

A quantitative trait nucleotide (QTN) in the RLK at rhg1 was inferred that alters A87 to V87 in the context of H274 rather than N274.

Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light...

Rising demand for food and bioenergy makes it imperative to breed for increased crop yield. Vegetative plant growth could be driven by resource acquisition or developmental programs. Metabolite profiling in 94 Arabidopsis accessions revealed that biomass correlates negatively with many metabolites, especially starch. Starch accumulates in the light...

Flavonol synthase (FLS) (EC-number 1.14.11.23), the enzyme that catalyses the conversion of flavonols into dihydroflavonols, is part of the flavonoid biosynthesis pathway. In Arabidopsis thaliana, this activity is thought to be encoded by several loci. In addition to the FLAVONOL SYNTHASE1 (FLS1) locus that has been confirmed by enzyme activity ass...

The tobamovirus resistance gene L3 of Capsicum chinense was mapped using an intra-specific F2 population (2,016 individuals) of Capsicum annuum cultivars, into one of which had been introduced the C. chinenseL3 gene, and an inter-specific F2 population (3,391 individuals) between C. chinense and Capsicum frutescence. Analysis of a BAC library with...

The genes MYB11, MYB12 and MYB111 share significant structural similarity and form subgroup 7 of the Arabidopsis thaliana R2R3-MYB gene family. To determine the regulatory potential of these three transcription factors, we used a combination of genetic, functional genomics and metabolite analysis approaches. MYB11, MYB12 and MYB111 show a high degr...

Table S2: Putative orthologs from R1-, r1-contig and haplotypes A, B and C of S. demissum and the corresponding accession numbers are shown. Putative pseudogenes are indicated by "PS". The identities between transposons (TP) are not shown.

Figure S3: Dot-Plot comparison computed by MUMmer of the DNA sequence of the R1-contig and individual BAC sequences of S. demissum. One column represents one BAC sequence of S. demissum. The first three columns (from left to right) are from haplotype A, the next seven from haplotype B and the last two columns from haplotype C. The figure shows high...

Table S1: Genomic sequence annotation of the R1- and r1-contig

Figure S4: Dot-Plot comparison computed by MUMmer of the DNA sequence of the r1-contig and BAC sequences of S. demissum. One column represents one BAC sequence of S. demissum. The first three columns (from left to right) are BAC sequences from haplotype A, the next seven from haplotype B and the last two columns from haplotype C. The figure shows t...

Figure S1: Gene annotation of R1-contig using APOLLO

Figure S2: Gene annotation of r1-contig using APOLLO

Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite...

Various plant secondary metabolites, including flavonoids, are involved in plant adaptation to different environments. The needs of sessile lifestyle of plants may have increased the variation of enzymes which are required in the modification and/or accumulation of different flavonol derivatives. The probable mechanism for generating variants of th...

The rhg1 gene or genes lie at a recessive or co-dominant locus, necessary for resistance to all Hg types of the soybean (Glycine max (L.) Merr.) cyst nematode (Heterodera glycines I.). The aim here was to identify nucleotide changes within a candidate gene found at the rhg1 locus that were capable of altering resistance to Hg types 0 (race 3). A 1....

IntroductionColony Hybridization Techniques for the Integration of DNA Sequences Into a Physical MapIntegrating Gene-rich Sequences into the Physical Map Via Overgo Hybridization Overlapping Oligo LabelingHybridizationWashingAutoradiographyPooling Strategy for the Integration of DNA Sequences Into a Physical Map DNA PoolingPCR MultiplexingDNA Isola...

Ustilago maydis, a basidiomycete, is a model organism among phytopathogenic fungi. A physical map of U. maydis strain 521 was developed from bacterial artificial chromosome (BAC) clones. BAC fingerprints used polyacrylamide gel electrophoresis to separate restriction fragments. Fragments were labeled at the HindIII site and co-digested with HaeIII...

On Jul 14, 2010 this sequence version replaced gi:21239381.

On Jul 14, 2010 this sequence version replaced gi:21239379.