Yoshiharu Y. Yamamoto

Gifu University | Gidai · Faculty of Applied Biological Sciences

Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lateral root primordia (LRP) emergence in nitrate-poor patches, by preferentially transporting auxin away from t...

Genes are transcribed from transcription start sites (TSSs), and their position in a genome is strictly controlled to avoid mis-expression of undesired regions. In this study, we designed and developed a methodology for the evaluation of promoter context, which detects proximal promoter regions from − 200 to − 60 bp relative to a TSS, in Arabidopsi...

Perception of pathogen-derived ligands by corresponding host receptors is a pivotal strategy in eukaryotic innate immunity. In plants, this is complemented by circadian anticipation of infection timing, promoting basal resistance even in the absence of pathogen threat. Here, we report that trichomes, hair-like structures on the epidermis, directly...

To elucidate the unknown regulatory mechanisms involved in aluminum (Al)-induced expression of POLYGALACTURONASE-INHIBITING PROTEIN 1 ( PGIP1 ), which is one of the downstream genes of SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) regulating Al-tolerance genes, we conducted a genome-wide association analysis of gene expression levels (eGWAS) of PGIP1...

Plants tailor immune responses to defend against pathogens with different lifestyles. In this process, antagonism between the immune hormones salicylic acid (SA) and jasmonic acid (JA) optimizes transcriptional signatures specifically to the attacker encountered. Antagonism is controlled by the transcription cofactor NPR1. The indispensable role of...

In gene‐trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different me...

The green oleaginous microalgae, Chlorella sorokiniana, is a highly productive Chlorella species and a potential host for the production of biofuel, nutraceuticals, and recombinant therapeutic proteins. The lack of a stable and efficient genetic transformation system is the major bottleneck in improving this species. We report an efficient and stab...

Malate-efflux from roots, which is regulated by the transcription factor STOP1 (SENSITIVE-TO-PROTON-RHIZOTOXICITY1), which mediates aluminum-induced expression of ALUMINUM-ACTIVATED-MALATE-TRANSPORTER1 (AtALMT1), is critical for aluminum-resistance in Arabidopsis thaliana. Several studies showed that root AtALMT1 expression is rapidly observed in r...

Metabolism, which is a flow of metabolites, is orchestrated by gene expression, and it is in turn regulated by metabolites. Some of the metabolites are known to act as signaling molecules that regulate metabolism and also developmental processes in plants. Here we summarize findings about metabolites-directed gene regulation, focusing on primary me...

In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. In this study, using Arabidopsis gene-trap lines in which a firefly luciferase ( LU...

Under acid soil conditions, Al stress and proton stress can occur, reducing root growth and function. However, these stressors are distinct, and tolerance to each is governed by multiple physiological processes. To better understand the genes that underlie these coincidental but experimentally separable stresses, a genome-wide association study (GW...

Nitrogen (N) is an essential macronutrient and the final form of endogenous inorganic N is ammonium, which is assimilated by glutamine synthetase (GS) into glutamine. However, how the multiple isoforms of cytosolic GSs contribute to metabolic systems via the regulation of ammonium assimilation remains unclear. In the present study, we compared the...

The transcription factor sensitive to proton rhizotoxicity 1 (STOP1) regulates multiple stress tolerances. In this study, we confirmed its involvement in NaCl and drought tolerance. The root growth of the T-DNA insertion mutant of STOP1 (stop1) was sensitive to NaCl-containing solidified MS media. Transcriptome analysis of stop1 under NaCl stress r...

Plant growth is strictly controlled by cell division, elongation, and differentiation for which adequate supplies of intracellular ATP are required. However, it is unclear how changes in the amount of intracellular ATP affect cell division and growth. To reveal the specific pathway dependent on ATP concentration, we performed analyses on the Arabid...

Expression levels of KIN10-dex and KIN11-dex in presence of DEX. (A) Real-time RT-PCR analysis of KIN10 expression in vector control (VC), KIN10-dex #1, and KIN10-dex #2. Total RNA prepared from 7-day-old dark-grown seedlings (approximately 20 seedlings) was amplified by RT-PCR. All values were normalized against the expression of the AtACTIN2 gene...

sd3kin10, sd3kin11 and sd3sog1 double mutants grew to adult stage and produced seeds. (A) Plant architecture of 80-day-old light-grown WT (left), kin10 mutant (middle) and sd3kin10 double mutant (right). (B) Plant architecture of 80-day-old light-grown WT (left), kin11 mutant (middle) and sd3kin11 double mutant (right). (C) Plant architecture of 80...

Expression of AOXa1 is altered in sd3. Total RNA prepared from 5-day-old dark-grown seedlings (approximately 20 seedlings) was amplified by RT-PCR. All values were normalized against expression of the AtACTIN2 gene. Error bars indicate standard deviation of 3 biological replicates.

Expression levels in kin10 and kin11 mutants. (A) Real-time RT-PCR analysis of KIN10 expression in WT and kin10. Total RNA prepared from 7-day-old dark-grown seedlings (approximately 20 seedlings) was amplified by RT-PCR. All values were normalized against expression of the AtACTIN2 gene. Error bars indicate the mean standard deviation of 3 biologi...

Accession number of genes and primer pairs used for qRT-PCR.

Hydrogen peroxide (H2O2) is a common signal molecule initiating transcriptional responses to all the known biotic and abiotic stresses of land plants. However, the degree of involvement of H2O2 in these stress responses has not yet been well studied. Here we identify time-dependent transcriptome profiles stimulated by H2O2 application in Arabidopsi...

Hydrogen peroxide (H2O2) is an important signaling molecule for various physiological processes that take place in higher plants during environmental adaptation. This article addresses the role of H2O2 in signal transduction and gene regulation in the context of a variety of biotic and abiotic stresses. Based on a comparative analysis using public...

Zinc finger transcription factors, STOP1-like proteins, are conserved among land plant species and control the expression of aluminum tolerance genes in various plant species. We performed transcriptome analyses in tobacco (Nicotiana tabacum) to identify NtSTOP1-regulating Al tolerance genes, the expression of which was regulated by their STOP1-lik...

The SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) transcription factor regulates gene expression associated with multiple stress tolerances in plant roots. In this study, we investigated the mechanism responsible for the sensitivity of the stop1 mutant to low-oxygen stress in Arabidopsis. Transcriptomic analyses revealed that two genes involved in lo...

This book summarizes the latest research results on the role of reactive oxygen species (ROS) in plants, particularly in many abiotic stresses, and their regulation. Redox homeostasis refers to maintaining a balance of oxidised and reduced state of biomolecules in a biological system for all-round sustenance. In a living system, redox reactions con...

In mammalian cells, the transcription factor p53 plays a crucial role in transmitting DNA damage signals to maintain genome integrity. However, in plants, orthologous genes for p53 and checkpoint proteins are absent. Instead, the plant-specific transcription factor SUPPRESSOR OF GAMMA RADIATION 1 (SOG1) controls most of the genes induced by gamma i...

Main conclusion: Al-responsive citrate-transporting CcMATE1 function and its regulation by CcSTOP1 were analyzed using NtSTOP1 -KD tobacco- and pigeonpea hairy roots, respectively, CcSTOP1 binding sequence of CcMATE1 showed similarity with AtALMT1 promoter. The molecular mechanisms of Aluminum (Al) tolerance in pigeonpea (Cajanus cajan) were chara...

ppdb (http:// ppdb. agr. gifu-u. ac. jp) is a web-based plant promoter database that provides promoter information of each gene in genomes of Arabidopsis, rice, poplar, and Physcomitrella patens. In this database, recognition of a promoter structure is achieved by annotating genome sequences with our sequence lists of bioinformatically identified o...

Alternative promoter usage is a proteome-expanding mechanism that allows multiple pre-mRNAs to be transcribed from a single gene. The impact of this mechanism on the proteome and whether it is positively exploited in normal organismal responses remain unclear. We found that the plant photoreceptor phytochrome induces genome-wide changes in alternat...

Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TS...

In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle...

Interactions between heat shock factor (HSF) and the heat shock response element (HSE) are important during the heat shock response (HSR) of flora and fauna. Moreover, plant HSFs that are involved in heat stress are also involved in abiotic stresses such as dehydration and cold as well as development, cell differentiation, and proliferation. Becaus...

The plant growth-promoting fungus (PGPF), Penicillium simplicissimum GP17-2 (GP17-2), induces systemic resistance against Pseudomonas syringae pv. tomato DC3000 (Pst) in Arabidopsis thaliana. The molecular mechanisms underlying induced systemic resistance (ISR) by GP17-2 were investigated in the present study. Microscopic observations revealed that...

Pyrenochaeta lycopersici is the causal agent of corky root, an important soilborne disease of tomato (Lycopersicon esculentum) and other solanaceous crops. P. lycopersici isolates are classified into Types 1 and 2 on the basis of several physiological and molecular features. In this study, we aimed to establish a loop-mediated isothermal amplificat...

The Arabidopsis Early Light Induced Protein (ELIP) is thought to act as a photoprotectant, reducing the damaging effects of high light (HL). Expression of ELIP2 is activated by multiple environmental stresses related to photoinhibition. We have identified putative regulatory elements in an ELIP2 promoter using octamer-based frequency comparison met...

Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H2O2, as well as biotic and abiotic induced redox signals. RRTF1 is highly conserved in angiosperms, however the physiological role remains elusive. Here we show that inactivation of RRTF1 restricts and overexpression promotes reactive oxygen spe...

In Arabidopsis thaliana the root apex is protected from aluminum (Al) rhizotoxicity by excretion of malate, an Al-chelator, by Al-activated malate transporter 1 (AtALMT1). AtALMT1 expression is fundamentally regulated by the STOP1 (Sensitive TO Proton rhizotoxicity 1) zinc finger protein, but other transcription factors have roles that enable Al-in...

Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a...

Chaetoceros gracilis belongs to the centric diatoms, and has recently been used in basic research on photosynthesis. In addition, it has been commercially used in fisheries and is also attracting interest as a feedstock for biofuels production and biorefinery. In this study, we developed an efficient genetic transformation system for C. gracilis. T...

Main conclusion VuDREB2A exists in cowpea as a canonical DREB2-type transcription factor, having the ability to bind dehydration-responsive elements in vitro and confer enhanced drought resistance in transgenic Arabidopsis. Cowpea (Vigna unguiculata L. Walp) is an important cultivated legume that can survive better in arid conditions than other c...

ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal,...

Hydrogen peroxide acts as a signaling molecule mediating the acquisition of tolerance to both biotic and abiotic stresses. Identification of marker genes for H2O2 response could help to intercept the signaling network of stress response of plants. Here, we describe application of marker genes for H2O2 responses to monitoring several abiotic stress...

The genomes of three plants, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and soybean (Glycine max), have been sequenced, and their many genes and promoters have been predicted. In Arabidopsis, cis-acting promoter elements involved in cold- and dehydration-responsive gene expression have been extensively analysed; however, the character...

It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent transcription. Several transcriptional characteristics are known to be associated with core types, including distribution patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive...

The transcription start site (TSS) is useful to predict gene and to understand transcription initiation. Although vast data on mRNA TSSs are available, little is known about tRNA genes because of rapid processing. Using a tobacco in vitro transcription system under conditions of impaired 5' end processing, TSSs were determined for 64 Arabidopsis tR...

Table S1: List of scanned promoters. Combinations of promoters and RARf tables used for promoter scan are shown. Totally 622 promoters that show response to any phytohormones were selected for the scanning. All the detected signals are shown in Additional file 2 (Table S2).

Figure S1: Filtering of octamers by RARf. Number of octamers showing high RAR values (> 3) is shown regarding total count of each octamers among 14,498 genic promoters. Rare octamers in the promoter region are shown to be filtered out by this statistical evaluation.

Table S3: Possible cross-talk at regulatory elements. Coincident detection by two different RARf tables is shown. If distance of two peaks by different RARf tables is within 4 bp, they are considered as co-localized and incorporated into the table. Totally 1188 co-localized peaks were detected. Position means distance from the major TSS used in ppd...

Table S2: Peaks of the scanned promoters. All the peaks detected by 730 scanning data for the 622 promoters shown in Additional file 2 (Table S1) were extracted and shown. Position means distance from the major TSS used in ppdb. Corresponding REG ID and recognition motif are also indicated.

Phytohormones organize plant development and environmental adaptation through cell-to-cell signal transduction, and their action involves transcriptional activation. Recent international efforts to establish and maintain public databases of Arabidopsis microarray data have enabled the utilization of this data in the analysis of various phytohormone...

Multiple biotic and abiotic environmental factors may constitute stresses that affect plant growth and yield in crop species. Advances in plant physiology, genetics, and molecular biology have greatly improved our understanding of plant responses to stresses. This book details on technologies that have emerged during the past decade and have been u...

Our limited understanding of plant promoters does not allow us to recognize any core promoter elements for the majority of plant promoters. To understand the promoter architecture of Arabidopsis, we used the combined approach of in silico detection of novel core promoter elements and large-scale determination of transcription start sites (TSSs). To...

Chloroplast division involves the tubulin-related GTPase FtsZ that assembles into a ring structure (Z-ring) at the mid-chloroplast division site, which is where invagination and constriction of the envelope membranes occur. Z-ring assembly is usually confined to the mid-chloroplast site by a well balanced counteraction of the stromal proteins MinD...

Some sacoglossan molluscs, including several species of Elysiidae, are known to incorporate algal chloroplasts, and the incorporated chlo-roplasts are functional for days to months, depending on species. This incorporation and maintenance of foreign chloroplasts are known as kleptoplasty. In this article, we surveyed photosynthetic activity of seve...

We irradiated Arabidopsis thaliana with several kinds of heavy-ion beams to investigate the linear energy transfer (LET)-dependent effects of heavy-ion beam irradiation. First, dry seeds were irradiated with C, N, Ne, Ar, or Fe ions at doses ranging from 5 to 400 Gy to compare the flowering and mutation rates among the ion species. The sensitivity...

High complementarity between plant microRNAs (miRNAs) and their messenger RNA targets is thought to cause silencing, prevalently by endonucleolytic cleavage. We have isolated Arabidopsis mutants defective in miRNA action. Their analysis provides evidence that plant miRNA–guided silencing has a widespread translational inhibitory component that is g...

ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures...

Arabidopsis REG octamers (Table S4.pdf). Contains octamer sequences and parameters.