Biomedical subjects

Taku Demura

Publications and source records attributed to Taku Demura.

At least 19 recordsLinked to original sources

PubMed2007

Transcriptional regulation in wood formation.

Wood (i.e. xylem tissue) in trees is mainly composed of two types of cells, fibres and tracheary elements. Recent molecular studies of various trees, as well as the non-tree species Arabidopsis thaliana and Zinnia elegans, have revealed coordinated gene expression during differentiation of these cells in wood and the presence of several transcription factors that might govern the complex networks of transcriptional regulation. This article reviews recent findings concerning the regulation of genes by transcription factors involved in wood formation such as AUXIN RESPONSE FACTOR (ARF), CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII), KANADI (KAN), MYB and NAM/ATAF/CUC (NAC).

Arabidopsis↗

PubMed2006

Co-regulation of brassinosteroid biosynthesis-related genes during xylem cell differentiation.

To understand the regulatory mechanisms of brassinosteroid (BR) biosynthesis in specific plant developmental processes, we first investigated the accumulation profiles of BRs and sterols in xylem differentiation in a Zinnia culture. The amounts of many substances in the late C28 sterol biosynthetic pathway to campesterol (CR), such as episterol and 24-methylenecholesterol, as well as those in the BR-specific biosynthetic pathway from CR to brassinolide (BL), were elevated in close association with tracheary element differentiation. Among them, 6-deoxotyphasterol (6-deoxoTY) accumulated to unusually high levels within cells cultured in tracheary element-inductive medium, while castasterone (CS) was not elevated either within or outside cells. To identify the molecular basis of this co-up-regulation of BRs and C28 sterols, we isolated Zinnia genes for the key enzymes of BR biosynthesis, ZeSTE1, ZeDIM, ZeDWF4, ZeCPD1 and ZeCPD2. RNA gel blot analysis of these genes indicated a coordinated increase in transcripts for ZeSTE1, ZeDIM, ZeDWF4 and ZeCPD1, and a tracheary element differentiation-specific increase in transcripts for ZeDWF4 and ZeCPD1. In situ hybridization experiments of ZeDWF4 and ZeCPD1 mRNAs revealed their preferential accumulation in procambium cells, immature xylem cells and xylem parenchyma cells. These results suggest that BR biosynthesis during tracheary element differentiation may be regulated by the coordinated regulation of broad sterol biosynthesis and specific regulation of BR biosynthesis, which occurs in part by elevated transcript levels of genes encoding BR biosynthetic enzymes, specifically ZeDWF4 and ZeCPD1. These data provide new insights into the regulation of BR biosynthesis and BR signaling during plant development.

Amino Acid Sequence↗

PubMed2006

SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis.

Secondary walls in fibers and tracheary elements constitute the most abundant biomass produced by plants. Although a number of genes involved in the biosynthesis of secondary wall components have been characterized, little is known about the molecular mechanisms underlying the coordinated expression of these genes. Here, we demonstrate that the Arabidopsis thaliana NAC (for NAM, ATAF1/2, and CUC2) domain transcription factor, SND1 (for secondary wall-associated NAC domain protein), is a key transcriptional switch regulating secondary wall synthesis in fibers. We show that SND1 is expressed specifically in interfascicular fibers and xylary fibers in stems and that dominant repression of SND1 causes a drastic reduction in the secondary wall thickening of fibers. Ectopic overexpression of SND1 results in activation of the expression of secondary wall biosynthetic genes, leading to massive deposition of secondary walls in cells that are normally nonsclerenchymatous. In addition, we have found that SND1 upregulates the expression of several transcription factors that are highly expressed in fibers during secondary wall synthesis. Together, our results reveal that SND1 is a key transcriptional activator involved in secondary wall biosynthesis in fibers.

Arabidopsis↗

PubMed2006

Fluorescence cross-correlation analyses of the molecular interaction between an Aux/IAA protein, MSG2/IAA19, and protein-protein interaction domains of auxin response factors of arabidopsis expressed in HeLa cells.

Since auxin may elicit numerous developmental responses by the use of a combination of auxin response factors (ARFs) and their Aux/IAA repressors, it is important to determine the interaction between the two protein families in a quantitative manner. We transiently expressed the C-terminal protein-protein interaction domains (CTDs) of Arabidopsis ARFs, MP/ARF5 and NPH4/ARF7, and MSG2/IAA19, fused to fluorescent proteins in HeLa cells, and determined their molecular interactions with fluorescence cross-correlation spectroscopy (FCCS). Almost complete association was found between MSG2 and MP-CTD and between MSG2 and NPH4-CTD. Approximately 20% association was found for MSG2 homodimers, NPH4-CTD homodimers and MP-CTD/NPH4-CTD heterodimers. Homotypic binding of MP-CTD may be weaker than that of MSG2. MSG2 was localized in cytoplasmic compartments in HeLa cells, whereas it was localized in the nuclei in plant cells. The fact that the heterotypic interaction between MSG2 and ARF-CTDs is stronger than each of the homotypic interactions appears to be the molecular basis for tight control of the transcriptional activity of ARFs by auxin. These results also show that FCCS is useful to examine protein-protein interactions especially for transcriptional regulators.

Arabidopsis↗

PubMed2006

Gene expression profiling using cDNA microarray analysis of the sexual reproduction stage of the unicellular charophycean alga Closterium peracerosum-strigosum-littorale complex.

The desmid Closterium peracerosum-strigosum-littorale complex, which is the closest unicellular sister to land plants, is the best characterized of the charophycean green algae with respect to the process of sexual reproduction. To elucidate the molecular mechanism of intercellular communication during sexual reproduction, we created a normalized cDNA library from mixed cells of the sexual and the vegetative phases and generated a cDNA microarray. In total, 3,236 expressed sequence tags, which were classified into 1,615 nonredundant groups, were generated for cDNA microarray construction. Candidate genes for key factors involved in fertilization, such as those that encode putative receptor-like protein kinase, leucine-rich-repeat receptor-like protein, and sex pheromone homologs, were up-regulated during sexual reproduction and/or by the addition of the purified sex pheromones, and the expression patterns of these genes were confirmed by quantitative real-time polymerase chain reaction analysis. This first transcriptome profile of Closterium will provide critical clues as to the mechanism and evolution of intercellular communication between the egg and sperm cells of land plants.

Algal Proteins↗

PubMed2006

A flexible representation of omic knowledge for thorough analysis of microarray data.

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site http://omicspace.riken.jp.

Journal Article↗

PubMed2006

Isolation and characterization of a novel peroxidase gene ZPO-C whose expression and function are closely associated with lignification during tracheary element differentiation.

In an attempt to elucidate the regulatory mechanism of vessel lignification, we isolated ZPO-C, a novel peroxidase gene of Zinnia elegans that is expressed specifically in differentiating tracheary elements (TEs). The ZPO-C transcript was shown to accumulate transiently at the time of secondary wall thickening of TEs in xylogenic culture of Zinnia cells. In situ hybridization indicated specific accumulation of the ZPO-C transcript in immature vessels in Zinnia seedlings. Immunohistochemical analysis using anti-ZPO-C antibody showed that the ZPO-C protein is abundant in TEs, especially at their secondary walls. For enzymatic characterization of ZPO-C, 6 x His-tagged ZPO-C was produced in tobacco cultured cells and purified. The ZPO-C:6 x His protein had a peroxidase activity preferring sinapyl alcohol as well as coniferyl alcohol as a substrate, with a narrow pH optimum around 5.25. The peroxidase activity required calcium ion and was elevated by increasing Ca2+ concentration in the range of 0-10 mM. An Arabidopsis homolog of ZPO-C, At5g51890, was examined for expression patterns with transgenic plants carrying a yellow fluorescent protein (YFP) gene under the control of the At5g51890 promoter. The YFP fluorescence localization demonstrated vessel-specific expression of At5g51890 in the Arabidopsis roots. Taken collectively, our results strongly suggest that ZPO-C and its homologs play an important role in lignification of secondary cell walls in differentiating TEs.

Amino Acid Sequence↗

PubMed2005

Change in the redox state of glutathione regulates differentiation of tracheary elements in Zinnia cells and Arabidopsis roots.

Exogenously applied GSH and GSSG can control the in vitro differentiation of mesophyll cells to tracheary elements (TEs) in Zinnia elegans, and de novo GSH synthesis is essential for the early differentiation. The purpose of the present study is to address how GSH and GSSG control TE differentiation. GSSG transiently accumulated during the in vitro TE differentiation and exogenously applied GSSG down-regulated transcript levels of GSSG reductase (GR), an enzyme maintaining glutathione in a reduced redox state, while there were no significant changes in transcript levels of enzymes involved in GSH synthesis. Transgenic Arabidopsis overexpressing the GR gene showed delayed TE formation in the root, which was attributed to the suppression of cell division. Exogenously applied GSH had an effect similar to overexpression of the GR gene. These findings suggest that reduced states of glutathione suppress TE differentiation. In wild-type Arabidopsis, TE formation was promoted by application of GSSG at an appropriate concentration, but was suppressed at higher concentrations. A T-DNA-inserted knockout mutant of cytosolic GR exhibited delayed TE formation; this phenotype was little affected by GSSG application. Taken together, the process of the redox changes in glutathione is considered to be controlled via GR activity for TE differentiation.

Arabidopsis↗

PubMed2005

Transcription switches for protoxylem and metaxylem vessel formation.

Land plants evolved xylem vessels to conduct water and nutrients, and to support the plant. Microarray analysis with a newly established Arabidopsis in vitro xylem vessel element formation system and promoter analysis revealed the possible involvement of some plant-specific NAC-domain transcription factors in xylem formation. VASCULAR-RELATED NAC-DOMAIN6 (VND6) and VND7 can induce transdifferentiation of various cells into metaxylem- and protoxylem-like vessel elements, respectively, in Arabidopsis and poplar. A dominant repression of VND6 and VND7 specifically inhibits metaxylem and protoxylem vessel formation in roots, respectively. These findings suggest that these genes are transcription switches for plant metaxylem and protoxylem vessel formation.

Arabidopsis Proteins↗

PubMed2005

Class III homeodomain leucine-zipper proteins regulate xylem cell differentiation.

Although it has been suggested that class III homeodomain leucine-zipper proteins (HD-Zip III) are involved in vascular development, details of the function of individual HD-Zip III proteins in vascular differentiation have not been resolved. To understand the function of each HD-Zip III protein in vascular differentiation precisely, we analyzed the in vitro transcriptional activity and in vivo function of Zinnia HD-Zip III genes, ZeHB-10, ZeHB-11 and ZeHB-12, which show xylem-related expression. Transgenic Arabidopsis plants harboring cauliflower mosaic virus 35S-driven ZeHB-10 and ZeHB-12 with a mutation in the START domain (mtZeHB-10, mtZeHB-12) showed a higher production of tracheary elements (TEs) and xylem precursor cells, respectively. A systematic analysis with Genechip arrays revealed that overexpression of mtZeHB-12 rapidly induced various genes, including brassinosteroid-signaling pathway-related genes and genes for transcription factors that are expressed specifically in vascular tissues in situ. Furthermore, mtZeHB-12 overexpression did not induce TE-specific genes, including genes related to programmed cell death and lignin polymerization, but did induce lignin monomer synthesis-related genes, which are expressed in xylem parenchyma cells. These results suggest that ZeHB-12 is involved in the differentiation of xylem parenchyma cells, but not of TEs.

Asteraceae↗

PubMed2005

DRP1A is responsible for vascular continuity synergistically working with VAN3 in Arabidopsis.

In most dicotyledonous plants, vascular tissues in the leaf have a reticulate venation pattern. We have isolated and characterized an Arabidopsis (Arabidopsis thaliana) mutant defective in the vascular network defective mutant, van3. van3 mutants show a discontinuous vascular pattern, and VAN3 is known to encode an ADP-ribosylation-factor-GTPase-activating protein that regulates membrane trafficking in the trans-Golgi network. To elucidate the molecular nature controlling the vein patterning process through membrane trafficking, we searched VAN3-interacting proteins using a yeast (Saccharomyces cerevisiae) two hybrid system. As a result, we isolated the plant Dynamin-Related Protein 1A (DRP1A) as a VAN3 interacting protein. The spatial and temporal expression patterns of DRP1AGUS and VAN3GUS were very similar. The subcellular localization of VAN3 completely overlapped to that of DRP1A. drp1a showed a disconnected vascular network, and the drp1a mutation enhanced the phenotype of vascular discontinuity of the van3 mutant in the drp1a van3 double mutant. Furthermore, the drp1 mutation enhanced the discontinuous vascular pattern of the gnom mutant, which had the same effect as that of the van3 mutation. These results indicate that DRP1 modulates the VAN3 function in vesicle budding from the trans-Golgi network, which regulates vascular formation in Arabidopsis.

ADP-Ribosylation Factors↗

PubMed2005

TONSOKU is expressed in S phase of the cell cycle and its defect delays cell cycle progression in Arabidopsis.

TONSOKU(TSK)/MGOUN3/BRUSHY1 of Arabidopsis thaliana encodes a nuclear leucine-glycine-aspargine (LGN) domain protein implicated to be involved in genome maintenance, and mutants with defects in TSK show a fasciated stem with disorganized meristem structures. We identified a homolog of TSK from tobacco BY-2 cells (NtTSK), which showed high sequence conservation both in the LGN domain and in leucine-rich repeats with AtTSK. The NtTSK gene was expressed during S phase of the cell cycle in tobacco BY-2 cells highly synchronized for cell division. The tsk mutants of Arabidopsis contained an increased proportion of cells with 4C nuclei and cells expressing cyclin B1 compared with the wild type. These results suggest that TSK is required during the cell cycle and defects of TSK cause the arrest of cell cycle progression at G2/M phase.

Amino Acid Sequence↗

PubMed2005

DcMYB1 acts as a transcriptional activator of the carrot phenylalanine ammonia-lyase gene (DcPAL1) in response to elicitor treatment, UV-B irradiation and the dilution effect.

Expression of a carrot phenylalanine ammonia-lyase (PAL) gene (DcPAL1) in suspension-cultured carrot cells is induced by treatment with a fungal elicitor, ultraviolet B (UV-B) irradiation, and by transferring and diluting cells with fresh medium (the dilution effect). Box-L-like sequences are known as important cis-elements of genes for enzymes involved in the phenylpropanoid biosynthetic pathway. Six sequences, box-L0 to box-L5, exist in the DcPAL1 gene promoter region. In this study, we isolated cDNA encoding the R2R3 type of MYB transcription factor, DcMYB1, using yeast one-hybrid screening with box-L1 or box-L5 as target elements. DcMYB1 bound to boxes-L0, L1, L3/4, and L5 sequences (ACC(A/T)(A/T)CC) in vitro, and in yeast cells and carrot protoplasts. Transient expression of DcMYB1 could up-regulate DcPAL1 promoter activity in carrot protoplasts. Results of the transient expression experiment for the deletion-mutated promoters of boxes-L0, L1, L3, and L5 suggest that these box-L-like sequences were required for the complete activation of the DcPAL1 promoter by DcMYB1. Expression of DcMYB1 transcripts was induced 0.5 h after elicitor treatment or UV-B irradiation, and 2 h after the dilution effect. Induction of DcPAL1 expression occurred 1 h after DcMYB1 expression in all stress treatments, and repression of DcMYB1 expression by RNA interference caused cessation of the up-regulation of DcPAL1 expression in the elicitor treatment or with UV-B irradiation. These results suggest that DcMYB1 is the main regulatory factor acting on box-L sequences in the DcPAL1 gene that respond to environmental cues.

Base Sequence↗

PubMed2004

The ATE genes are responsible for repression of transdifferentiation into xylem cells in Arabidopsis.

We isolated three recessive mutants of Arabidopsis (Arabidopsis thaliana) showing ectopic expression of the xylem-specific marker, pAtxyn3::YFP. Genetic analysis indicated that the phenotypes were caused by mutations in three different genes, designated Abnormal Tracheary Element formation-related gene expression (ate1-3). The ate1 mutants showed a normal DR5::GUS gene expression pattern, and the ate1 mutation did not affect the abnormal vascular pattern formation in the van3 and pin1 mutants, indicating that the ate1 mutation does not affect the vascular pattern organization governed by auxin. The ate mutants showed ectopic lignin deposition, patterned secondary wall thickenings, and cell death, which are characteristic of mature tracheary elements (TEs) in cells ectopically expressing the pAtxyn3::YFP gene. Ectopic TE formation was rapidly induced in parenchymal tissue of the ate mutants in a TE-inducible system with excised hypocotyl. Furthermore, reverse transcription-polymerase chain reaction experiments showed that the expression of TE formation-related genes is up-regulated in the ate mutants. The ate1 mutation also caused ectopic expression of another xylem-specific marker gene, pAt3g62160::YFP. Overall, our results suggest that the ATE genes are responsible for the in situ repression of transdifferentiation into TEs in Arabidopsis and could be participants in the transdifferentiation-masking system.

Arabidopsis↗

PubMed2004

Expression of photosynthesis-related genes and their regulation by light during somatic embryogenesis in Daucus carota.

To clarify the spatial and temporal pattern of gene expression for photosynthesis-associated proteins during somatic embryogenesis in Daucus carota L., the localization of mRNAs for three genes, rbcL, Lhcb and por, was examined in dark-grown and light-irradiated somatic embryos by in situ hybridization. The three mRNAs were expressed in common in the mesophyll precursor cells of light-irradiated embryos at the late torpedo and plantlet stages, but characteristic expression patterns of each photosynthesis-related gene were also observed. Expression of rbcL mRNA first occurred throughout the embryo but gradually became localized in the mesophyll precursor cells and cortex during early embryogenesis. Localization of Lhcb mRNA in the mesophyll precursor cells and shoot apical meristem became clear in the early torpedo stage. Expression of Lhcb mRNA was not affected by light during early embryogenesis, but could be induced by light in the torpedo stage, suggesting that light-inducible expression of Lhcb mRNA arises within the torpedo stage. At the late torpedo stage, clear localization of por mRNA started in mesophyll precursor cells of the cotyledon in light-irradiated embryos. Greening potency of the embryo also appeared first at this stage. Therefore, greening and initial differentiation of photosynthetic tissues during somatic embryogenesis seem to be associated with coordinated expression of mRNA for rbcL, Lhcb and por in late torpedo-shaped embryos.

Darkness↗

PubMed2004

A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells.

To understand how plant cell changes gene expression during cell division and after termination of cell division, we analyzed the change of gene expression during the growth of tobacco BY-2 cell lines using a cDNA microarray, which contained about 9,200 expression sequence tag fragments and corresponded to about 7,000 genes. We found that log phase cells predominantly expressed DNA/chromosome duplication gene homologs. In addition, many genes for basic transcription and translation machineries, as well as proteasomal genes, were up-regulated at the log phase. About half of the kinesin homolog genes, but not myosin homolog genes, were predominantly expressed at the dividing phase as well. In contrast, stationary phase cells expressed genes for many receptor kinases, signal transduction machineries and transcription factors. Several hundreds of genes showed differential expression after incubation of stationary phase cells with medium containing either salicylic acid or abscisic acid. These findings suggested that BY-2 cells at the stationary phase express genes for perceiving extracellular signals.

Base Sequence↗

PubMed2004

Spatial and temporal tracing of vessel differentiation in young Arabidopsis seedlings by the expression of an immature tracheary element-specific promoter.

The vascular system is a complex tissue composed of several vascular cell types. However, little is known about the differentiation process of each vascular cell in situ. In this study, we found that the expression of the Zinnia cysteine protease 4 (ZCP4) promoter is restricted to only immature tracheary elements (TEs) in situ. Therefore, we monitored the early TE differentiation process in young Arabidopsis seedlings using a fusion gene of the ZCP4 promoter and the beta-glucuronidase gene as a molecular marker. This approach revealed unique processes of vessel differentiation during early seedling development, in which discontinuous initiation of vessel element differentiation occurs at distinct regions, followed by the simultaneous differentiation of protoxylem vessels and bidirectional differentiation of metaxylem vessels to form a vessel in the plant body.

Arabidopsis↗

PubMed2004

Overexpression of a novel small peptide ROTUNDIFOLIA4 decreases cell proliferation and alters leaf shape in Arabidopsis thaliana.

Leaf shape is determined by polar cell expansion and polar cell proliferation along the leaf axes. However, the genes controlling polar cell proliferation during leaf morphogenesis are largely unknown. We identified a dominant mutant of Arabidopsis thaliana, rotundifolia4-1D (rot4-1D), which possessed short leaves and floral organs. We showed that the altered leaf shape is caused by reduced cell proliferation, specifically in the longitudinal (proximal-distal) axis of the leaf, suggesting that the ROT4 gene controls polar cell proliferation in lateral organs. The ROT4 open-reading frame (ORF) encodes a novel small peptide that had not been identified in the Arabidopsis genome annotation. Overexpression of a ROT4-green fluorescence protein (GFP) fusion protein in transgenic plants recapitulated the rot4 phenotype, suggesting that ROT4 acts to restrict cell proliferation. The ROT4-GFP fusion protein localized to the plasma membrane when expressed in transgenic Arabidopsis plants. Phylogenetic analysis indicates that ROT4 defines a novel seed plant-specific family of small peptides with 22 members in Arabidopsis, ROT FOUR LIKE1-22 (RTFL1-22). All RTFL members share a conserved 29-amino acid domain, the RTF domain, and overexpression of the ROT4 RTF domain alone is sufficient to confer a rot4-1D phenotype. Loss-of-function mutations in several RTFL genes were aphenotypic, suggesting that there may be some functional redundancy between family members. Analyses by reverse transcription-polymerase chain reaction (RT-PCR) and in situ hybridization revealed that ROT4 is expressed in the shoot apex and young leaves of wild-type plants, consistent with a role for ROT4 in controlling polarity-dependent cell proliferation during wild-type leaf morphogenesis.

Amino Acid Sequence↗