Faculty Profiles - YAMASHINO, Takafumi

Papers - YAMASHINO, Takafumi

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Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway. Reviewed

Nakamichi N, Kita M, Niinuma K, Ito S, Yamashino T, Mizoguchi T, Mizuno T.

Plant Cell Physiol. Vol. 48 ( 6 ) page： 822-832 2007.6

Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa. Reviewed

Nakamura Y, Kato T, Yamashino T, Murakami M, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 5 ) page： 1183-1191 2007.5

A link between cytokinin and ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) that belongs to the AS2/LOB (LATERAL ORGAN BOUNDARIES) family genes in Arabidopsis thaliana. Reviewed

Naito T, Yamashino T, Kiba T, Koizumi N, Kojima M, Sakakibara H, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 5 ) page： 1269-1278 2007.5

The SskA and SrrA response regulators are implicated in oxidative stress responses of hyphae and asexual spores in the phosphorelay signaling network of Aspergillus nidulans. Reviewed

Hagiwara D, Asano Y, Marui J, Furukawa K, Kanamaru K, Kato M, Abe K, Kobayashi T, Yamashino T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 4 ) page： 1003-1014 2007.4

Characterization of the rice circadian clock-associated pseudo-response regulators in Arabidopsis thaliana. Reviewed

Murakami M, Tago Y, Yamashino T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 4 ) page： 1107-1110 2007.4

Mutants of circadian-associated PRR genes display a novel and visible phenotype as to light responses during de-etiolation of Arabidopsis thaliana seedlings. Reviewed

Kato T, Murakami M, Nakamura Y, Ito S, Nakamichi N, Yamashino T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 3 ) page： 834-839 2007.3

Characterization of the NikA histidine kinase implicated in the phosphorelay signal transduction of Aspergillus nidulans, with special reference to fungicide responses. Reviewed

Hagiwara D, Matsubayashi Y, Marui J, Furukawa K, Yamashino T, Kanamaru K, Kato M, Abe K, Kobayashi T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 3 ) page： 844-847 2007.3

Characterization of Circadian-associated pseudo-response regulators: I. Comparative studies on a series of transgenic lines misexpressing five distinctive PRR Genes in Arabidopsis thaliana. Reviewed

Matsushika A, Murakami M, Ito S, Nakamichi N, Yamashino T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 2 ) page： 527-534 2007.2

*AHK5 histidine kinase regulates root elongation through an ETR1-dependent abscisic acid and ethylene signaling pathway in Arabidopsis thaliana. Reviewed

Iwama A, Yamashino T, Tanaka Y, Sakakibara H, Kakimoto T, Sato S, Kato T, Tabata S, Nagatani A, Mizuno T.

Plant Cell Physiol. Vol. 48 ( 2 ) page： 375-380 2007.2

Characterization of circadian-associated pseudo-response regulators: II. The function of PRR5 and its molecular dissection in Arabidopsis thaliana. Reviewed

Matsushika A, Kawamura M, Nakamura Y, Kato T, Murakami M, Yamashino T, Mizuno T.

Biosci Biotechnol Biochem. Vol. 71 ( 2 ) page： 535-544 2007.2

Type-B ARR transcription factors, ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of Arabidopsis thaliana. Reviewed

Yokoyama A, Yamashino T, Amano Y, Tajima Y, Imamura A, Sakakibara H, Mizuno T.

Plant Cell Physiol. Vol. 48 ( 1 ) page： 84-96 2007.1

Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Reviewed

Murakami M, Tago Y, Yamashino T, Mizuno T.

Plant Cell Physiol. Vol. 48 ( 1 ) page： 110-121 2007.1

PSEUDO-RESPONSE REGULATORS, PRR9, PRR7 and PRR5, together play essential roles close to the circadian clock of Arabidopsis thaliana. Reviewed

Nakamichi N, Kita M, Ito S, Yamashino T, Mizuno T.

Vol. 46 ( 5 ) page： 686-698 2005.5

Language：English Publishing type：Research paper (scientific journal)

In Arabidopsis thaliana, a number of clock-associated protein components have been identified. Among them, CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL) and TOC1 (TIMING OF CAB EXPRESSION 1) are believed to be the essential components of the central oscillator. CCA1 and LHY are homologous and partially redundant Myb-related DNA-binding proteins, whereas TOC1 is a member of a small family of proteins, designated as PSEUDO-RESPONSE REGULATOR. It is also believed that these two different types of clock components form an autoregulatory positive/negative feedback loop at the levels of transcription/translation that generates intrinsic rhythms. Nonetheless, it was not yet certain whether or not other PRR family members (PRR9, PRR7, PRR5 and PRR3) are implicated in clock function per se. Employing a set of prr9, prr7 and prr5 mutant alleles, here we established all possible single, double and triple prr mutants. They were examined extensively by comparing them with each other with regard to their phenotypes of circadian rhythms, photoperiodicity-dependent control of flowering time and photomorphogenic responses to red light during de-etiolation. Notably, the prr9 prr7 prr5 triple lesions in plants resulted in severe phenotypes: (i) arrhythmia in the continuous light conditions, and an anomalous phasing of diurnal oscillation of certain circadian-controlled genes even in the entrained light/dark cycle conditions; (ii) late flowering that was no longer sensitive to the photoperiodicity; and (iii) hyposensitivity (or blind) to red light in the photomorphogenic responses. The phenotypes of the single and double mutants were also characterized extensively, showing that they exhibited circadian-associated phenotypes characteristic for each. These results are discussed from the viewpoint that PRR9/PRR7/PRR5 together act as period-controlling factors, and they play overlapping and distinctive roles close to (or within) the central oscillator in which the rela

PRR5 (PSEUDO-RESPONSE REGULATOR 5) plays antagonistic roles to CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) in Arabidopsis thaliana Reviewed

Fujimori T, Sato E, Yamashino T, Mizuno T

Biosci. Biotechnol. Biochem. Vol. 69 ( 2 ) page： 426-430 2005.2

Language：English Publishing type：Research paper (scientific journal)

In general, the clock (or oscillator) is central to circadian rhythms in many organisms. In the model higher plant Arabidopsis thaliana, the best candidates for clock components are CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) and LHY (LATE ELONGATED HYPOCOTYL), which are homologous Myb-related transcription factors. It is also believed that TOC1 (TIMING OF CAB EXPRESSION 1) is another component of the central oscillator. In this connection, we have been characterizing a small family of proteins, designated ARABIDOPSIS PSEUDO-RESPONSE REGULATOR (PRR1, PRR3, PRR5, PRR7, and PRR9), based on the fact that one of the members (PRR1) is identical to TOC1. Nevertheless, it is not yet certain whether other PRR family members are also implicated in clock function per se. To address this issue, in this study we examined a functional interaction between the CCA1 clock component and one of the PRR family members, PRR5, by employing transgenic lines overexpressing both the CCA1 and PRR5 genes. Evidence will be provided that PRR5 plays an antagonistic role(s) to the putative CCA1 clock component.

The Arabidopsis pseudo-response regulators, PRR5 and PRR7, coordinately play essential roles for circadian clock function Reviewed

Nakamichi N, Kita M, Ito S, Sato E, Yamashino T, Mizuno T

Plant Cell Physiol. Vol. 46 ( 4 ) page： 609-619 2005.2

Language：English Publishing type：Research paper (scientific journal)

In Arabidopsis thaliana, a number of clock-associated protein factors have been identified. Among them, TOC1 (TIMING OF CAB EXPRESSION 1) is believed to be a component of the central oscillator. TOC1 is a member of a small family of proteins, designated as ARABIDOPSIS PSEUDO-RESPONSE REGULATOR, including PRR1/TOC1, PRR3, PRR5, PRR7 and PRR9. It has not been certain whether or not other PRR family members are also implicated in clock function per se. To clarify this problem, here we constructed a double mutant line, which is assumed to have severe lesions in both the PRR5 and PRR7 genes. Resulting homozygous prr5-11 prr7-11 young seedlings showed a marked phenotype of hyposensitivity to red light during de-etiolation. In addition, they displayed a phenotype of extremely late flowering under long-day photoperiod conditions, but not short-day conditions. The rhythms at the level of transcription of certain clock-controlled genes were severely perturbed in the double mutant plants when they were released into continuous light (LL) and darkness (DD). The observed phenotype was best interpreted as 'arrhythmic in both LL and DD' and/or 'very short period with markedly reduced amplitude'. Even under the light entrainment (LD) conditions, the mutant plants showed anomalous diurnal oscillation profiles with altered amplitude and/or phase with regard to certain clock-controlled genes, including the clock component CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1) gene. Such events were observed even under temperature entrainment conditions, suggesting that the prr5-11 prr7-11 lesions cannot simply be attributed to a defect in the light signal input pathway. These pleiotropic circadian-associated phenotypes of the double mutant were very remarkable, as compared with those observed previously for each single mutant. Taking these results together, we propose for the first time that PRR5 and PRR7 coordinately (or synergistically) play essential clock-associated roles close to the central oscill

Combinatorial microarray analysis revealing Arabidopsis genes implicated in cytokinin responses through the His->Asp Phosphorelay circuitry Reviewed

Kiba T, Naitou T, Koizumi N, Yamashino T, Sakakibara H, Mizuno T

Plant Cell Physiol. Vol. 46 ( 2 ) page： 339-355 2005.2

Language：English Publishing type：Research paper (scientific journal)

In Arabidopsis thaliana, the immediate early response of plants to cytokinin is formulated as the multistep histidine kinase (AHK)-->histidine-containing phosphotransmitter (AHP)-->response regulator (ARR) phosphorelay signaling circuitry, which is initiated by the cytokinin receptor histidine protein kinases. In the hope of finding components (or genes) that function downstream of the cytokinin-mediated His-->Asp phosphorelay signaling circuitry, we carried out genome-wide microarray analyses. To this end, we used a combinatorial microarray strategy by employing not only wild-type plants, but also certain transgenic lines in which the cytokinin-mediated His-->Asp phosphorelay signaling circuitry has been genetically manipulated. These transgenic lines employed were ARR21-overexpressing and ARR22-overexpressing plants, each of which exhibits a characteristic phenotype with regard to the cytokinin-mediated His-->Asp phosphorelay. The results of extensive microarray analyses with these plants allowed us systematically to identify a certain number of genes that were up-regulated at the level of transcription in response to cytokinin directly or indirectly. Among them, some representatives were examined further in wild-type plants to support the idea that certain genes encoding transcription factors are rapidly and specifically induced at the level of transcription by cytokinin in a manner similar to that of the type-A ARR genes, which are the hallmarks of the His-->Asp phosphorelay signaling circuitry. Several interesting transcription factors were thus identified as being cytokinin responsive, including those belonging to the AP2/EREBP family, MYB family, GATA family or bHLH family. Including these, the presented list of cytokinin-up-regulated genes (214) will provide us with valuable bases for understanding the His-->Asp phosphorelay in A. thaliana.

Molecular dissection of the promoter of the light-induced and circadian-controlled APRR9 gene encoding a clock-associated component of Arabidopsis thaliana. Reviewed

Ito S, Nakamichi N, Matsushika A, Fujimori T, Yamashino T, Mizuno T.

Biosci. Biotechnol. Biochem. Vol. 69 ( 2 ) page： 382-390 2005.2

Language：English Publishing type：Research paper (scientific journal)

In the model higher plant Arabidopsis thaliana, a number of circadian clock-associated protein components have recently been identified. Among them, a small family of ARABIDOPSIS PSEUDO-RESPONSE REGULATORS (APRR1/TOC1, APRR3, APRR5, APRR7, and APRR9) is interesting because the most probable clock component TIMING OF CAB EXPRESSION 1 (TOC1) belongs to this family. Several lines of evidence have already been accumulated to support the view that not only APRR1/TOC1 but also other APRR family members are crucial for a better understanding of the molecular link between circadian rhythm and light-signal transduction. Among the APRR1/TOC1 family members, the circadian-controlled APRR9 gene is unique in that its expression is rapidly induced by light at the level of transcription. In this study we dissected the regulatory cis-elements of the light-induced and/or circadian-controlled APRR9 promoter by employing not only a mutant plant carrying a T-DNA insertion in the APRR9 promoter, but also a series of APRR9-promoter::LUC (luciferase) reporters that were introduced into an Arabidopsis cultured cell line (T87 cells). Taking the results of these approaches together, we provide several lines of evidence that the APRR9 promoter contains at least two distinctive and separable regulatory cis-elements: an "L element" responsible for the light-induced expression, followed by an "R element" necessary for the fundamental rhythmic expression of APRR9. Furthermore, APRR1/TOC1 was implicated in the L-element-mediated light response of APRR9, directly or indirectly.

Circadian-associated rice pseudo response regulators (OsPRRs): insight into the control of flowering time. Reviewed

Murakami M, Matsushika A, Ashikari M, Yamashino T, Mizuno T

Biosci. Biotechnol. Biochem. Vol. 69 ( 2 ) page： 410-414 2005.2

Language：English Publishing type：Research paper (scientific journal)

A small family of plant proteins, designated PSEUDO RESPONSE REGULATORS (PRRs), is crucial for a better understanding of the molecular link between circadian rhythm and photoperiodic control of flowering time in the dicotyledonous model plant Arabidopsis thaliana. Recently, we showed that the monocotyledonous model plant Oryza sativa also has homologous members of the OsPRR family (Oryza sativa PRR). In the previous experiments with rice, we mainly characterized a japonica variety (Nipponbare). By employing an indica variety (Kasalath), in this study we further characterized OsPRRs with reference to the photoperiod sensitivity Hd (Heading date) QTL (quantitative trait loci) implicated in the control of flowering time in rice. The circadian-controlled and sequential expression profiles of the five OsPRR genes were observed not only for Nipponbare but also for Kasalath. Then each of these OsPRR genes was mapped on the rice chromosomes. Among these OsPRR genes, OsPRR37 was mapped very closely to Hd2-QTL, which was identified as the major locus that enhances the photoperiod sensitivity of flowering in Nipponbare. Furthermore, we found that Kasalath has a severe mutational lesion in the OsPRR37 coding sequence.

Molecular basis for promoter selectivity of the transcriptional activator OmpR of Escherichia coli: isolation of mutants that can activate the non-cognate kdpABC promoter. Reviewed

Ohashi K, Yamashino T, Mizuno T

J. Biochem. (Tokyo) Vol. 137 ( 1 ) page： 51-59 2005.1

Language：English Publishing type：Research paper (scientific journal)

Escherichia coli has two osmo-responsive two-component regulatory systems, the EnvZ-OmpR and KdpD-KdpE systems, each of which consists of a sensor histidine protein kinase and a response regulator. The OmpR and KdpE response regulators belong to the same family of DNA-binding proteins, and act as positive transcriptional factors in response to the medium osmolarity. However, OmpR specifically activates the ompC gene encoding the OmpC outer membrane protein, whereas KdpE exclusively activates the kdpABC operon encoding the high-affinity Kdp potassium-transporter. To gain insight into the molecular basis for such strict promoter selectivity, we isolated OmpR mutants that can activate the non-cognate kdpABC promoter in vivo. For these OmpR mutants, it was found that a few common and crucial amino acids are responsible for the altered property of OmpR (e.g., Gly-164, Glu-193). In vitro properties of these OmpR mutants were further examined by means of DNA-binding assays and DNA-footprinting analyses with reference to the kdpABC promoter. These results were interpreted on the basis of the three-dimensional structure of the C-terminal half of OmpR, which consists of a DNA-binding helix-turn-helix motif and a RNA polymerase-interacting surface. The results of this study were best explained by assuming that the isolated OmpR mutants have an altered property with regard to the interaction with RNA polymerase on the kdpABC promoter. We propose that the promoter selectivity of OmpR is determined not only by its DNA-binding specificity, but also by the spatial configuration of the promoter on which OmpR must properly associate with RNA polymerase.

Rapid response of Arabidopsis T87 cultured cells to cytokinin through His-to-Asp phosphorelay signal transduction Reviewed

Yamada H, Koizumi N, Nakamichi N, Kiba T, Yamashino T, Mizuno T.

Biosci. Biotechnol. Biochem. Vol. 68 ( 9 ) page： 1966-1976 2004.9

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Papers - YAMASHINO, Takafumi