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1.
PLoS Genet ; 17(5): e1009292, 2021 05.
Article in English | MEDLINE | ID: mdl-33970916

ABSTRACT

The plastochron, the time interval between the formation of two successive leaves, is an important determinant of plant architecture. We genetically and phenotypically investigated many-noded dwarf (mnd) mutants in barley. The mnd mutants exhibited a shortened plastochron and a decreased leaf blade length, and resembled previously reported plastochron1 (pla1), pla2, and pla3 mutants in rice. In addition, the maturation of mnd leaves was accelerated, similar to pla mutants in rice. Several barley mnd alleles were derived from three genes-MND1, MND4, and MND8. Although MND4 coincided with a cytochrome P450 family gene that is a homolog of rice PLA1, we clarified that MND1 and MND8 encode an N-acetyltransferase-like protein and a MATE transporter-family protein, which are respectively orthologs of rice GW6a and maize BIGE1 and unrelated to PLA2 or PLA3. Expression analyses of the three MND genes revealed that MND1 and MND4 were expressed in limited regions of the shoot apical meristem and leaf primordia, but MND8 did not exhibit a specific expression pattern around the shoot apex. In addition, the expression levels of the three genes were interdependent among the various mutant backgrounds. Genetic analyses using the double mutants mnd4mnd8 and mnd1mnd8 indicated that MND1 and MND4 regulate the plastochron independently of MND8, suggesting that the plastochron in barley is controlled by multiple genetic pathways involving MND1, MND4, and MND8. Correlation analysis between leaf number and leaf blade length indicated that both traits exhibited a strong negative association among different genetic backgrounds but not in the same genetic background. We propose that MND genes function in the regulation of the plastochron and leaf growth and revealed conserved and diverse aspects of plastochron regulation via comparative analysis of barley and rice.


Subject(s)
Gene Expression Regulation, Plant , Genes, Plant , Hordeum/growth & development , Hordeum/genetics , Plant Leaves/growth & development , Plant Leaves/genetics , Alleles , CRISPR-Cas Systems/genetics , Cell Division , Hordeum/cytology , Mutation , Oryza/genetics , Phenotype , Plant Cells , Plant Leaves/cytology , Time Factors
2.
Plant Cell Physiol ; 63(2): 265-278, 2022 Feb 15.
Article in English | MEDLINE | ID: mdl-35166362

ABSTRACT

The molecular basis for leaf development, a major focus in developmental biology, remains unclear in the monocotyledonous grass, rice (Oryza sativa). Here, we performed a mutant screen in rice and identified an AP2-type transcription factor family protein, NARROW AND DWARF LEAF1 (NDL1). NDL1 is the ortholog of Arabidopsis thaliana (subsequently called Arabidopsis) ENHANCER OF SHOOT REGENERATION1 (ESR1)/DORNRÖSCHEN (DRN) and mediates leaf development and maintenance of the shoot apical meristem (SAM). Loss of function of NDL1 results in bladeless leaves and SAMs that are flat, rather than dome-shaped, and lack cell proliferation activity. This loss of function also causes reduced auxin signaling. Moreover, as is the case with Arabidopsis ESR1/DRN, NDL1 plays crucial roles in shoot regeneration. Importantly, we found that NDL1 is not expressed in the SAM but is expressed in leaf primordia. We propose that NDL1 cell autonomously regulates leaf development, but non-cell autonomously regulates SAM maintenance in rice.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Oryza , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Gene Expression Regulation, Plant , Meristem/genetics , Meristem/metabolism , Mutation/genetics , Oryza/genetics , Oryza/metabolism
3.
Plant Cell Physiol ; 63(2): 265-278, 2022 Feb 15.
Article in English | MEDLINE | ID: mdl-34865135

ABSTRACT

The molecular basis for leaf development, a major focus in developmental biology, remains unclear in the monocotyledonous grass, rice (Oryza sativa). Here, we performed a mutant screen in rice and identified an AP2-type transcription factor family protein, NARROW AND DWARF LEAF1 (NDL1). NDL1 is the ortholog of Arabidopsis thaliana (subsequently called Arabidopsis) ENHANCER OF SHOOT REGENERATION1 (ESR1)/DORNRÖSCHEN (DRN) and mediates leaf development and maintenance of the shoot apical meristem (SAM). Loss of function of NDL1 results in bladeless leaves and SAMs that are flat, rather than dome-shaped, and lack cell proliferation activity. This loss of function also causes reduced auxin signaling. Moreover, as is the case with Arabidopsis ESR1/DRN, NDL1 plays crucial roles in shoot regeneration. Importantly, we found that NDL1 is not expressed in the SAM but is expressed in leaf primordia. We propose that NDL1 cell autonomously regulates leaf development, but non-cell autonomously regulates SAM maintenance in rice.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Oryza , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Gene Expression Regulation, Plant , Meristem/genetics , Meristem/metabolism , Mutation/genetics , Oryza/genetics , Oryza/metabolism
4.
Development ; 146(13)2019 06 21.
Article in English | MEDLINE | ID: mdl-31118231

ABSTRACT

Asymmetric cell division is a key step in cellular differentiation in multicellular organisms. In plants, asymmetric zygotic division produces the apical and basal cells. The mitogen-activated protein kinase (MPK) cascade in Arabidopsis acts in asymmetric divisions such as zygotic division and stomatal development, but whether the effect on cellular differentiation of this cascade is direct or indirect following asymmetric division is not clear. Here, we report the analysis of a rice mutant, globular embryo 4 (gle4). In two- and four-cell-stage embryos, asymmetric zygotic division and subsequent cell division patterns were indistinguishable between the wild type and gle4 mutants. However, marker gene expression and transcriptome analyses showed that specification of the basal region was compromised in gle4 We found that GLE4 encodes MPK6 and that GLE4/MPK6 is essential in cellular differentiation rather than in asymmetric zygotic division. Our findings provide a new insight into the role of MPK in plant development. We propose that the regulation of asymmetric zygotic division is separate from the regulation of cellular differentiation that leads to apical-basal polarity.


Subject(s)
Asymmetric Cell Division/genetics , Mitogen-Activated Protein Kinase 6/physiology , Oryza , Zygote/cytology , Cell Division/genetics , Cloning, Molecular , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Plant , Mitogen-Activated Protein Kinase 6/genetics , Oryza/embryology , Oryza/enzymology , Oryza/genetics , Plants, Genetically Modified , Seeds/genetics , Seeds/metabolism
5.
BMC Genomics ; 22(1): 169, 2021 Mar 09.
Article in English | MEDLINE | ID: mdl-33750294

ABSTRACT

BACKGROUND: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. RESULTS: In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. CONCLUSIONS: Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.


Subject(s)
Oryza , Gene Expression Regulation, Plant , Oryza/genetics , Oryza/metabolism , Plant Leaves/genetics , Plant Leaves/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Transcriptome
6.
Development ; 145(7)2018 04 05.
Article in English | MEDLINE | ID: mdl-29567670

ABSTRACT

Regulation of cell proliferation is crucial for establishing the shape of plant leaves. We have identified MAKIBA3 (MKB3), a loss-of-function mutant of which exhibits a narrowed- and rolled-leaf phenotype in rice. MKB3 was found to be an ortholog of Arabidopsis ANGUSTIFOLIA3 (AN3), which positively regulates cell proliferation. The reduced leaf size of mkb3 plants with enlarged cells and the increased size of MKB3-overexpressing leaves with normal-sized cells indicate that MKB3 is a positive regulator of leaf proliferation and that mkb3 mutation triggers a compensation syndrome, as does Arabidopsis an3 Expression analysis revealed that MKB3 is predominantly expressed on the epidermis of leaf primordia, which is different from the location of AN3 A protein movement assay demonstrated that MKB3 moves from an MKB3-expressing domain to a non-expressing domain, which is required for normal leaf development. Our results suggest that rice MKB3 and Arabidopsis AN3 have conserved functions and effects on leaf development. However, the expression pattern of MKB3 and direction of protein movement are different between rice and Arabidopsis, which might reflect differences in leaf primordia development in these two species.


Subject(s)
Arabidopsis/metabolism , Cell Proliferation/genetics , Oryza/metabolism , Plant Leaves/growth & development , Trans-Activators/metabolism , Arabidopsis Proteins/metabolism , Cell Enlargement , Gene Expression Regulation, Plant , Mutation , Oryza/genetics , Phenotype , Plant Leaves/metabolism , Trans-Activators/genetics
7.
Endocr J ; 68(3): 329-343, 2021 Mar 28.
Article in English | MEDLINE | ID: mdl-33390421

ABSTRACT

This study was aimed to evaluate the effects of intensive exercise in addition to the administration of sodium-glucose cotransporter 2 inhibitor dapagliflozin (DAPA) on body composition, including fat-free mass, in type 2 diabetes. We randomly assigned 146 patients to 24 weeks of treatment with intensive exercise, including resistance training, plus 5 mg (up to 10 mg) of DAPA daily (IT group) or DAPA alone (CT group). The primary endpoint was the difference in the change in fat-free mass from baseline to 24 weeks between the groups. The skeletal muscle mass index (SMI); metabolic profile, including HbA1c; and regional fat mass were also determined. ANCOVA was used for the group comparison, with least squares mean (LSM) differences and 95% confidence interval (CI). There was no significant difference in the change in fat-free mass (LSM difference -0.1 kg (95% CI: -0.5 to 0.4) and SMI (LSM difference -0.1 kg (95% CI: -0.2 to 0.1) between the groups. In contrast, the reduction of trunk fat mass was significantly higher in the IT group than in the CT group ((LSM difference -0.5 kg [95% CI -0.9 to -0.1]). Higher adherence to the resistance training tended to be associated with changes in HbA1c and high-sensitivity CRP levels. Our study suggests that intensive exercise do not prevent the reduction of fat-free mass after administration of SGLT2 inhibitors but can increase the reduction in abdominal fat, presumably leading to further improvements of hyperglycemia and chronic inflammation than DAPA alone in type 2 diabetes patients.


Subject(s)
Benzhydryl Compounds/therapeutic use , Body Composition , Diabetes Mellitus, Type 2/therapy , Glucosides/therapeutic use , Resistance Training/methods , Sodium-Glucose Transporter 2 Inhibitors/therapeutic use , Adipose Tissue/pathology , Aged , Diabetes Mellitus, Type 2/metabolism , Exercise Therapy/methods , Female , Glycated Hemoglobin/metabolism , Humans , Male , Middle Aged , Muscle, Skeletal/pathology , Organ Size
8.
Development ; 143(7): 1217-27, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26903508

ABSTRACT

Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.


Subject(s)
Arabidopsis/embryology , Gene Expression Regulation, Developmental/genetics , Gene Expression Regulation, Plant/genetics , Oryza/embryology , Plant Growth Regulators/genetics , Cell Division/physiology , Gene Expression Profiling , Oligonucleotide Array Sequence Analysis
9.
Development ; 143(18): 3407-16, 2016 09 15.
Article in English | MEDLINE | ID: mdl-27578792

ABSTRACT

Juvenile-to-adult phase transition is an important shift for the acquisition of adult vegetative characteristics and subsequent reproductive competence. We identified a recessive precocious (pre) mutant exhibiting a long leaf phenotype in rice. The long leaf phenotype is conspicuous in the second to the fourth leaves, which are juvenile and juvenile-to-adult transition leaves. We found that morphological and physiological traits, such as midrib formation, shoot meristem size, photosynthetic rate and plastochron, in juvenile and juvenile-to-adult transition stages of the pre mutant have precociously acquired adult characteristics. In agreement with these results, expression patterns of miR156 and miR172, which are microRNAs regulating phase change, support the accelerated juvenile-to-adult phase change in the pre mutant. The mutated gene encodes an allene oxide synthase (OsAOS1), which is a key enzyme for the biosynthesis of jasmonic acid (JA). The pre mutant showed a low level of JA and enhanced sensitivity to gibberellic acid, which promotes the phase change in some plant species. We also show that prolonged plastochron in the pre mutant is caused by accelerated PLASTOCHRON1 (PLA1) function. The present study reveals a substantial role of JA as a negative regulator of vegetative phase change.


Subject(s)
Cyclopentanes/metabolism , Oryza/metabolism , Oxylipins/metabolism , Plant Proteins/metabolism , Gene Expression Regulation, Plant/genetics , Gene Expression Regulation, Plant/physiology , Oryza/genetics , Plant Proteins/genetics
10.
Plant Cell Physiol ; 59(2): 376-391, 2018 Feb 01.
Article in English | MEDLINE | ID: mdl-29272531

ABSTRACT

In several eudicot species, one copy of each member of the WUSCHEL-RELATED HOMEOBOX (WOX) gene family, WOX1 and WOX3, is redundantly or differentially involved in lateral leaf outgrowth, whereas only the WOX3 gene regulating the lateral domain of leaf development has been reported in grass. In this study, we show that a WOX3 gene, LEAF LATERAL SYMMETRY1 (LSY1), regulates lateral leaf development in a different manner ftom that of other duplicated paralogs of WOX3, NARROW LEAF2 (NAL2)/NAL3, in rice. A loss-of-function mutant of LSY1 exhibited an asymmetrical defect from early leaf development, which is different from a symmetric defect in a double loss-of-function mutant of NAL2/3, whereas the expression of both genes was observed in a similar domain in the margins of leaf primordia. Unlike NAL2/3, overexpression of LSY1 produced malformed leaves whose margins were curled adaxially. Expression domains and the level of adaxial/abaxial marker genes were affected in the LSY1-overexpressing plants, indicating that LSY1 is involved in regulation of adaxial-abaxial patterning at the margins of the leaf primordia. Additive phenotypes in some leaf traits of lsy1 nal2/3 triple mutants and the unchanged level of NAL2/3 expression in the lsy1 background suggested that LSY1 regulates lateral leaf development independently of NAL2/3. Our results indicated that all of the rice WOX3 genes are involved in leaf lateral outgrowth, but the functions of LSY1 and NAL2/3 have diverged. We propose that the function of WOX3 and the regulatory mode of leaf development in rice are comparable with those of WOX1/WOX3 in eudicot species.


Subject(s)
Multigene Family , Organogenesis/genetics , Oryza/genetics , Oryza/metabolism , Plant Proteins/metabolism , Sequence Homology, Amino Acid , Base Sequence , Gene Expression Regulation, Plant , Genes, Plant , Models, Biological , Phenotype , Plant Leaves/cytology , Plant Leaves/metabolism , Plant Proteins/genetics , Plants, Genetically Modified , Reproduction
11.
New Phytol ; 218(4): 1558-1569, 2018 06.
Article in English | MEDLINE | ID: mdl-29498045

ABSTRACT

Floods impede gas (O2 and CO2 ) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown. We used a rice mutant (dripping wet leaf 7, drp7) which does not retain gas films on leaves, and its wild-type (Kinmaze), in gene discovery for this trait. Gene complementation was tested in transgenic lines. Functional properties of leaves as related to gas film retention and underwater photosynthesis were evaluated. Leaf Gas Film 1 (LGF1) was identified as the gene determining leaf gas films. LGF1 regulates C30 primary alcohol synthesis, which is necessary for abundant epicuticular wax platelets, leaf hydrophobicity and gas films on submerged leaves. This trait enhanced underwater photosynthesis 8.2-fold and contributes to submergence tolerance. Gene function was verified by a complementation test of LGF1 expressed in the drp7 mutant background, which restored C30 primary alcohol synthesis, wax platelet abundance, leaf hydrophobicity, gas film retention, and underwater photosynthesis. The discovery of LGF1 provides an opportunity to better understand variation amongst rice genotypes for gas film retention ability and to target various alleles in breeding for improved submergence tolerance for yield stability in flood-prone areas.


Subject(s)
Adaptation, Physiological , Floods , Gases/metabolism , Genes, Plant , Hydrophobic and Hydrophilic Interactions , Oryza/genetics , Plant Leaves/physiology , Waxes/metabolism , Base Sequence , Biosynthetic Pathways , Genetic Complementation Test , Mutation/genetics , Oryza/physiology , Photosynthesis , Plant Epidermis/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism
12.
Breed Sci ; 73(1): 1-2, 2023 Mar.
Article in English | MEDLINE | ID: mdl-37168812
13.
Nihon Shokakibyo Gakkai Zasshi ; 115(6): 544-553, 2018.
Article in Japanese | MEDLINE | ID: mdl-29887590

ABSTRACT

We diagnosed distal cholangiocarcinoma in a 76-year-old woman who was then treated by subtotal stomach-preserving pancreaticoduodenectomy. Histopathological examination revealed a well-differentiated tubular adenocarcinoma on the side of the bile duct, and a neuroendocrine carcinoma in an area outside the bile duct where the tumor had infiltrated. Immunohistochemical staining identified homology between cytokeratins and MUC, indicating a similar origin. This report discusses problems associated with diagnosis and treatment by summarizing 22 patients who underwent curative resection and subsequently had a confirmed prognosis.


Subject(s)
Adenocarcinoma/diagnosis , Bile Duct Neoplasms/diagnosis , Carcinoma, Neuroendocrine/diagnosis , Adenocarcinoma/surgery , Aged , Bile Duct Neoplasms/surgery , Bile Ducts , Bile Ducts, Intrahepatic , Carcinoma, Neuroendocrine/surgery , Female , Humans , Pancreaticoduodenectomy
14.
Glycoconj J ; 34(2): 267-273, 2017 04.
Article in English | MEDLINE | ID: mdl-28205070

ABSTRACT

Disialosyl globopentaosylceramide (DSGb5) is a ganglioside originally isolated from tissue extracts of renal cell carcinoma (RCC) with metastasis. Previous in vitro experiments have suggested that DSGb5 promotes metastasis by enhancing the migration of RCC cells and downregulating NK cell cytotoxicity against RCC cells. In this study, we investigated the clinicopathological significance of DSGb5 expression in RCC and outcomes of RCC patients. A total of 156 RCC patients who underwent surgical treatments at our hospital from January 2007 through December 2012 were analyzed in this study. The expression of DSGb5 in RCC specimens was examined by immunohistochemical staining with monoclonal antibody 5F3. The immunostaining intensity of RCC tissues was assessed in comparison with that in benign renal tubules as an internal positive control. The relationship between DSGb5 expression and clinicopathological characteristics was investigated and recurrence free survival following surgery was evaluated. Microvascular invasion was observed in 68% (n = 19/28) and in 45% (n = 58/128) of the DSGb5 high expression group and low expression group, respectively (p = 0.031). Of 156 patients with a median follow up of 51 months, 18 patients (12%) developed metastasis following surgery. Patients in the DSGb5 high expression group showed significantly lower recurrence-free survival as compared with those in the DSGb5 low expression group (log-rank P = 0.047). In the present study, DSGb5 expression was associated with microvascular invasion in RCC tissues, and patients with DSGb5 high expression showed significantly lower recurrence-free survival rates. These findings suggest that DSGb5 expressed in RCC is correlated with metastasis and is a potential predictor for identifying patients who experience metastasis after surgery.


Subject(s)
Carcinoma, Renal Cell , Gene Expression Regulation, Neoplastic , Globosides/biosynthesis , Kidney Neoplasms , Kidney Tubules, Distal , Aged , Antibodies, Monoclonal, Murine-Derived/chemistry , Antineoplastic Agents, Immunological/chemistry , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/mortality , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/surgery , Disease-Free Survival , Female , Humans , Immunohistochemistry , Kidney Neoplasms/metabolism , Kidney Neoplasms/mortality , Kidney Neoplasms/pathology , Kidney Neoplasms/surgery , Kidney Tubules, Distal/metabolism , Kidney Tubules, Distal/pathology , Male , Middle Aged , Neoplasm Metastasis , Survival Rate
15.
Breed Sci ; 66(3): 416-24, 2016 Jun.
Article in English | MEDLINE | ID: mdl-27436952

ABSTRACT

Barley (Hordeum vulgare L.) is the fourth most-produced cereal in the world and is mainly utilized as animal feed and malts. Recently barley attracts considerable attentions as healthy food rich in dietary fiber. However, limited knowledge is available about developmental aspects of barley leaves. In the present study, we investigated barley narrow leafed dwarf1 (nld1) mutants, which exhibit thin leaves accompanied by short stature. Detailed histological analysis revealed that leaf marginal tissues, such as sawtooth hairs and sclerenchymatous cells, were lacked in nld1, suggesting that narrowed leaf of nld1 was attributable to the defective development of the marginal regions in the leaves. The defective marginal developments were also appeared in internodes and glumes in spikelets. Map-based cloning revealed that NLD1 encodes a WUSCHEL-RELATED HOMEOBOX 3 (WOX3), an ortholog of the maize NARROW SHEATH genes. In situ hybridization showed that NLD1 transcripts were localized in the marginal edges of leaf primordia from the initiating stage. From these results, we concluded that NLD1 plays pivotal role in the increase of organ width and in the development of marginal tissues in lateral organs in barley.

16.
Plant J ; 78(6): 927-36, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24654985

ABSTRACT

Auxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development. Analysis of many Arabidopsis mutants that were defective in auxin biosynthesis revealed that the indole-3-pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the major biosynthetic pathway of indole-3-acetic acid (IAA). In contrast, little information is known about the molecular mechanisms of auxin biosynthesis in rice. In this study, we identified a auxin-related rice mutant, fish bone (fib). FIB encodes an orthologue of TAA genes and loss of FIB function resulted in pleiotropic abnormal phenotypes, such as small leaves with large lamina joint angles, abnormal vascular development, small panicles, abnormal organ identity and defects in root development, together with a reduction in internal IAA levels. Moreover, we found that auxin sensitivity and polar transport activity were altered in the fib mutant. From these results, we suggest that FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated.


Subject(s)
Indoleacetic Acids/metabolism , Oryza/genetics , Plant Growth Regulators/metabolism , Plant Proteins/physiology , Tryptophan Transaminase/physiology , Amino Acid Sequence , Biological Transport/genetics , Cloning, Molecular , Molecular Sequence Data , Oryza/enzymology , Oryza/metabolism , Phenotype , Plant Proteins/chemistry , Plant Proteins/genetics , Sequence Alignment , Sequence Analysis, Protein , Tryptophan Transaminase/chemistry , Tryptophan Transaminase/genetics
17.
Nucleic Acids Res ; 41(Database issue): D1214-21, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23180784

ABSTRACT

Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, 'single guide gene search' and 'multiple guide gene search' to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.


Subject(s)
Databases, Genetic , Gene Expression Profiling , Gene Regulatory Networks , Genes, Plant , Oryza/genetics , Internet , Molecular Sequence Annotation , Oryza/growth & development , Oryza/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Software
18.
PLoS Genet ; 8(9): e1002953, 2012 Sep.
Article in English | MEDLINE | ID: mdl-23028360

ABSTRACT

RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE), which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs) and are processed into small RNAs (small interfering RNAs, siRNAs) that suppress TEs by RNA-directed DNA methylation. Thus, the majority of TEs are epigenetically silenced. On the other hand, most of the eukaryotic genome is composed of TEs and their remnants, suggesting that TEs have evolved countermeasures against host-mediated silencing. Under some circumstances, TEs can become active and increase in copy number. Knowledge is accumulating on the mechanisms of TE silencing by the host; however, the mechanisms by which TEs counteract silencing are poorly understood. Here, we show that a class of TEs in rice produces a microRNA (miRNA) to suppress host silencing. Members of the microRNA820 (miR820) gene family are located within CACTA DNA transposons in rice and target a de novo DNA methyltransferase gene, OsDRM2, one of the components of epigenetic silencing. We confirmed that miR820 negatively regulates the expression of OsDRM2. In addition, we found that expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci. Furthermore, we found that the nucleotide sequence of miR820 and its recognition site within the target gene in some Oryza species have co-evolved to maintain their base-pairing ability. The co-evolution of these sequences provides evidence for the functionality of this regulation. Our results demonstrate how parasitic elements in the genome escape the host's defense machinery. Furthermore, our analysis of the regulation of OsDRM2 by miR820 sheds light on the action of transposon-derived small RNAs, not only as a defense mechanism for host genomes but also as a regulator of interactions between hosts and their parasitic elements.


Subject(s)
DNA Transposable Elements/genetics , Host-Parasite Interactions/genetics , MicroRNAs , Oryza/genetics , RNA, Small Interfering/genetics , DNA Methylation/genetics , Epigenetic Repression , Evolution, Molecular , Gene Expression Regulation, Plant , Gene Silencing , Genome, Plant , Interspersed Repetitive Sequences/genetics , MicroRNAs/genetics , MicroRNAs/metabolism
19.
Tohoku J Exp Med ; 236(1): 1-7, 2015 05.
Article in English | MEDLINE | ID: mdl-25864532

ABSTRACT

About one third of renal cell carcinoma (RCC) patients exhibit metastasis upon initial presentation. However, the molecular basis for RCC metastasis is not fully understood. A ganglioside, disialosyl globopentaosylceramide (DSGb5), was originally isolated from RCC tissue extracts, and its expression is correlated with RCC metastatic potential. DSGb5 is synthesized by GalNAc α2,6-sialyltransferase VI (ST6GalNAcVI) and is expressed on the surface of RCC cells. Importantly, DSGb5 binds to sialic acid-binding Ig-like lectin-7 (Siglec-7) expressed on natural killer (NK) cells, thereby inhibiting NK-cell cytotoxicity. However, the role of DSGb5 in RCC progression remains obscure. To address this issue, we used ACHN cells derived from malignant pleural effusion of a patient with metastatic RCC. Using the limiting dilution method, we isolated three independent clones with different DSGb5 expression levels. Comparison of these clones indicated that the cloned cells with high DSGb5 expression levels exhibited greater migration potential, compared to the clone with low DSGb5 expression levels. In contrast, DSGb5 expression levels exerted no significant effect on cell proliferation. We then established the ACHN-derived cell lines that stably expressed siRNA against ST6GalNAcVI mRNA or control siRNA. Importantly, the ST6GalNAcVI-knockdown cells expressed low levels of DSGb5. We thus demonstrated the significantly decreased migration potential of the ST6GalNAcVI-knockdown cells with low DSGb5 expression levels, compared to the control siRNA-transfected cells expressing high DSGb5 levels, but no significant difference in the cell proliferation. Thus, DSGb5 expression may ensure the migration of RCC cells. We propose that DSGb5 expressed on RCC cells may determine their metastatic capability.


Subject(s)
Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Cell Movement , Globosides/metabolism , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Carcinoma, Renal Cell/genetics , Cell Line, Tumor , Cell Proliferation , Cell Separation , Flow Cytometry , Gene Expression Regulation, Neoplastic , Globosides/chemistry , Humans , Kidney Neoplasms/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transfection
20.
Nihon Hinyokika Gakkai Zasshi ; 106(1): 53-8, 2015 Jan.
Article in Japanese | MEDLINE | ID: mdl-26399133

ABSTRACT

A 44-year-old man discovered a swollen right testis more than 4 years earlier. He was brought to our hospital because of abdominal pain and vomiting. Enhanced computed tomography (CT) showed a swollen right testis, lung nodules, and swollen retroperitoneal and mediastinal lymph nodes. The swollen lymph nodes compressed the duodenum, causing ileus. HCG, HCG-ß, and AFP levels were normal, but the LDH level was high (2,933 IU/L). A diagnosis of testicular cancer with lung and lymph node metastases was made, and a right orchidectomy was performed. However, the pathological diagnosis was unclear, and it was necessary to consult another pathologist, but this took .6 weeks. While awaiting the pathological diagnosis, the patient was given chemotherapy with two 3-week courses of BEP. On pathological examination, the tumor consisted of small round cells with a rosette-like arrangement. Cartilage and keratinized tissues were also present. Immunohistochemical staining was positive for CD56, synaptophysin, vimentin, GFAP, and CD99 (MIC2), but negative for AE1/AE3, OCT-4, chromogranin, INI-1, and desmin. The patient was then diagnosed as having a primitive neuroectodermal tumor and teratoma. The metastatic lymph nodes decreased in size after chemotherapy; therefore, two further courses of BEP were added. However, CT showed disease progression. The patient refused further therapy and returned home. Eight months later, he was hospitalized because of swollen retroperitoneal and mediastinal lymph nodes and ileus. Despite treatment with radiation therapy, which resulted in decreased lymph nodes, the patient died. This was a very rare case, the first such case in Japan.


Subject(s)
Neuroectodermal Tumors, Primitive/therapy , Testicular Neoplasms/therapy , Adult , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Fatal Outcome , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/secondary , Lymphatic Metastasis , Male , Neuroectodermal Tumors, Primitive/secondary , Orchiectomy , Testicular Neoplasms/pathology
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