90 results on '"Yong-Mei Bi"'
Search Results
2. Identification of differentially-expressed genes of rice in overlapping responses to bacterial infection by Xanthomonas oryzae pv. oryzae and nitrogen deficiency
- Author
-
Chao YU, Hua-min CHEN, Fang TIAN, Yong-mei BI, Rothstein J Steven, Leach E Jan, and Chen-yang HE
- Subjects
rice ,differentially-expressed genes (DEGs) ,bacterial infection ,nitrogen deficiency ,co-regulation ,Agriculture (General) ,S1-972 - Abstract
Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of high nitrogen (N) responsive diseases. Rice plants became more disease resistant with decreasing N suggesting that the crosstalk between disease resistance and N utilization pathways might exist. However, the co-regulatory components in such crosstalk have not been elucidated. Here, we comparatively analyzed the gene expression profiling of rice under Xoo inoculation, low N treatment, or a combination of both stresses, and identified the differentially-expressed genes (DEGs) in overlapping responses. These DEGs were involved in different biological processes, including innate immunity and nitrogen metabolism. The randomly-selected DEGs expression was validated by quantitative real-time PCR assays. Temporal expression of six genes from different functional categories suggested that N condition was the dominant factor when both stresses were present. These DEGs identified provide novel insights into the coordinated regulatory mechanism in biotic and abiotic stress responses in rice.
- Published
- 2015
- Full Text
- View/download PDF
3. Altered Expression of OsNLA1 Modulates Pi Accumulation in Rice (Oryza sativa L.) Plants
- Author
-
Sihui Zhong, Kashif Mahmood, Yong-Mei Bi, Steven J. Rothstein, and Kosala Ranathunge
- Subjects
homeostasis ,nitrogen ,OsNLA1 ,permeability ,phosphorous ,toxicity ,Plant culture ,SB1-1110 - Abstract
Current agricultural practices rely on heavy use of fertilizers for increased crop productivity. However, the problems associated with heavy fertilizer use, such as high cost and environmental pollution, require the development of crop species with increased nutrient use efficiency. In this study, by using transgenic approaches, we have revealed the critical role of OsNLA1 in phosphate (Pi) accumulation of rice plants. When grown under sufficient Pi and nitrate levels, OsNLA1 knockdown (Osnla1-1, Osnla1-2, and Osnla1-3) lines accumulated higher Pi content in their shoot tissues compared to wild-type, whereas, over-expression lines (OsNLA1-OE1, OsNLA1-OE2, and OsNLA1-OE3) accumulated the least levels of Pi. However, under high Pi levels, knockdown lines accumulated much higher Pi content compared to wild-type and exhibited Pi toxicity symptoms in the leaves. In contrast, the over-expression lines had 50–60% of the Pi content of wild-type and did not show such symptoms. When grown under limiting nitrate levels, OsNLA1 transgenic lines also displayed a similar pattern in Pi accumulation and Pi toxicity symptoms compared to wild-type suggesting an existence of cross-talk between nitrogen (N) and phosphorous (P), which is regulated by OsNLA1. The greater Pi accumulation in knockdown lines was a result of enhanced Pi uptake/permeability of roots compared to the wild-type. The cross-talk between N and P was found to be nitrate specific since the knockdown lines failed to over-accumulate Pi under low (sub-optimal) ammonium level. Moreover, OsNLA1 was also found to interact with OsPHO2, a known regulator of Pi homeostasis, in a Yeast Two-Hybrid (Y2H) assay. Taken together, these results show that OsNLA1 is involved in Pi homeostasis regulating Pi uptake and accumulation in rice plants and may provide an opportunity to enhance P use efficiency by manipulating nitrate supply in the soil.
- Published
- 2017
- Full Text
- View/download PDF
4. The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism.
- Author
-
Ashraf El-Kereamy, Yong-Mei Bi, Kosala Ranathunge, Perrin H Beatty, Allen G Good, and Steven J Rothstein
- Subjects
Medicine ,Science - Abstract
Temperatures higher than the optimum negatively affects plant growth and development. Tolerance to high temperature is a complex process that involves several pathways. Understanding this process, especially in crops such as rice, is essential to prepare for predicted climate changes due to global warming. Here, we show that OsMYB55 is induced by high temperature and overexpression of OsMYB55 resulted in improved plant growth under high temperature and decreased the negative effect of high temperature on grain yield. Transcriptome analysis revealed an increase in expression of several genes involved in amino acids metabolism. We demonstrate that OsMYB55 binds to the promoter regions of target genes and directly activates expression of some of those genes including glutamine synthetase (OsGS1;2) glutamine amidotransferase (GAT1) and glutamate decarboxylase 3 (GAD3). OsMYB55 overexpression resulted in an increase in total amino acid content and of the individual amino acids produced by the activation of the above mentioned genes and known for their roles in stress tolerance, namely L-glutamic acid, GABA and arginine especially under high temperature condition. In conclusion, overexpression of OsMYB55 improves rice plant tolerance to high temperature, and this high tolerance is associated with enhanced amino acid metabolism through transcription activation.
- Published
- 2012
- Full Text
- View/download PDF
5. GNC and CGA1 modulate chlorophyll biosynthesis and glutamate synthase (GLU1/Fd-GOGAT) expression in Arabidopsis.
- Author
-
Darryl Hudson, David Guevara, Mahmoud W Yaish, Carol Hannam, Nykoll Long, Joseph D Clarke, Yong-Mei Bi, and Steven J Rothstein
- Subjects
Medicine ,Science - Abstract
Chloroplast development is an important determinant of plant productivity and is controlled by environmental factors including amounts of light and nitrogen as well as internal phytohormones including cytokinins and gibberellins (GA). The paralog GATA transcription factors GNC and CGA1/GNL up-regulated by light, nitrogen and cytokinin while also being repressed by GA signaling. Modifying the expression of these genes has previously been shown to influence chlorophyll content in Arabidopsis while also altering aspects of germination, elongation growth and flowering time. In this work, we also use transgenic lines to demonstrate that GNC and CGA1 exhibit a partially redundant control over chlorophyll biosynthesis. We provide novel evidence that GNC and CGA1 influence both chloroplast number and leaf starch in proportion to their transcript level. GNC and CGA1 were found to modify the expression of chloroplast localized GLUTAMATE SYNTHASE (GLU1/Fd-GOGAT), which is the primary factor controlling nitrogen assimilation in green tissue. Altering GNC and CGA1 expression was also found to modulate the expression of important chlorophyll biosynthesis genes (GUN4, HEMA1, PORB, and PORC). As previously demonstrated, the CGA1 transgenic plants demonstrated significantly altered timing to a number of developmental events including germination, leaf production, flowering time and senescence. In contrast, the GNC transgenic lines we analyzed maintain relatively normal growth phenotypes outside of differences in chloroplast development. Despite some evidence for partial divergence, results indicate that regulation of both GNC and CGA1 by light, nitrogen, cytokinin, and GA acts to modulate nitrogen assimilation, chloroplast development and starch production. Understanding the mechanisms controlling these processes is important for agricultural biotechnology.
- Published
- 2011
- Full Text
- View/download PDF
6. The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice.
- Author
-
Mahmoud W Yaish, Ashraf El-Kereamy, Tong Zhu, Perrin H Beatty, Allen G Good, Yong-Mei Bi, and Steven J Rothstein
- Subjects
Genetics ,QH426-470 - Abstract
The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key abscisic acid (ABA) biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI) protein, an enzyme that catalyzes 16α, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs) in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production.
- Published
- 2010
- Full Text
- View/download PDF
7. Overexpression of miR169o, an Overlapping MicroRNA in Response to Both Nitrogen Limitation and Bacterial Infection, Promotes Nitrogen Use Efficiency and Susceptibility to Bacterial Blight in Rice
- Author
-
Chao Yu, Jichun Wang, Fang Tian, Steven J. Rothstein, Yong-Mei Bi, Chen Yutong, Cao Yaqian, Xueping Zhou, Huamin Chen, Fenghuan Yang, and Chenyang He
- Subjects
0301 basic medicine ,Xanthomonas ,Nitrogen ,Physiology ,Gene Expression ,Plant Science ,Biology ,Plant disease resistance ,Microbiology ,03 medical and health sciences ,Xanthomonas oryzae ,Gene Expression Regulation, Plant ,Gene expression ,Gene ,Disease Resistance ,Plant Diseases ,Regulation of gene expression ,Oryza sativa ,Nitrogen deficiency ,Wild type ,food and beverages ,Oryza ,Cell Biology ,General Medicine ,biology.organism_classification ,MicroRNAs ,030104 developmental biology ,RNA, Plant - Abstract
Limiting nitrogen (N) supply contributes to improved resistance to bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) in susceptible rice (Oryza sativa). To understand the regulatory roles of microRNAs (miRNAs) in this phenomenon, 63 differentially expressed overlapping miRNAs in response to Xoo infection and N limitation stress in rice were identified through deep RNA sequencing and stem-loop quantitative real-time PCR. Among these, miR169o was further assessed as a typical overlapping miRNA through the overexpression of the miR169o primary gene. Osa-miR169o-OX plants were taller, and had more biomass accumulation with significantly increased nitrate and total amino acid contents in roots than the wild type (WT). Transcript level assays showed that under different N supply conditions, miR169o oppositely regulated NRT2, and this is reduced under normal N supply conditions but remarkably induced under N-limiting stress. On the other hand, osa-miR169o-OX plants also displayed increased disease lesion lengths and reduced transcriptional levels of defense gene (PR1b, PR10a, PR10b and PAL) compared with the WT after inoculation with Xoo. In addition, miR169o impeded Xoo-mediated NRT transcription. Therefore, the overlapping miR169o contributes to increase N use efficiency and negatively regulates the resistance to BB in rice. Consistently, transient expression of NF-YA genes in rice protoplasts promoted the transcripts of PR genes and NRT2 genes, while it reduced the transcripts of NRT1 genes. Our results provide novel and additional insights into the co ordinated regulatory mechanisms of cross-talk between Xoo infection and N deficiency responses in rice.
- Published
- 2018
8. Overexpression of OsGATA12 regulates chlorophyll content, delays plant senescence and improves rice yield under high density planting
- Author
-
Kashif Mahmood, Guangwen Lu, Yong-Mei Bi, Steven J. Rothstein, José A. Casaretto, Shan Ying, and Fang Liu
- Subjects
Chlorophyll ,0106 biological sciences ,0301 basic medicine ,Plant Science ,Genetically modified crops ,Biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Genetics ,Promoter Regions, Genetic ,Plant Proteins ,Panicle ,2. Zero hunger ,Plant senescence ,Zinc finger transcription factor ,Oryza sativa ,food and beverages ,Agriculture ,Oryza ,General Medicine ,Plants, Genetically Modified ,Chloroplast ,030104 developmental biology ,chemistry ,Agronomy ,Seeds ,GATA transcription factor ,Agronomy and Crop Science ,Transcription Factors ,010606 plant biology & botany - Abstract
Agronomic traits controlling the formation, architecture and physiology of source and sink organs are main determinants of rice productivity. Semi-dwarf rice varieties with low tiller formation but high seed production per panicle and dark green and thick leaves with prolonged source activity are among the desirable traits to further increase the yield potential of rice. Here, we report the functional characterization of a zinc finger transcription factor, OsGATA12, whose overexpression causes increased leaf greenness, reduction of leaf and tiller number, and affects yield parameters. Reduced tillering allowed testing the transgenic plants under high density which resulted in significantly increased yield per area and higher harvest index compared to wild-type. We show that delayed senescence of transgenic plants and the corresponding longer stay-green phenotype is mainly due to increased chlorophyll and chloroplast number. Further, our work postulates that the increased greenness observed in the transgenic plants is due to more chlorophyll synthesis but most significantly to decreased chlorophyll degradation, which is supported by the reduced expression of genes involved in the chlorophyll degradation pathway. In particular we show evidence for the down-regulation of the STAY GREEN RICE gene and in vivo repression of its promoter by OsGATA12, which suggests a transcriptional repression function for a GATA transcription factor for prolonging the onset of senescence in cereals.
- Published
- 2017
9. Overexpression of ANAC046 Promotes Suberin Biosynthesis in Roots of
- Author
-
Kashif, Mahmood, Viktoria Valeska, Zeisler-Diehl, Lukas, Schreiber, Yong-Mei, Bi, Steven J, Rothstein, and Kosala, Ranathunge
- Subjects
Cell Nucleus ,Chlorophyll ,roots ,transcription activator ,Arabidopsis thaliana ,Arabidopsis Proteins ,suberin biosynthesis ,fungi ,Arabidopsis ,food and beverages ,Plants, Genetically Modified ,Lipids ,Plant Roots ,Article ,ANAC046 ,Plant Leaves ,Gene Expression Regulation, Plant ,Waxes ,Trans-Activators ,permeability - Abstract
NAC (NAM (no apical meristem), ATAF1/2, and CUC2 (cup-shaped cotyledon)) proteins are one of the largest families of plant-specific transcription factors, and this family is present in a wide range of land plants. Here, we have investigated the role of ANAC046 in the regulation of suberin biosynthesis and deposition in Arabidopsis. Subcellular localization and transcriptional activity assays showed that ANAC046 localizes in the nucleus, where it functions as a transcription activator. Analysis of the PANAC046:GUS lines revealed that ANAC046 is mainly expressed in the root endodermis and periderm, and is also induced in leaves by wounding. The transgenic lines overexpressing ANAC046 exhibited defective surfaces on the aerial plant parts compared to the wild-type (WT) as characterized by increased permeability for Toluidine blue stain and greater chlorophyll leaching. Quantitative RT-PCR analysis showed that the expression of suberin biosynthesis genes was significantly higher in the roots and leaves of overexpression lines compared to the WT. The biochemical analysis of leaf cuticular waxes showed that the overexpression lines accumulated 30% more waxes than the WT. Concurrently, overexpression lines also deposited almost twice the amount of suberin content in their roots compared with the WT. Taken together, these results showed that ANAC046 is an important transcription factor that promotes suberin biosynthesis in Arabidopsis thaliana roots.
- Published
- 2019
10. Overexpression of ANAC046 Promotes Suberin Biosynthesis in Roots of Arabidopsis thaliana
- Author
-
Steven J. Rothstein, Lukas Schreiber, Kashif Mahmood, Viktoria Zeisler-Diehl, Yong-Mei Bi, and Kosala Ranathunge
- Subjects
roots ,0106 biological sciences ,0301 basic medicine ,food.ingredient ,01 natural sciences ,Catalysis ,Inorganic Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,food ,Biosynthesis ,Suberin ,Arabidopsis ,Arabidopsis thaliana ,Physical and Theoretical Chemistry ,Molecular Biology ,Transcription factor ,Spectroscopy ,transcription activator ,biology ,suberin biosynthesis ,fungi ,Organic Chemistry ,food and beverages ,General Medicine ,15. Life on land ,Meristem ,biology.organism_classification ,ANAC046 ,Computer Science Applications ,Cell biology ,030104 developmental biology ,chemistry ,Endodermis ,permeability ,Cotyledon ,010606 plant biology & botany - Abstract
NAC (NAM (no apical meristem), ATAF1/2, and CUC2 (cup-shaped cotyledon)) proteins are one of the largest families of plant-specific transcription factors, and this family is present in a wide range of land plants. Here, we have investigated the role of ANAC046 in the regulation of suberin biosynthesis and deposition in Arabidopsis. Subcellular localization and transcriptional activity assays showed that ANAC046 localizes in the nucleus, where it functions as a transcription activator. Analysis of the PANAC046:GUS lines revealed that ANAC046 is mainly expressed in the root endodermis and periderm, and is also induced in leaves by wounding. The transgenic lines overexpressing ANAC046 exhibited defective surfaces on the aerial plant parts compared to the wild-type (WT) as characterized by increased permeability for Toluidine blue stain and greater chlorophyll leaching. Quantitative RT-PCR analysis showed that the expression of suberin biosynthesis genes was significantly higher in the roots and leaves of overexpression lines compared to the WT. The biochemical analysis of leaf cuticular waxes showed that the overexpression lines accumulated 30% more waxes than the WT. Concurrently, overexpression lines also deposited almost twice the amount of suberin content in their roots compared with the WT. Taken together, these results showed that ANAC046 is an important transcription factor that promotes suberin biosynthesis in Arabidopsis thaliana roots.
- Published
- 2019
11. Identification of differentially-expressed genes of rice in overlapping responses to bacterial infection by Xanthomonas oryzae pv. oryzae and nitrogen deficiency
- Author
-
Fang Tian, Leach E. Jan, Rothstein J. Steven, Chen-yang He, Chao Yu, Yong-mei Bi, and Huamin Chen
- Subjects
co-regulation ,Agriculture (General) ,Plant Science ,Plant disease resistance ,Biochemistry ,S1-972 ,Microbiology ,Xanthomonas oryzae ,Food Animals ,nitrogen deficiency ,Xanthomonas oryzae pv. oryzae ,differentially-expressed genes (DEGs) ,Gene ,Ecology ,biology ,Abiotic stress ,Nitrogen deficiency ,rice ,bacterial infection ,food and beverages ,biology.organism_classification ,Gene expression profiling ,Crosstalk (biology) ,Animal Science and Zoology ,Agronomy and Crop Science ,Food Science - Abstract
Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of high nitrogen (N) responsive diseases. Rice plants became more disease resistant with decreasing N suggesting that the crosstalk between disease resistance and N utilization pathways might exist. However, the co-regulatory components in such crosstalk have not been elucidated. Here, we comparatively analyzed the gene expression profiling of rice under Xoo inoculation, low N treatment, or a combination of both stresses, and identified the differentially-expressed genes (DEGs) in overlapping responses. These DEGs were involved in different biological processes, including innate immunity and nitrogen metabolism. The randomly-selected DEGs expression was validated by quantitative real-time PCR assays. Temporal expression of six genes from different functional categories suggested that N condition was the dominant factor when both stresses were present. These DEGs identified provide novel insights into the coordinated regulatory mechanism in biotic and abiotic stress responses in rice.
- Published
- 2015
12. Genome‐wide binding analysis of AtGNC and AtCGA1 demonstrates their cross‐regulation and common and specific functions
- Author
-
José A. Casaretto, Steven J. Rothstein, Yong-Mei Bi, and Zhenhua Xu
- Subjects
0106 biological sciences ,0301 basic medicine ,Senescence ,Arabidopsis thaliana ,Plant Science ,01 natural sciences ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Genome ,03 medical and health sciences ,Transcription (biology) ,plant greening ,Gene ,Transcription factor ,Ecology, Evolution, Behavior and Systematics ,Original Research ,Genetics ,Ecology ,biology ,Ubiquitin ligase ,Plant development ,ChIP‐seq ,030104 developmental biology ,biology.protein ,GATA transcription factors ,GATA transcription factor ,plant development ,010606 plant biology & botany - Abstract
GATA transcription factors are involved in multiple processes in plant growth and development. Two GATA factors, NITRATE‐INDUCIBLE,CARBON METABOLISM‐INVOLVED (GNC) and CYTOKININ‐RESPONSIVE GATA FACTOR 1 (CGA1, also named GNL), are important regulators in greening, flowering, senescence, and hormone signaling. However, their direct target genes related to these biological processes are poorly characterized. Here, GNC and CGA1 are shown to be transcription activators and by using chromatin immunoprecipitation sequencing (ChIP‐seq), 1475 and 638 genes are identified to be associated with GNC and CGA1 binding, respectively. Enrichment of diverse motifs in the peak binding regions for GNC and CGA1 suggests the possibility that these two transcription factors also interact with other transcription factors and in addition genes coding for DNA‐binding proteins are highly enriched among GNC‐ and CGA1‐associated genes. Despite the fact that these two GATA factors are known to share a large portion of co‐expressed genes, our analysis revealed a low percentage of overlapping binding‐associated genes for these two homologues. This suggests a possible cross‐regulation between these, which is verified using ChIP‐qPCR. The common and specific biological processes regulated by GNC and CGA1 also support this notion. Functional analysis of the binding‐associated genes revealed that those encoding transcription factors, E3 ligase, as well as genes with roles in plant development are highly enriched, indicating that GNC and CGA1 mediate complex genetic networks in regulating different aspects of plant growth and development.
- Published
- 2017
13. AMT1;1 transgenic rice plants with enhanced NH4+ permeability show superior growth and higher yield under optimal and suboptimal NH4+ conditions
- Author
-
Ashraf El-Kereamy, Satinder K. Gidda, Steven J. Rothstein, Yong Mei Bi, and Kosala Ranathunge
- Subjects
Chlorophyll ,0106 biological sciences ,Physiology ,Glutamine ,Nitrogen assimilation ,Gene Expression ,Plant Science ,Plant Roots ,01 natural sciences ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Genes, Reporter ,Ammonium Compounds ,Onions ,Biomass ,Cation Transport Proteins ,Plant Proteins ,2. Zero hunger ,0303 health sciences ,assimilation ,food and beverages ,Plants, Genetically Modified ,Ammonium transporter ,Horticulture ,Phenotype ,Shoot ,Carbohydrate Metabolism ,Plant Shoots ,Research Paper ,inorganic chemicals ,Nitrogen ,Transgene ,Biology ,Models, Biological ,Permeability ,03 medical and health sciences ,Xylem ,Botany ,Ammonium ,transgenic ,030304 developmental biology ,Oryza sativa ,rice ,Oryza ,15. Life on land ,Genetically modified rice ,chemistry ,Edible Grain ,010606 plant biology & botany - Abstract
The major source of nitrogen for rice (Oryza sativa L.) is ammonium (NH4(+)). The NH4(+) uptake of roots is mainly governed by membrane transporters, with OsAMT1;1 being a prominent member of the OsAMT1 gene family that is known to be involved in NH4(+) transport in rice plants. However, little is known about its involvement in NH4(+) uptake in rice roots and subsequent effects on NH4(+) assimilation. This study shows that OsAMT1;1 is a constitutively expressed, nitrogen-responsive gene, and its protein product is localized in the plasma membrane. Its expression level is under the control of circadian rhythm. Transgenic rice lines (L-2 and L-3) overexpressing the OsAMT1;1 gene had the same root structure as the wild type (WT). However, they had 2-fold greater NH4(+) permeability than the WT, whereas OsAMT1;1 gene expression was 20-fold higher than in the WT. Analogous to the expression, transgenic lines had a higher NH4(+) content in the shoots and roots than the WT. Direct NH4(+) fluxes in the xylem showed that the transgenic lines had significantly greater uptake rates than the WT. Higher NH4(+) contents also promoted higher expression levels of genes in the nitrogen assimilation pathway, resulting in greater nitrogen assimilates, chlorophyll, starch, sugars, and grain yield in transgenic lines than in the WT under suboptimal and optimal nitrogen conditions. OsAMT1;1 also enhanced overall plant growth, especially under suboptimal NH4(+) levels. These results suggest that OsAMT1;1 has the potential for improving nitrogen use efficiency, plant growth, and grain yield under both suboptimal and optimal nitrogen fertilizer conditions.
- Published
- 2014
14. Rice Cytokinin GATA Transcription Factor1 Regulates Chloroplast Development and Plant Architecture
- Author
-
Darryl Hudson, Andrew J. Hand, Lixin Hao, Yong-Mei Bi, Xi Chen, Tong Zhu, Steven J. Rothstein, Zhenhua Xu, and David Guevara
- Subjects
Chlorophyll ,Chloroplasts ,Cytokinins ,Light ,Nitrogen ,Physiology ,Gene Expression ,Flowers ,Plant Science ,Biology ,GATA Transcription Factors ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Transcription (biology) ,RNA interference ,Botany ,Genetics ,Biomass ,Photosynthesis ,Oligonucleotide Array Sequence Analysis ,Plant Proteins ,Gene knockdown ,Oryza sativa ,Gene Expression Profiling ,food and beverages ,Oryza ,Starch ,Darkness ,Plants, Genetically Modified ,Genes, Development, and Evolution ,Gibberellins ,Cell biology ,Plant Leaves ,Chloroplast ,chemistry ,Seeds ,Cytokinin ,RNA Interference ,Gibberellin - Abstract
Chloroplast biogenesis has been well documented in higher plants, yet the complex methods used to regulate chloroplast activity under fluctuating environmental conditions are not well understood. In rice (Oryza sativa), the CYTOKININ-RESPONSIVE GATA TRANSCRIPTION FACTOR1 (Cga1) shows increased expression following light, nitrogen, and cytokinin treatments, while darkness and gibberellin reduce expression. Strong overexpression of Cga1 produces dark green, semidwarf plants with reduced tillering, whereas RNA interference knockdown results in reduced chlorophyll and increased tillering. Coexpression, microarray, and real-time expression analyses demonstrate a correlation between Cga1 expression and the expression of important nucleus-encoded, chloroplast-localized genes. Constitutive Cga1 overexpression increases both chloroplast biogenesis and starch production but also results in delayed senescence and reduced grain filling. Growing the transgenic lines under different nitrogen regimes indicates potential agricultural applications for Cga1, including manipulation of biomass, chlorophyll/chloroplast content, and harvest index. These results indicate a conserved mechanism by which Cga1 regulates chloroplast development in higher plants.
- Published
- 2013
15. A Developmental Transcriptional Network for Maize Defines Coexpression Modules
- Author
-
Lewis Lukens, Wenqing Wu, Tong Zhu, Joseph Colasanti, Steven J. Rothstein, Xi Chen, Yong-Mei Bi, and Gregory S Downs
- Subjects
Regulation of gene expression ,Senescence ,Genetics ,Physiology ,Transcription (biology) ,Gene expression ,Transcriptional regulation ,RNA ,Plant Science ,Biology ,Gene ,Genome - Abstract
Here, we present a genome-wide overview of transcriptional circuits in the agriculturally significant crop species maize (Zea mays). We examined transcript abundance data at 50 developmental stages, from embryogenesis to senescence, for 34,876 gene models and classified genes into 24 robust coexpression modules. Modules were strongly associated with tissue types and related biological processes. Sixteen of the 24 modules (67%) have preferential transcript abundance within specific tissues. One-third of modules had an absence of gene expression in specific tissues. Genes within a number of modules also correlated with the developmental age of tissues. Coexpression of genes is likely due to transcriptional control. For a number of modules, key genes involved in transcriptional control have expression profiles that mimic the expression profiles of module genes, although the expression of transcriptional control genes is not unusually representative of module gene expression. Known regulatory motifs are enriched in several modules. Finally, of the 13 network modules with more than 200 genes, three contain genes that are notably clustered (P < 0.05) within the genome. This work, based on a carefully selected set of major tissues representing diverse stages of maize development, demonstrates the remarkable power of transcript-level coexpression networks to identify underlying biological processes and their molecular components.
- Published
- 2013
16. NIN-like protein 8 is a master regulator of nitrate-promoted seed germination in Arabidopsis
- Author
-
Vanathy Easwaran, Masanori Okamoto, Ryoichi Yano, Anne Krapp, Yunchen Gong, Steven J. Rothstein, Dawei Yan, Akira Endo, Yong-Mei Bi, David S. Guttman, Vivian Chau, Matthew Ierullo, Nicolas Provart, Eiji Nambara, Mitsuhiro Kimura, Asher Pasha, Department of Cell & Systems Biology, University of Toronto, JST, PRESTO, Tottori University, Shimane University, Université de Tsukuba = University of Tsukuba, Centre for the Analysis of Genome Evolution and Function, Department of Molecular and Cellular Biology, University of Guelph, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, NSERC [RGPIN 355784, RGPIN-2014-03621], JST PRESTO [11105], Labex Saclay Plant Sciences [ANR-10-LABX-0040-SPS], and Nambara, Eiji
- Subjects
0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Science ,Mutant ,Arabidopsis ,General Physics and Astronomy ,Germination ,Biology ,01 natural sciences ,Genetic analysis ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,chemistry.chemical_compound ,Cytochrome P-450 Enzyme System ,Plant Growth Regulators ,Nitrate ,Gene Expression Regulation, Plant ,Botany ,[SDV.IDA]Life Sciences [q-bio]/Food engineering ,Protein Isoforms ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,Promoter Regions, Genetic ,Abscisic acid ,Conserved Sequence ,Plant Proteins ,chemistry.chemical_classification ,Nitrates ,Multidisciplinary ,Arabidopsis Proteins ,Catabolism ,fungi ,Gene Expression Regulation, Developmental ,food and beverages ,General Chemistry ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Enzyme ,chemistry ,Seeds ,Abscisic Acid ,Transcription Factors ,010606 plant biology & botany - Abstract
Seeds respond to multiple different environmental stimuli that regulate germination. Nitrate stimulates germination in many plants but how it does so remains unclear. Here we show that the Arabidopsis NIN-like protein 8 (NLP8) is essential for nitrate-promoted seed germination. Seed germination in nlp8 loss-of-function mutants does not respond to nitrate. NLP8 functions even in a nitrate reductase-deficient mutant background, and the requirement for NLP8 is conserved among Arabidopsis accessions. NLP8 reduces abscisic acid levels in a nitrate-dependent manner and directly binds to the promoter of CYP707A2, encoding an abscisic acid catabolic enzyme. Genetic analysis shows that NLP8-mediated promotion of seed germination by nitrate requires CYP707A2. Finally, we show that NLP8 localizes to nuclei and unlike NLP7, does not appear to be activated by nitrate-dependent nuclear retention of NLP7, suggesting that seeds have a unique mechanism for nitrate signalling., Nitrate stimulates seed germination in many plant species. Here, Yan et al. show that the Arabidopsis transcription factor NIN-like protein 8 is required to stimulate germination in response to nitrate and induces expression of an enzyme involved in ABA catabolism.
- Published
- 2016
17. Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants
- Author
-
Eiji Nambara, Kashif Mahmood, Mahmoud W. Yaish, Steven J. Rothstein, Yong Mei Bi, Kosala Ranathunge, and Ashraf El-Kereamy
- Subjects
0106 biological sciences ,CC-type ,Plant Science ,lcsh:Plant culture ,01 natural sciences ,nitrogen ,03 medical and health sciences ,chemistry.chemical_compound ,cytokinin ,Glutaredoxin ,lcsh:SB1-1110 ,Gene ,030304 developmental biology ,Original Research ,2. Zero hunger ,Genetics ,0303 health sciences ,biology ,rice ,GA ,Wild type ,food and beverages ,Glutathione ,glutaredoxin ,biology.organism_classification ,Cell biology ,chemistry ,Cytokinin ,Gibberellin ,Plant hormone ,Thioredoxin ,010606 plant biology & botany - Abstract
Glutaredoxins (GRXs) are small glutathione dependent oxidoreductases that belong to the Thioredoxin (TRX) superfamily and catalyze the reduction of disulfide bonds of their substrate proteins. Plant GRXs include three different groups based on the motif sequence, namely CPYC, CGFS, and CC-type proteins. The rice CC-type proteins, OsGRX6 was identified during the screening for genes whose expression changes depending on the level of available nitrate. Overexpression of OsGRX6 in rice displayed a semi-dwarf phenotype. The OsGRX6 overexpressors contain a higher nitrogen content than the wild type, indicating that OsGRX6 plays a role in homeostatic regulation of nitrogen use. Consistent with this, OsGRX6 overexpressors displayed delayed chlorophyll degradation and senescence compared to the wild type plants. To examine if the growth defect of these transgenic lines attribute to disturbed plant hormone actions, plant hormone levels were measured. The levels of two cytokinins (CKs), 2-isopentenyladenine and trans-zeatin, and gibberellin A1 (GA1) were increased in these lines. We also found that these transgenic lines were less sensitive to exogenously applied GA, suggesting that the increase in GA1 is a result of the feedback regulation. These data suggest that OsGRX6 affects hormone signaling and nitrogen status in rice plants.
- Published
- 2015
18. Reappraisal of nitrogen use efficiency in rice overexpressing glutamine synthetase1
- Author
-
Barry J. Shelp, Elizabeth K. Brauer, Gale G. Bozzo, Steven J. Rothstein, Yong-Mei Bi, and Amanda Rochon
- Subjects
Nitrogen ,Physiology ,Plant Science ,Oryza ,Gene Expression Regulation, Enzymologic ,Gene Expression Regulation, Plant ,Glutamate-Ammonia Ligase ,Glutamine synthetase ,Genetics ,Plant Proteins ,Panicle ,biology ,food and beverages ,Plant physiology ,Cell Biology ,General Medicine ,Herbaceous plant ,Plants, Genetically Modified ,biology.organism_classification ,Glutamine ,Mutagenesis, Insertional ,Horticulture ,Agronomy ,Shoot ,Backcrossing ,Plant Shoots - Abstract
Cytosolic glutamine synthetase (GS1) is responsible for the primary assimilation of ammonia, and a role in nitrogen (N) remobilization is implicated from its vascular localization and enhanced expression during senescence. This paper tested the hypothesis that overexpression (OX) of GS1 in rice improves utilization N use efficiency (UtE = spikelet yield/shoot N content). Three GS1 OX lines were identified using activity assays and quantitative polymerase chain reaction. Physiological analysis of the OX lines, as well as azygous and wild-type (Wt) controls, was conducted with mature plants after growth under varying nitrate conditions (non-limiting N, limiting N, transfer from non-limiting N to limiting N at panicle emergence) and growth environments (growth chamber vs greenhouse). Overall, OX lines did not differ from azygous controls in vegetative yield or shoot N content. In two of the three growth trials (i.e. the growth chamber trials) harvest index, N harvest index (spikelet N content/shoot N content) and UtE were generally enhanced in the OX lines relative to their azygous controls. These characteristics were highly correlated with percent spikelets filled and spikelet number. Thus, N partitioning in rice during grain filling could be altered by GS1 OX, resulting in improved UtE. Unfortunately, GS OX did not result in more efficient use of N under limiting N than under non-limiting N, and is therefore unlikely to result in the use of less N under field conditions. Transformation effects significantly hindered the productivity of the OX lines, but backcrossing to the Wt should overcome this.
- Published
- 2011
19. SAUR39, a Small Auxin-Up RNA Gene, Acts as a Negative Regulator of Auxin Synthesis and Transport in Rice
- Author
-
Tong Zhu, Steven J. Rothstein, Yong-Mei Bi, and Surya Kant
- Subjects
chemistry.chemical_classification ,Physiology ,fungi ,food and beverages ,Plant physiology ,Plant Science ,Meristem ,Biology ,Genetically modified rice ,Cell biology ,chemistry.chemical_compound ,chemistry ,Auxin ,Cytokinin ,Botany ,Genetics ,Gene family ,Polar auxin transport ,Abscisic acid - Abstract
The phytohormone auxin plays a critical role for plant growth by regulating the expression of a set of genes. One large auxin-responsive gene family of this type is the small auxin-up RNA (SAUR) genes, although their function is largely unknown. The expression of the rice (Oryza sativa) SAUR39 gene showed rapid induction by transient change in different environmental factors, including auxin, nitrogen, salinity, cytokinin, and anoxia. Transgenic rice plants overexpressing the SAUR39 gene resulted in lower shoot and root growth, altered shoot morphology, smaller vascular tissue, and lower yield compared with wild-type plants. The SAUR39 gene was expressed at higher levels in older leaves, unlike auxin biosynthesis, which occurs largely in the meristematic region. The transgenic plants had a lower auxin level and a reduced polar auxin transport as well as the down-regulation of some putative auxin biosynthesis and transporter genes. Biochemical analysis also revealed that transgenic plants had lower chlorophyll content, higher levels of anthocyanin, abscisic acid, sugar, and starch, and faster leaf senescence compared with wild-type plants at the vegetative stage. Most of these phenomena have been shown to be negatively correlated with auxin level and transport. Transcript profiling revealed that metabolic perturbations in overexpresser plants were largely due to transcriptional changes of genes involved in photosynthesis, senescence, chlorophyll production, anthocyanin accumulation, sugar synthesis, and transport. The lower growth and yield of overexpresser plants was largely recovered by exogenous auxin application. Taken together, the results suggest that SAUR39 acts as a negative regulator for auxin synthesis and transport.
- Published
- 2009
20. Over-expression ofSTP13, a hexose transporter, improves plant growth and nitrogen use inArabidopsis thalianaseedlings
- Author
-
R. A. Schofield, Steven J. Rothstein, Surya Kant, and Yong-Mei Bi
- Subjects
Sucrose ,Monosaccharide Transport Proteins ,Nitrogen ,Physiology ,Transgene ,Anion Transport Proteins ,Arabidopsis ,Plant Science ,Carbohydrate metabolism ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Tobacco ,Arabidopsis thaliana ,Hexose ,Biomass ,Cloning, Molecular ,Promoter Regions, Genetic ,Cells, Cultured ,Regulation of gene expression ,chemistry.chemical_classification ,Symporters ,biology ,Arabidopsis Proteins ,food and beverages ,Metabolism ,Plants, Genetically Modified ,biology.organism_classification ,Carbon ,Glucose ,chemistry ,Biochemistry ,RNA, Plant ,Seedlings - Abstract
In Arabidopsis thaliana, the regulation of hexose levels by the large monosaccharide transporter (MST) gene family influences many aspects of plant growth. The cloning and transgenic expression of one family member (STP13) enabled the manipulation of carbon (C) and nitrogen (N) metabolism in Arabidopsis. Transgenic seedlings constitutively over-expressing STP13 (STP13OX) had increased rates of glucose uptake, higher endogenous sucrose levels and accumulated more total C and biomass per plant when grown on soil-less media supplemented with 55 mM glucose and sufficient N (9 mM nitrate). Furthermore, STP13OX seedlings acquired 90% more total N than the Col-0 seedlings, and had higher levels of expression of the nitrate transporter NRT2.2. In addition, STP13OX seedlings were larger and had higher biomass than Col-0 seedlings when grown under a limiting N condition (3 mM nitrate). Transgene analysis of STP13 reveals that its gene product is localized to the plasma membrane (PM) in tobacco BY-2 suspension cells, that it encodes a functional MST in planta, and that the STP13 promoter directs GUS expression to the vasculature and to leaf mesophyll cells. This work highlights the link between C and N metabolism, demonstrating that a plant's N use may be improved by increasing the availability of C.
- Published
- 2009
21. Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene
- Author
-
Steven J. Rothstein, Raymond Yang, Andrew Schofield, Mingsheng Peng, Darryl Hudson, Yong-Mei Bi, Honglan Gu, and Rong Tsao
- Subjects
0106 biological sciences ,Anthocyanin ,Physiology ,Nitrogen ,Ubiquitin-Protein Ligases ,Mutant ,Arabidopsis ,lignin ,phosphorus limitation ,Plant Science ,adaptation ,medicine.disease_cause ,01 natural sciences ,Anthocyanins ,03 medical and health sciences ,chemistry.chemical_compound ,N limitation ,medicine ,Gene ,030304 developmental biology ,2. Zero hunger ,Regulation of gene expression ,0303 health sciences ,Mutation ,biology ,Phenylpropanoid ,Arabidopsis Proteins ,fungi ,food and beverages ,nla mutant ,Phosphorus ,biology.organism_classification ,Research Papers ,Biosynthetic Pathways ,Phenotype ,chemistry ,Biochemistry ,Gene Expression Regulation ,Flux (metabolism) ,010606 plant biology & botany - Abstract
Plants can survive a limiting nitrogen (N) supply by developing a set of N limitation adaptive responses. However, the Arabidopsis nla (nitrogen limitation adaptation) mutant fails to produce such responses, and cannot adapt to N limitation. In this study, the nla mutant was utilized to understand further the effect of NLA on Arabidopsis adaptation to N limitation. Grown with limiting N, the nla mutant could not accumulate anthocyanins and instead produced an N limitation-induced early senescence phenotype. In contrast, when supplied with limiting N and limiting phosphorus (Pi), the nla mutants accumulated abundant anthocyanins and did not show the N limitation-induced early senescence phenotype. These results support the hypothesis that Arabidopsis has a specific pathway to control N limitation-induced anthocyanin synthesis, and the nla mutation disrupts this pathway. However, the nla mutation does not affect the Pi limitation-induced anthocyanin synthesis pathway. Therefore, Pi limitation induced the nla mutant to accumulate anthocyanins under N limitation and allowed this mutant to adapt to N limitation. Under N limitation, the nla mutant had a significantly down-regulated expression of many genes functioning in anthocyanin synthesis, and an enhanced expression of genes involved in lignin production. Correspondingly, the nla mutant grown with limiting N showed a significantly lower production of anthocyanins (particularly cyanidins) and an increase in lignin contents compared with wild-type plants. These data suggest that NLA controls Arabidopsis adaptability to N limitation by channelling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis, which is important for Arabidopsis to adapt to N limitation.
- Published
- 2008
22. The Arabidopsis Halophytic RelativeThellungiella halophilaTolerates Nitrogen-Limiting Conditions by Maintaining Growth, Nitrogen Uptake, and Assimilation
- Author
-
Surya Kant, Yong-Mei Bi, Simon Barak, Steven J. Rothstein, and Elizabeth A. Weretilnyk
- Subjects
biology ,Physiology ,chemistry.chemical_element ,Plant Science ,biology.organism_classification ,Nitrate reductase ,Nitrogen ,chemistry.chemical_compound ,Nitrate ,chemistry ,Arabidopsis ,Halophyte ,Shoot ,Botany ,Genetics ,Thellungiella ,Regulator gene - Abstract
A comprehensive knowledge of mechanisms regulating nitrogen (N) use efficiency is required to reduce excessive input of N fertilizers while maintaining acceptable crop yields under limited N supply. Studying plant species that are naturally adapted to low N conditions could facilitate the identification of novel regulatory genes conferring better N use efficiency. Here, we show that Thellungiella halophila, a halophytic relative of Arabidopsis (Arabidopsis thaliana), grows better than Arabidopsis under moderate (1 mm nitrate) and severe (0.4 mm nitrate) N-limiting conditions. Thellungiella exhibited a lower carbon to N ratio than Arabidopsis under N limitation, which was due to Thellungiella plants possessing higher N content, total amino acids, total soluble protein, and lower starch content compared with Arabidopsis. Furthermore, Thellungiella had higher amounts of several metabolites, such as soluble sugars and organic acids, under N-sufficient conditions (4 mm nitrate). Nitrate reductase activity and NR2 gene expression in Thellungiella displayed less of a reduction in response to N limitation than in Arabidopsis. Thellungiella shoot GS1 expression was more induced by low N than in Arabidopsis, while in roots, Thellungiella GS2 expression was maintained under N limitation but was decreased in Arabidopsis. Up-regulation of NRT2.1 and NRT3.1 expression was higher and repression of NRT1.1 was lower in Thellungiella roots under N-limiting conditions compared with Arabidopsis. Differential transporter gene expression was correlated with higher nitrate influx in Thellungiella at low 15NO3 − supply. Taken together, our results suggest that Thellungiella is tolerant to N-limited conditions and could act as a model system to unravel the mechanisms for low N tolerance.
- Published
- 2008
23. Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA
- Author
-
Mingsheng Peng, Steven J. Rothstein, Yong-Mei Bi, and Tong Zhu
- Subjects
Nitrogen ,Ubiquitin-Protein Ligases ,Mutant ,Arabidopsis ,Plant Science ,Biology ,Protein degradation ,Anthocyanins ,Transcriptome ,Gene Expression Regulation, Plant ,Gene expression ,Genetics ,RNA, Messenger ,Photosynthesis ,Gene ,Oligonucleotide Array Sequence Analysis ,Arabidopsis Proteins ,Microarray analysis techniques ,Gene Expression Profiling ,Biological Transport ,General Medicine ,biology.organism_classification ,Ubiquitin ligase ,Biochemistry ,biology.protein ,Agronomy and Crop Science ,Genome, Plant ,Signal Transduction - Abstract
Nitrogen is an essential mineral nutrient and is required in great abundance for plant growth and development. Insufficient nitrogen triggers extensive physiological and biochemical changes in plants which constitute a set of adaptive responses to nitrogen limitation. In this study, to determine the genome-wide transcriptome response to nitrogen limitation, Arabidopsis plants were grown with limiting (3 mM) and sufficient (10 mM) nitrate, respectively, and their gene expression profiles were analyzed using Affymetrix GeneChip arrays. In addition to inducing the adaptive responses in Arabidopsis, nitrogen limitation altered the expression levels of 629 genes with 340 up-regulated and 289 down-regulated. The up-regulated group included the genes involved in protein degradation and the biosynthesis of anthocyanin and phenylpropanoids. The down-regulated group contained the genes functioning in photosynthesis and in the synthesis of nitrogenous macromolecules such as chlorophyll, proteins, amino acids and nucleotides. Numerous nitrogen limitation responsive genes encode transcription factors, signal transduction components, and proteins required for hormone synthesis and response. The Arabidopsis nitrogen limitation adaptation mutant (nla) is defective in developing the nitrogen limitation adaptive responses. The microarray analysis revealed that the absence of the functional NLA in the nla mutant extensively altered its responsive transcriptome to nitrogen limitation. In this mutant 1122 genes were up-regulated and 622 repressed. It was also found that the nla mutant phenotype was associated with the early induction of senescence-associated genes. This study presents a genome-wide view of Arabidopsis transcriptome response to nitrogen limitation and its regulation by NLA, and provides information to probe the molecular mechanism controlling plant adaptability to nitrogen limitation.
- Published
- 2007
24. A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation
- Author
-
Steven J. Rothstein, Mingsheng Peng, Carol Hannam, Yong-Mei Bi, and Honglan Gu
- Subjects
Cloning ,Genetics ,Mutation ,biology ,Mutant ,Wild type ,Cell Biology ,Plant Science ,biology.organism_classification ,medicine.disease_cause ,Ubiquitin ligase ,Cell biology ,Ubiquitin ,Arabidopsis ,biology.protein ,medicine ,Gene - Abstract
Summary Abundant nitrogen is required for the optimal growth and development of plants, while numerous biotic and abiotic factors that consume soil nitrogen frequently create a nitrogen limitation growth condition. To cope with this, plants have evolved a suite of adaptive responses to nitrogen limitation. However, the molecular mechanism governing the adaptability of plants to nitrogen limitation is totally unknown because no reported mutant defines this trait. Here we isolated an Arabidopsis mutant, nla (nitrogen limitation adaptation), and identified the NLA gene as an essential component in this molecular mechanism. Supplied with insufficient inorganic nitrogen (nitrate or ammonium), the nla mutant failed to develop the essential adaptive responses to nitrogen limitation, but senesced much earlier and more rapidly than did the wild type. Under other stress conditions including low phosphorus nutrient, drought and high temperature, the nla mutant did not show this early senescence phenotype, but closely resembled the wild type in growth and development. Map-based cloning of NLA revealed that this gene encodes a RING-type ubiquitin ligase, and nla is a deletion mutation which does not code for the RING domain in the NLA protein. The NLA protein is localized to the nuclear speckles, where this protein interacts with the Arabidopsis ubiquitin conjugase 8 (AtUBC8). In the nla mutant, the deletion of the RING domain from NLA altered its subcellular localization, disrupted the interaction between NLA and AtUBC8 and caused the early senescence phenotype induced by low inorganic nitrogen. All the results indicate that NLA is a positive regulator for the development of the adaptability of Arabidopsis to nitrogen limitation.
- Published
- 2007
25. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution
- Author
-
Eiji Nambara, Steven J. Rothstein, Guangwen Lu, Viktoriya Coneva, Kashif Mahmood, José A. Casaretto, Shan Ying, Yong-Mei Bi, and Fang Liu
- Subjects
0106 biological sciences ,Auxin efflux ,Crops, Agricultural ,Arabidopsis ,Tiller (botany) ,Plant Science ,Root system ,Biology ,Endoplasmic Reticulum ,01 natural sciences ,Plant Roots ,03 medical and health sciences ,Auxin ,Gene Expression Regulation, Plant ,Botany ,Genetics ,Homeostasis ,Biomass ,Phylogeny ,030304 developmental biology ,Panicle ,Plant Proteins ,2. Zero hunger ,chemistry.chemical_classification ,0303 health sciences ,Oryza sativa ,Auxin homeostasis ,Indoleacetic Acids ,fungi ,food and beverages ,Biological Transport ,Oryza ,Cell Biology ,15. Life on land ,Plants, Genetically Modified ,chemistry ,Shoot ,010606 plant biology & botany - Abstract
Plant architecture attributes such as tillering, plant height and panicle size are important agronomic traits that determine rice (Oryza sativa) productivity. Here, we report that altered auxin content, transport and distribution affect these traits, and hence rice yield. Overexpression of the auxin efflux carrier-like gene OsPIN5b causes pleiotropic effects, mainly reducing plant height, leaf and tiller number, shoot and root biomass, seed-setting rate, panicle length and yield parameters. Conversely, reduced expression of OsPIN5b results in higher tiller number, more vigorous root system, longer panicles and increased yield. We show that OsPIN5b is an endoplasmic reticulum (ER) -localized protein that participates in auxin homeostasis, transport and distribution in vivo. This work describes an example of an auxin-related gene where modulating its expression can simultaneously improve plant architecture and yield potential in rice, and reveals an important effect of hormonal signaling on these traits.
- Published
- 2014
26. Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity
- Author
-
Steven J. Rothstein, Yu Zhang, Yong-Mei Bi, Rong Zhao, Tong Zhu, and Tara Signorelli
- Subjects
Mutation ,Mutant ,Cell Biology ,Plant Science ,Biology ,biology.organism_classification ,medicine.disease_cause ,Molecular biology ,Gene expression profiling ,Arabidopsis ,Gene expression ,Genetics ,medicine ,Gene family ,GATA transcription factor ,Gene - Abstract
The Arabidopsis GATA transcription factor family has 30 members, the biological function of most of which is poorly understood. Homozygous T-DNA insertion lines for 23 of the 30 members were identified and analyzed. Genetic screening of the insertion lines in defined growth conditions revealed one line with an altered phenotype, while the other lines showed no obvious change. This line, SALK_001778, has a T-DNA insertion in the second exon of At5g56860 which prevents the expression of the GATA domain. Genetic analysis of the mutant demonstrated that the phenotypic change is caused by a single gene effect and is recessive to the wild-type allele. In wild-type plants, the expression of At5g56860 is shoot-specific, occurs at an early stage of development and is inducible by nitrate. Loss of expression of At5g56860 in the loss-of-function mutant plants resulted in reduced chlorophyll levels. A transcript profiling experiment revealed that a considerable proportion of genes downregulated in the loss-of-function mutants are involved in carbon metabolism and At5g56860 is thus designated GNC (GATA, nitrate-inducible, carbon metabolism-involved). gnc mutants with no GNC expression are more sensitive to exogenous glucose, and two hexose transporter genes, with a possible connection to glucose signaling, are significantly downregulated, while GNC over-expressing transgenic plants upregulate their expression and are less sensitive to exogenous glucose. These observations suggest a function for GNC in regulating carbon and nitrogen metabolism.
- Published
- 2005
27. The challenges of commercializing second-generation transgenic crop traits necessitate the development of international public sector research infrastructure
- Author
-
Mei Han, Allen G. Good, Viktoriya Coneva, Steven J. Rothstein, and Yong-Mei Bi
- Subjects
Crops, Agricultural ,Insecta ,Public Sector ,Physiology ,business.industry ,Natural resource economics ,Nitrogen ,Public sector ,Environmental resource management ,Plant Science ,Breeding ,Plants, Genetically Modified ,Droughts ,Phenotype ,Work (electrical) ,Plant species ,Animals ,business ,Biotechnology ,Herbicide Resistance - Abstract
It has been 30 years since the first transformation of a gene into a plant species, and since that time a number of biotechnology products have been developed, with the most important being insect- and herbicide-resistant crops. The development of second-generation products, including nutrient use efficiency and tolerance to important environmental stressors such as drought, has, up to this time, been less successful. This is in part due to the inherent complexities of these traits and in part due to limitations in research infrastructure necessary for public sector researchers to test their best ideas. Here we discuss lessons from previous work in the generation of the first-generation traits, as well as work from our labs and others on identifying genes for nitrogen use efficiency. We then describe some of the issues that have impeded rapid progress in this area. Finally, we propose the type of public sector organization that we feel is necessary to make advances in important second-generation traits such as nitrogen use efficiency.
- Published
- 2014
28. The AtPP gene of the Brassica napus S locus region is specifically expressed in the stigma and encodes a protein similar to a methyltransferase involved in plant defense
- Author
-
Yong-Mei Bi, Yuhai Cui, Norbert Brugière, and Steven J. Rothstein
- Subjects
Genetics ,biology ,Protein family ,Nucleic acid sequence ,food and beverages ,Cell Biology ,Plant Science ,biology.organism_classification ,Homology (biology) ,Arabidopsis ,Gene expression ,Gene family ,Gene ,Pollen-pistil interaction - Abstract
Self-incompatibility (SI) in Brassica is controlled by the S locus. The specificity of the SI response is controlled on the stigma side by the S receptor kinase (SRK) and on the pollen side by the SCR (S locus cysteine-rich) protein, but other proteins might be involved in the process of self-pollen rejection. In this study, we show that the AtPP gene linked to the S locus of Brassica napus is expressed in the stigmas of SI lines. AtPP has a developmental pattern of expression similar to the SRK gene. The AtPP protein has similarity with members of an Arabidopsis protein family and with an S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, which is a plant defense-related protein of Clarkia breweri representing a new class of methyltransferases. A member of the AtPP gene family is present in the homeolog region of the S locus in Arabidopsis. Therefore, this gene might have co-evolved with S genes from an ancestral S locus of Brassicaceae. Possible functions of the AtPP protein in the self-recognition process are discussed.
- Published
- 2001
29. Transformation of Arabidopsis with a Brassica SLG/SRK region and ARC1 gene is not sufficient to transfer the self-incompatibility phenotype
- Author
-
N. Brugière, Steven J. Rothstein, Daphne R. Goring, Yong-Mei Bi, and Yuhai Cui
- Subjects
DNA, Bacterial ,Transcription, Genetic ,Ubiquitin-Protein Ligases ,Transgene ,Genetic Vectors ,Restriction Mapping ,Arabidopsis ,Brassica ,Genetically modified crops ,Transformation, Genetic ,Genetics ,Molecular Biology ,Gene ,Glycoproteins ,Plant Proteins ,biology ,fungi ,food and beverages ,Plant transformation vector ,Plants, Genetically Modified ,biology.organism_classification ,Phenotype ,Crucifer ,Carrier Proteins ,Protein Kinases ,Rhizobium - Abstract
Self-incompatibility (SI) promotes outbreeding in flowering plants, and in Brassica SI is genetically controlled by the S locus. Self-incompatible Brassica and self-fertile Arabidopsis belong to the same crucifer family. In addition, a comparative analysis reveals a high degree of microsynteny between the B. campestris S locus and its homologous region in Arabidopsis--with the notable exception that the Brassica SI genes, SLG and SRK, are missing. Brassica ARC1 encodes a component of the SRK signal transduction pathway leading to self-pollen rejection, and no closely related ARC1 homolog has been identified in Arabidopsis. The purpose of the research reported here was to introduce Brassica SI components into Arabidopsis in an attempt to compensate for the missing genes and to investigate whether the SI phenotype can be transferred. Inserts of approximately 40 kb from the fosmid clones F20 and F22, which span the B. napus W1 SLG-SRK region, were cloned into the plant transformation vector pBIBAC2. Transgenic plants were generated that expressed the Brassica SI genes in the flower buds. In addition, the endogenous, SLG-like, gene AtS1 was not co-suppressed by the Brassica SLG transgene. No SI phenotype was observed among the T1 BIBAC2-F20 and BIBAC2-F22 transgenic plants. When the ARC1 gene was transformed into BIBAC2-F20 or BIBAC2-F22 plants, the resulting BIBAC2-F20-ARC1 and BIBAC2-F22-ARC1 plants still set seeds normally, and no rejection response was observed when self-incompatible B. napus W1 pollen was placed on BIBAC2-F20-ARC1 or BIBAC2-F22-ARC1 Arabidopsis stigmas. Taken together, our results suggest that complementing Arabidopsis genome with Brassica SLG, SRK and ARC1 genes is unlikely to be sufficient to transfer the SI phenotype.
- Published
- 2000
30. Cell-specific expression of salicylate hydroxylase in an attempt to separate localized HR and systemic signalling establishing SAR in tobacco
- Author
-
Yong-Mei Bi, Luis A. J. Mur, John Draper, Anne Louise Maddison, and Robert M. Darby
- Subjects
Transgene ,Nicotiana tabacum ,fungi ,food and beverages ,Soil Science ,Plant Science ,Biology ,biology.organism_classification ,Virology ,Cell biology ,body regions ,Lesion ,chemistry.chemical_compound ,chemistry ,Gene expression ,medicine ,Tobacco mosaic virus ,Phloem ,medicine.symptom ,skin and connective tissue diseases ,Agronomy and Crop Science ,Molecular Biology ,Salicylic acid ,Systemic acquired resistance - Abstract
There is conflicting evidence concerning the nature of the long-distance signal responsible for establishing the systemic acquired resistance (SAR) state following a local response to an incompatible plant/pathogen interaction. We outline standard inoculation procedures and terminology for experiments used to characterize SAR in Nicotiana tabacum and show that leaf development (age) has dramatic affects on TMV lesion size which needs to be taken into account in experimental design. TMV infection was more efficient at inducing SAR than primary infection with avirulent bacteria. We have examined the effect on SAR induction of altering the accumulation of salicylic acid (SA), through the expression of a salicylate hydroxylase gene (SH-L), in different phases of lesion development using the hydrogen peroxide-responsive AoPR1 promoter and the salicylate-responsive PR1a promoter. Suppression of SA accumulation during the early phases of lesion development in AoPR1-SH-L transgenic tobacco resulted in an attenuated form of SAR compared to wild-type plants, whereas SAR was not exhibited in PR1a-SH-L plants. However, interpretation of data from these experiments was complicated by virus escape from inoculated leaves. Using a GUS reporter it was discovered that the CaMV35S promoter was not expressed constitutively in all cell types of petioles and stems, particularly phloem tissue, whereas the PR1a promoter demonstrated induced expression in the phloem following TMV infection. We suggest two hypotheses for why PR1a-SH-L transgenics do not display SAR: either the systemic expression of PR1a-SH-L is sufficient to suppress SAR, or SA synthesis or translocation in the phloem is essential for SAR.
- Published
- 2000
31. Compromising early salicylic acid accumulation delays the hypersensitive response and increases viral dispersal during lesion establishment in TMV-infected tobacco
- Author
-
Simon Firek, John Draper, Robert Darby, Luis A. J. Mur, and Yong-Mei Bi
- Subjects
Hypersensitive response ,Programmed cell death ,Time Factors ,Cell Survival ,Recombinant Fusion Proteins ,Plant Science ,Polymerase Chain Reaction ,Mixed Function Oxygenases ,Lesion ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Tobacco ,Gene expression ,Genetics ,Tobacco mosaic virus ,medicine ,DNA Primers ,Glucuronidase ,Plant Diseases ,Nicotiana ,biology ,Tobamovirus ,Cell Biology ,Plants, Genetically Modified ,biology.organism_classification ,Virology ,Molecular biology ,Salicylates ,Artificial Gene Fusion ,Tobacco Mosaic Virus ,Plants, Toxic ,chemistry ,medicine.symptom ,Salicylic Acid ,Salicylic acid - Abstract
Summary To investigate the role of salicylic acid (SA) in the hypersensitive response (HR) its accumulation was compromised during different phases of lesion development by differential expression of a salicylate hydroxylase gene (SH-L). Constitutive suppression of SA accumulation was achieved by expression of a gene fusion between the CaMV35S promoter (35S) and SH-L. Using the H2O2-responsive AoPR1 promoter to drive SH-L SA accumulation could be compromised at an early stage, on lesion formation and possibly prior to visible necrosis, whilst use of the salicylate-responsive PR1a promoter reduced SA accumulation at a later stage as lesions expand. TMV infection of 35S-SH-L and AoPR1-SH-L, but not PR1a-SH-L, tobacco resulted in significantly greater rates of lesion growth than in wild-type tobacco. TMV was detected in asymptomatic tissue surrounding lesions only in 35S-SH-L and AoPR1-SH-L lines; subsequently these transgenic lines exhibited a ‘spreading-necrosis’ originating from the lesion which entered the stem and eventually other leaves, a phenotype which could be correlated with the presence of TMV particles. Analysis of TMV-infected and ‘temperature-shifted’ tobacco indicated that both 35S-SH-L and AoPR1-SH-L, but not PR1a-SH-L, transgenics exhibited delayed cell-death compared to wild-type infections. We propose that the SH-L phenotypes indicate that early SA accumulation is a major factor in preventing viral escape, via mechanism(s) which may include influencing the rate of host-cell death and, possibly, an effect on viral function.
- Published
- 1997
32. Somatic embryogenesis and Agrobacterium -mediated transformation system for scented geraniums ( Pelargonium sp. 'Frensham')
- Author
-
Sankaran KrishnaRaj, Yong-Mei Bi, and Praveen K. Saxena
- Subjects
Somatic embryogenesis ,Agrobacterium ,fungi ,food and beverages ,Kanamycin ,Plant Science ,Pelargonium ,Agrobacterium tumefaciens ,Biology ,biology.organism_classification ,Transformation (genetics) ,Murashige and Skoog medium ,Micropropagation ,Botany ,Genetics ,medicine ,medicine.drug - Abstract
Plant regeneration via somatic embryogenesis was achieved from leaf petioles of Pelargonium sp. `Frensham' cultured on Murashige and Skoog medium containing 15 μM N6-benzyladenine, and 5 μM α-naphthaleneacetic acid (NAA). More than 80% of these somatic embryos converted into plants when isolated and cultured on Murashige and Skoog medium supplemented with 15 μM NAA. Stable transgenic plants were obtained by co-cultivation of the petioles (prior to culture) with Agrobacterium tumefaciens strains LBA4404 (harbouring a binary vector pBI121 carrying the nptII and gus genes) and LBG66 (harbouring a binary plasmid pJQ418 carrying the gus/int:nptII fusion gene). Transformants were selected using kanamycin and transformation was verified by β-glucuronidase histochemical assay and polymerase chain reaction. Southern analysis further confirmed the integration of these genes into the genome of transgenic plants. We report here for the first time, an Agrobacterium-mediated model transformation system coupled with regeneration via somatic embryogenesis for production of transgenics in Pelargonium sp.
- Published
- 1997
33. The Rice R2R3-MYB Transcription Factor OsMYB55 Is Involved in the Tolerance to High Temperature and Modulates Amino Acid Metabolism
- Author
-
Allen G. Good, Kosala Ranathunge, Perrin H. Beatty, Ashraf El-Kereamy, Steven J. Rothstein, and Yong Mei Bi
- Subjects
0106 biological sciences ,Arginine ,Agricultural Biotechnology ,lcsh:Medicine ,Plant Science ,01 natural sciences ,Gene Expression Regulation, Plant ,Molecular Cell Biology ,Amino Acids ,lcsh:Science ,Promoter Regions, Genetic ,Phylogeny ,gamma-Aminobutyric Acid ,Cellular Stress Responses ,Plant Proteins ,2. Zero hunger ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,Genetically Modified Organisms ,Temperature ,Agriculture ,Amino acid ,Chemistry ,Organic Acids ,Biochemistry ,Research Article ,Biotechnology ,Signal Transduction ,Transcriptional Activation ,Cereals ,Glutamic Acid ,Crops ,Biology ,Molecular Genetics ,03 medical and health sciences ,Stress, Physiological ,Glutamine synthetase ,Plant-Environment Interactions ,Genetics ,Gene Regulation ,Proline ,Heat shock ,030304 developmental biology ,Glutamine amidotransferase ,Plant Ecology ,Gene Expression Profiling ,lcsh:R ,Organic Chemistry ,Oryza ,Metabolism ,Glutamic acid ,chemistry ,lcsh:Q ,Rice ,Transcriptome ,Heat-Shock Response ,010606 plant biology & botany ,Transcription Factors - Abstract
Temperatures higher than the optimum negatively affects plant growth and development. Tolerance to high temperature is a complex process that involves several pathways. Understanding this process, especially in crops such as rice, is essential to prepare for predicted climate changes due to global warming. Here, we show that OsMYB55 is induced by high temperature and overexpression of OsMYB55 resulted in improved plant growth under high temperature and decreased the negative effect of high temperature on grain yield. Transcriptome analysis revealed an increase in expression of several genes involved in amino acids metabolism. We demonstrate that OsMYB55 binds to the promoter regions of target genes and directly activates expression of some of those genes including glutamine synthetase (OsGS1;2) glutamine amidotransferase (GAT1) and glutamate decarboxylase 3 (GAD3). OsMYB55 overexpression resulted in an increase in total amino acid content and of the individual amino acids produced by the activation of the above mentioned genes and known for their roles in stress tolerance, namely L-glutamic acid, GABA and arginine especially under high temperature condition. In conclusion, overexpression of OsMYB55 improves rice plant tolerance to high temperature, and this high tolerance is associated with enhanced amino acid metabolism through transcription activation.
- Published
- 2012
34. Exploring the molecular and metabolic factors contributing to the adaptation of maize seedlings to nitrate limitation
- Author
-
David Guevara, Xi Chen, Ashraf El-Kereamy, Yong-Mei Bi, and Steven J. Rothstein
- Subjects
biology ,business.industry ,seedlings ,nitrogen limitation ,Plant Science ,lcsh:Plant culture ,biology.organism_classification ,Zea mays ,N fertilizer ,Biotechnology ,chemistry.chemical_compound ,NUE ,Nitrate ,chemistry ,Agronomy ,Nitrate transport ,Seedling ,N application ,Genotype ,lcsh:SB1-1110 ,Transcriptional analysis ,business ,Sugar ,Original Research - Abstract
Crop production on soils containing sub-optimal levels of nitrogen (N) severely compromises yield potential. The development of plant varieties displaying high N use efficiency (NUE) will optimize N fertilizer use and reduce the environmental damage caused by excess N application. Maize is one of the most important crops cultivated worldwide. Identification of the genotypes with an enhanced NUE in the field is both time and resource consuming and sometime is difficult due to the regulation in the biotechnology programs. Identification of traits associated with adaptation to N limitation at an early vegetative stage which could reflect NUE at maturity is in need. We developed a hydroponic growth system and used it to test two genotypes that were different in their NUE at maturity under N limitation. One genotype SRG-200 showed a higher NUE than the other genotype SRG-100 and we used its hybrid SRG-150 as a reference for NUE. A number of phenotypic, molecular, and metabolic factors were tested using these three genetic lines at an early vegetative stage to determine which of these could be more indicative of predicting improved NUE at an early seedling stage. These include a transcriptional analysis which showed that the higher NUE in SRG-200 genotype is associated with higher transcript levels for the genes involved in nitrate transport, N assimilation, and GS and that the SRG-200 genotype maintained higher sugar content in leaves. Those identified in this study could be useful indicators for selecting promising maize lines at early stages to help develop elite varieties showing an enhanced NUE.
- Published
- 2011
35. Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots
- Author
-
Wen-Xue Li, Yong-Mei Bi, Sihui Zhong, Zhenhua Xu, Chuanxiao Xie, Shihuang Zhang, Xinhai Li, and Steven J. Rothstein
- Subjects
0106 biological sciences ,Time Factors ,Plant Science ,01 natural sciences ,Plant Roots ,Transcriptome ,chemistry.chemical_compound ,RNA interference ,Nitrate ,Gene Expression Regulation, Plant ,Plant Genomics ,Arabidopsis thaliana ,Gene Regulatory Networks ,2. Zero hunger ,Regulation of gene expression ,0303 health sciences ,Multidisciplinary ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Agriculture ,Genomics ,RNA, Plant ,Medicine ,Epigenetics ,DNA microarray ,Genome, Plant ,Research Article ,Limiting factor ,Nitrogen ,Science ,Genes, Plant ,Zea mays ,Molecular Genetics ,03 medical and health sciences ,Genetics ,Gene Regulation ,Biology ,030304 developmental biology ,Nitrates ,business.industry ,Abiotic stress ,Gene Expression Profiling ,Reproducibility of Results ,Computational Biology ,biology.organism_classification ,Sustainable Agriculture ,Biotechnology ,Plant Leaves ,MicroRNAs ,chemistry ,Plant Biotechnology ,business ,Function (biology) ,010606 plant biology & botany - Abstract
BackgroundNitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation.Methodology/principal findingsIn this study, we used the SmartArray™ and GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. Nine miRNA families (miR164, miR169, miR172, miR397, miR398, miR399, miR408, miR528, and miR827) were identified in leaves, and nine miRNA families (miR160, miR167, miR168, miR169, miR319, miR395, miR399, miR408, and miR528) identified in roots. They were verified by real time stem loop RT-PCR, and some with additional time points of nitrate limitation. The miRNAs identified showed overlapping or unique responses to chronic and transient nitrate limitation, as well as tissue specificity. The potential target genes of these miRNAs in maize were identified. The expression of some of these was examined by qRT-PCR. The potential function of these miRNAs in responding to nitrate limitation is described.Conclusions/significanceGenome-wide miRNAs responding to nitrate limiting conditions in maize leaves and roots were identified. This provides an insight into the timing and tissue specificity of the transcriptional regulation to low nitrate availability in maize. The knowledge gained will help understand the important roles miRNAs play in maize responding to a nitrogen limiting environment and eventually develop strategies for the improvement of maize genetics.
- Published
- 2011
36. Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency
- Author
-
Yong-Mei Bi, Steven J. Rothstein, and Surya Kant
- Subjects
Crops, Agricultural ,Physiology ,Nitrogen ,chemistry.chemical_element ,Plant Development ,Plant Science ,Agricultural engineering ,Biology ,Breeding ,Environment ,Genes, Plant ,Plant Roots ,Crop ,Sustainable agriculture ,Fertilizers ,Nitrogen cycle ,Gene Expression Profiling ,fungi ,food and beverages ,Assimilation (biology) ,Plants ,Adaptation, Physiological ,Plant development ,Transcription profiling ,Agronomy ,chemistry ,Genetic Engineering - Abstract
Development of genetic varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Generally, NUE can be divided into two parts. First, assimilation efficiency involves nitrogen (N) uptake and assimilation and second utilization efficiency involves N remobilization. Understanding the mechanisms regulating these processes is crucial for the improvement of NUE in crop plants. One important approach is to develop an understanding of the plant response to different N regimes, especially to N limitation, using various methods including transcription profiling, analysing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions. One can then attempt to improve NUE in crop plants using the knowledge gained from these studies. There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review. Increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required to achieve this.
- Published
- 2010
37. A mutation in NLA, which encodes a RING-type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation
- Author
-
Mingsheng, Peng, Carol, Hannam, Honglan, Gu, Yong-Mei, Bi, and Steven J, Rothstein
- Subjects
Cell Nucleus ,Arabidopsis Proteins ,Nitrogen ,Reverse Transcriptase Polymerase Chain Reaction ,Recombinant Fusion Proteins ,Ubiquitin-Protein Ligases ,Molecular Sequence Data ,Arabidopsis ,Adaptation, Physiological ,Gene Expression Regulation, Plant ,Two-Hybrid System Techniques ,Mutation ,Onions ,Ubiquitin-Conjugating Enzymes ,Amino Acid Sequence ,Protein Binding - Abstract
Abundant nitrogen is required for the optimal growth and development of plants, while numerous biotic and abiotic factors that consume soil nitrogen frequently create a nitrogen limitation growth condition. To cope with this, plants have evolved a suite of adaptive responses to nitrogen limitation. However, the molecular mechanism governing the adaptability of plants to nitrogen limitation is totally unknown because no reported mutant defines this trait. Here we isolated an Arabidopsis mutant, nla (nitrogen limitation adaptation), and identified the NLA gene as an essential component in this molecular mechanism. Supplied with insufficient inorganic nitrogen (nitrate or ammonium), the nla mutant failed to develop the essential adaptive responses to nitrogen limitation, but senesced much earlier and more rapidly than did the wild type. Under other stress conditions including low phosphorus nutrient, drought and high temperature, the nla mutant did not show this early senescence phenotype, but closely resembled the wild type in growth and development. Map-based cloning of NLA revealed that this gene encodes a RING-type ubiquitin ligase, and nla is a deletion mutation which does not code for the RING domain in the NLA protein. The NLA protein is localized to the nuclear speckles, where this protein interacts with the Arabidopsis ubiquitin conjugase 8 (AtUBC8). In the nla mutant, the deletion of the RING domain from NLA altered its subcellular localization, disrupted the interaction between NLA and AtUBC8 and caused the early senescence phenotype induced by low inorganic nitrogen. All the results indicate that NLA is a positive regulator for the development of the adaptability of Arabidopsis to nitrogen limitation.
- Published
- 2007
38. AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis
- Author
-
Steven J. Rothstein, Yong-Mei Bi, Yuhai Cui, and Mingsheng Peng
- Subjects
DNA, Complementary ,DNA, Plant ,Mutant ,Arabidopsis ,Plant Science ,Flowers ,Biology ,Plant Roots ,Flowering Locus C ,Genetics ,Epigenetics ,DNA Primers ,Base Sequence ,Indoleacetic Acids ,Reverse Transcriptase Polymerase Chain Reaction ,fungi ,Wild type ,food and beverages ,Cell Biology ,DNA Methylation ,biology.organism_classification ,Chromatin ,Methyl-CpG-binding domain ,DNA methylation ,Dinucleoside Phosphates ,Plant Shoots - Abstract
*Summary The functional characterization of mammalian proteins containing a methyl-CpG-binding domain (MBD) has revealed that MBD proteins can decipher the epigenetic information encoded by DNA methylation, and integrate DNA methylation, modification of chromatin structure and repression of gene expression. The Arabidopsis genome has 13 putative genes encoding MBD proteins, and no specific biological function has been defined for any AtMBD genes. In this study, we identified three T-DNA insertion mutant alleles at the AtMBD9 locus, and found that all of them exhibited obvious developmental abnormalities. First, the atmbd9 mutants flowered significantly earlier than wild-type plants. The expression of FLOWERING LOCUS C (FLC), a major repressor of Arabidopsis flowering, was markedly attenuated by the AtMBD9 mutations. This FLC transcription reduction was associated with a significant decrease in the acetylation level in histone H3 and H4 of FLC chromatin in the atmbd9 mutants. Secondly, the atmbd9 mutants produced more shoot branches by increasing the outgrowth of axillary buds when compared with wild-type plants. The two known major factors controlling the outgrowth of axillary buds in Arabidopsis, auxin and the more axillary growth (MAX) pathway, were found not to be involved in producing this enhanced shoot branching phenotype in atmbd9 mutants, indicating that AtMBD9 may regulate a novel pathway to control shoot branching. This pathway is not related to FLCexpression as over-expression of FLCin atmbd9-2 restored itsflowering time to one similar to that of the wild type, but did not alter the shoot branching phenotype.
- Published
- 2006
39. Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity
- Author
-
Yong-Mei, Bi, Yu, Zhang, Tara, Signorelli, Rong, Zhao, Tong, Zhu, and Steven, Rothstein
- Subjects
Chlorophyll ,DNA, Bacterial ,Nitrates ,Base Sequence ,DNA, Plant ,Arabidopsis Proteins ,Nitrogen ,Gene Expression Profiling ,Arabidopsis ,Drug Resistance ,Gene Expression ,Genes, Plant ,GATA Transcription Factors ,Carbon ,Mutagenesis, Insertional ,Glucose ,Phenotype ,Multigene Family - Abstract
The Arabidopsis GATA transcription factor family has 30 members, the biological function of most of which is poorly understood. Homozygous T-DNA insertion lines for 23 of the 30 members were identified and analyzed. Genetic screening of the insertion lines in defined growth conditions revealed one line with an altered phenotype, while the other lines showed no obvious change. This line, SALK_001778, has a T-DNA insertion in the second exon of At5g56860 which prevents the expression of the GATA domain. Genetic analysis of the mutant demonstrated that the phenotypic change is caused by a single gene effect and is recessive to the wild-type allele. In wild-type plants, the expression of At5g56860 is shoot-specific, occurs at an early stage of development and is inducible by nitrate. Loss of expression of At5g56860 in the loss-of-function mutant plants resulted in reduced chlorophyll levels. A transcript profiling experiment revealed that a considerable proportion of genes downregulated in the loss-of-function mutants are involved in carbon metabolism and At5g56860 is thus designated GNC (GATA, nitrate-inducible, carbon metabolism-involved). gnc mutants with no GNC expression are more sensitive to exogenous glucose, and two hexose transporter genes, with a possible connection to glucose signaling, are significantly downregulated, while GNC over-expressing transgenic plants upregulate their expression and are less sensitive to exogenous glucose. These observations suggest a function for GNC in regulating carbon and nitrogen metabolism.
- Published
- 2005
40. Functional Characterization of the Rice UDP-glucose 4-epimerase 1, OsUGE1: A Potential Role in Cell Wall Carbohydrate Partitioning during Limiting Nitrogen Conditions
- Author
-
Ashraf El-Kereamy, David Guevara, Yong Mei-Bi, Mahmoud W. Yaish, and Steven J. Rothstein
- Subjects
0106 biological sciences ,Sucrose ,Agricultural Biotechnology ,Glycobiology ,lcsh:Medicine ,Carbohydrate Biosynthesis ,Plant Science ,Biochemistry ,01 natural sciences ,UDPglucose 4-Epimerase ,chemistry.chemical_compound ,Cell Wall ,Gene Expression Regulation, Plant ,Molecular Cell Biology ,lcsh:Science ,Plant Proteins ,2. Zero hunger ,chemistry.chemical_classification ,0303 health sciences ,Multidisciplinary ,Plant Biochemistry ,Organic Compounds ,Genetically Modified Organisms ,food and beverages ,Agriculture ,Plants, Genetically Modified ,Chemistry ,Physical Sciences ,Carbohydrate Metabolism ,Genetic Engineering ,Plant Shoots ,Research Article ,Biotechnology ,Uridine Diphosphate Glucose ,Nitrogen ,Carbohydrates ,Genetically Modified Foods ,Crops ,Carbohydrate metabolism ,Biology ,Biosynthesis ,Polysaccharide ,Cell wall ,03 medical and health sciences ,Botany ,Cellulose ,030304 developmental biology ,Oryza sativa ,lcsh:R ,Chemical Compounds ,Biology and Life Sciences ,Oryza ,Cell Biology ,Carbohydrate ,Genetically modified rice ,chemistry ,lcsh:Q ,Plant Biotechnology ,Rice ,Cereal Crops ,010606 plant biology & botany - Abstract
Plants grown under inadequate mineralized nitrogen (N) levels undergo N and carbon (C) metabolic re-programming which leads to significant changes in both soluble and insoluble carbohydrate profiles. However, relatively little information is available on the genetic factors controlling carbohydrate partitioning during adaptation to N-limitation conditions in plants. A gene encoding a uridine-diphospho-(UDP)-glucose 4-epimerase (OsUGE-1) from rice (Oryza sativa) was found to be N-responsive. We developed transgenic rice plants to constitutively over-express the OsUGE-1 gene (OsUGE1-OX1-2). The transgenic rice lines were similar in size to wild-type plants at the vegetative stage and at maturity regardless of the N-level tested. However, OsUGE1-OX lines maintained 18-24% more sucrose and 12-22% less cellulose in shoots compared to wild-type when subjected to sub-optimal N-levels. Interestingly, OsUGE1-OX lines maintained proportionally more galactose and glucose in the hemicellulosic polysaccharide profile of plants compared to wild-type plants when grown under low N. The altered cell wall C-partitioning during N-limitation in the OsUGE1-OX lines appears to be mediated by OsUGE1 via the repression of the cellulose synthesis associated genes, OsSus1, OsCesA4, 7, and 9. This relationship may implicate a novel control point for the deposition of UDP-glucose to the complex polysaccharide profiles of rice cell walls. However, a direct relationship between OsUGE1 and cell wall C-partitioning during N-limitation requires further investigation.
- Published
- 2014
41. A novel strategy for regulated expression of a cytotoxic gene
- Author
-
Yong-Mei Bi, Steven J. Rothstein, and Alan G. Wildeman
- Subjects
Programmed cell death ,Tetracycline ,Cell Survival ,Recombinant Fusion Proteins ,Green Fluorescent Proteins ,Cytomegalovirus ,Transfection ,Cell Line ,Transactivation ,Ribonucleases ,Bacterial Proteins ,Gene expression ,Genetics ,medicine ,Humans ,Cytotoxicity ,Luciferases ,Promoter Regions, Genetic ,Gene ,Barnase ,biology ,General Medicine ,Molecular biology ,Luminescent Proteins ,Gene Expression Regulation ,biology.protein ,Trans-Activators ,Barstar ,medicine.drug ,Plasmids - Abstract
The tetracycline (Tet) transactivator system is a powerful promoter system to control gene expression. However, expression of a cytotoxic gene in this system has been limited due to the lethal effect caused by low levels of basal expression of the toxic gene. In this report, we describe a novel strategy to express a toxic gene using the Tet system. The barstar gene is placed downstream of a minimal promoter and the barnase gene downstream of the tetracycline responsive element minimal promoter. When barnase is expressed at a basal level, its toxicity in human cell culture is offset by the similar basal level expression of barstar. However, when the barnase expression is induced with the transactivator protein, its overproduction leads to cell death. Therefore, this strategy allows cytotoxicity to be effectively regulated by tetracycline.
- Published
- 2001
42. Expression of OsMYB55 in maize activates stress-responsive genes and enhances heat and drought tolerance.
- Author
-
Casaretto, José A., El-kereamy, Ashraf, Bin Zeng, Stiegelmeyer, Suzy M., Xi Chen, Yong-Mei Bi, and Rothstein, Steven J.
- Subjects
CORN genetics ,EFFECT of heat on plants ,DROUGHT tolerance ,TRANSGENIC plants ,RNA sequencing - Abstract
Background: Plant response mechanisms to heat and drought stresses have been considered in strategies for generating stress tolerant genotypes, but with limited success. Here, we analyzed the transcriptome and improved tolerance to heat stress and drought of maize plants over-expressing the OsMYB55 gene. Results: Over-expression of OsMYB55 in maize decreased the negative effects of high temperature and drought resulting in improved plant growth and performance under these conditions. This was evidenced by the higher plant biomass and reduced leaf damage exhibited by the transgenic lines compared to wild type when plants were subjected to individual or combined stresses and during or after recovery from stress. A global transcriptomic analysis using RNA sequencing revealed that several genes induced by heat stress in wild type plants are constitutively up-regulated in OsMYB55 transgenic maize. In addition, a significant number of genes up-regulated in OsMYB55 transgenic maize under control or heat treatments have been associated with responses to abiotic stresses including high temperature, dehydration and oxidative stress. The latter is a common and major consequence of imposed heat and drought conditions, suggesting that this altered gene expression may be associated with the improved stress tolerance in these transgenic lines. Functional annotation and enrichment analysis of the transcriptome also pinpoint the relevance of specific biological processes for stress responses. Conclusions: Our results show that expression of OsMYB55 can improve tolerance to heat stress and drought in maize plants. Enhanced expression of stress-associated genes may be involved in OsMYB55-mediated stress tolerance. Possible implications for the improved tolerance to heat stress and drought of OsMYB55 transgenic maize are discussed. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
43. Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants.
- Author
-
El-Kereamy, Ashraf, Yong-Mei Bi, Mahmood, Kashif, Ranathunge, Kosala, Yaish, Mahmoud W., Nambara, Eiji, and Rothstein, Steven J.
- Subjects
RICE genetics ,GENETIC overexpression ,GLUTAREDOXIN - Abstract
Glutaredoxins (GRXs) are small glutathione dependent oxidoreductases that belong to the Thioredoxin (TRX) superfamily and catalyze the reduction of disulfide bonds of their substrate proteins. Plant GRXs include three different groups based on the motif sequence, namely CPYC, CGFS, and CC-type proteins. The rice CC-type proteins, OsGRX6 was identified during the screening for genes whose expression changes depending on the level of available nitrate. Overexpression of OsGRX6 in rice displayed a semi-dwarf phenotype. The OsGRX6 overexpressors contain a higher nitrogen content than the wild type, indicating that OsGRX6 plays a role in homeostatic regulation of nitrogen use. Consistent with this, OsGRX6 overexpressors displayed delayed chlorophyll degradation and senescence compared to the wild type plants. To examine if the growth defect of these transgenic lines attribute to disturbed plant hormone actions, plant hormone levels were measured. The levels of two cytokinins (CKs), 2-isopentenyladenine and trans-zeatin, and gibberellin A1 (GA1) were increased in these lines. We also found that these transgenic lines were less sensitive to exogenously applied GA, suggesting that the increase in GA1 is a result of the feedback regulation. These data suggest that OsGRX6 affects hormone signaling and nitrogen status in rice plants. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
44. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea maysL.) associated with distinctcis-acting promoter motifs
- Author
-
Xi Chen, Joseph Colasanti, Steven J. Rothstein, Manish N. Raizada, Christophe Liseron-Monfils, Eddie Bondo, Lewis Lukens, Guangwen Lu, Wenqing Wu, Tara Signorelli, Yong-Mei Bi, Gregory S Downs, and Tong Zhu
- Subjects
phase change ,Response element ,E-box ,Plant Science ,Biology ,maize ,Nitrate reductase ,Zea mays ,nitrogen ,nitrite transporter ,Gene Expression Regulation, Plant ,Arabidopsis ,Promoter Regions, Genetic ,Gene ,Plant Proteins ,2. Zero hunger ,Genetics ,promoter ,assimilation ,motif ,adult ,Promoter ,biology.organism_classification ,Nitrite reductase ,G-box ,juvenile ,Regulon ,nitrate response element ,transporter ,NRE ,transcriptome ,Research Paper - Abstract
Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination. Four nitrogen-related expression clusters were identified in roots and shoots corresponding to, or overlapping, juvenile, adult, and reproductive phases of development. Quantitative real time PCR data was consistent with the existence of these distinct expression clusters. Promoters corresponding to each cluster were screened for over-represented cis-acting elements. The 8-bp distal motif of the Arabidopsis 43-bp nitrogen response element (NRE) was over-represented in nitrogen-related maize gene promoters. This conserved motif, referred to here as NRE43-d8, was previously shown to be critical for nitrate-activated transcription of nitrate reductase (NIA1) and nitrite reductase (NIR1) by the NIN-LIKE PROTEIN 6 (NLP6) in Arabidopsis. Here, NRE43-d8 was over-represented in the promoters of maize nitrate and ammonium transporter genes, specifically those that showed peak expression during early-stage vegetative development. This result predicts an expansion of the NRE-NLP6 regulon and suggests that it may have a developmental component in maize. We also report leaf expression of putative orthologs of nitrite transporters (NiTR1), a transporter not previously reported in maize. We conclude by discussing how each of the four transcriptional modules may be responsible for the different nitrogen uptake and assimilation requirements of leaves and roots at different stages of maize development.
- Published
- 2013
45. Metabolic and co-expression network-based analyses associated with nitrate response in rice.
- Author
-
Coneva, Viktoriya, Simopoulos, Caitlin, Casaretto, José A., El-kereamy, Ashraf, Guevara, David R., Cohn, Jonathan, Tong Zhu, Lining Guo, Alexander, Danny C., Yong-Mei Bi, McNicholas, Paul D., and Rothstein, Steven J.
- Subjects
NITRATES ,GENE expression ,NITROGEN ,CROPS ,METABOLIC profile tests ,GENE ontology ,NUCLEOSIDES ,GLUTAMINE ,PHOSPHORYLATION - Abstract
Background Understanding gene expression and metabolic re-programming that occur in response to limiting nitrogen (N) conditions in crop plants is crucial for the ongoing progress towards the development of varieties with improved nitrogen use efficiency (NUE). To unravel new details on the molecular and metabolic responses to N availability in a major food crop, we conducted analyses on a weighted gene co-expression network and metabolic profile data obtained from leaves and roots of rice plants adapted to sufficient and limiting N as well as after shifting them to limiting (reduction) and sufficient (induction) N conditions. Results A gene co-expression network representing clusters of rice genes with similar expression patterns across four nitrogen conditions and two tissue types was generated. The resulting 18 clusters were analyzed for enrichment of significant gene ontology (GO) terms. Four clusters exhibited significant correlation with limiting and reducing nitrate treatments. Among the identified enriched GO terms, those related to nucleoside/nucleotide, purine and ATP binding, defense response, sugar/carbohydrate binding, protein kinase activities, cell-death and cell wall enzymatic activity are enriched. Although a subset of functional categories are more broadly associated with the response of rice organs to limiting N and N reduction, our analyses suggest that N reduction elicits a response distinguishable from that to adaptation to limiting N, particularly in leaves. This observation is further supported by metabolic profiling which shows that several compounds in leaves change proportionally to the nitrate level (i.e. higher in sufficient N vs. imitimg N) and respond with even higher levels when the nitrate level is reduced. Notably, these compounds are directly involved in N assimilation, transport, and storage (glutamine, asparagine, glutamate and allantoin) and extend to most amino acids. Based on these data, we hypothesize that plants respond by rapidly mobilizing stored vacuolar nitrate when N deficit is perceived, and that the response likely involves phosphorylation signal cascades and transcriptional regulation. Conclusions The co-expression network analysis and metabolic profiling performed in rice pinpoint the relevance of signal transduction components and regulation of N mobilization in response to limiting N conditions and deepen our understanding of N responses and N use in crops. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
46. Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis
- Author
-
Steven J. Rothstein, Tong Zhu, Rong-Lin Wang, and Yong-Mei Bi
- Subjects
0106 biological sciences ,lcsh:QH426-470 ,Transcription, Genetic ,Nitrogen ,lcsh:Biotechnology ,Arabidopsis ,Proteomics ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,lcsh:TP248.13-248.65 ,Gene expression ,Genetics ,Gene ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,biology ,Mechanism (biology) ,Gene Expression Profiling ,15. Life on land ,biology.organism_classification ,Gene expression profiling ,lcsh:Genetics ,Transcription profiling ,DNA microarray ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
Background A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and identifying N-responsive genes in order to manipulate their expression, thus enabling plants to use N more efficiently. No studies have yet delineated these responses at the transcriptional level when plants are grown under chronic N stress and the understanding of regulatory elements involved in N response is very limited. Results To further our understanding of the response of plants to varying N levels, a growth system was developed where N was the growth-limiting factor. An Arabidopsis whole genome microarray was used to evaluate global gene expression under different N conditions. Differentially expressed genes under mild or severe chronic N stress were identified. Mild N stress triggered only a small set of genes significantly different at the transcriptional level, which are largely involved in various stress responses. Plant responses were much more pronounced under severe N stress, involving a large number of genes in many different biological processes. Differentially expressed genes were also identified in response to short- and long-term N availability increases. Putative N regulatory elements were determined along with several previously known motifs involved in the responses to N and carbon availability as well as plant stress. Conclusion Differentially expressed genes identified provide additional insights into the coordination of the complex N responses of plants and the components of the N response mechanism. Putative N regulatory elements were identified to reveal possible new components of the regulatory network for plant N responses. A better understanding of the complex regulatory network for plant N responses will help lead to strategies to improve N use efficiency.
- Published
- 2007
47. Identification of regulatory genes to improve nitrogen use efficiency.
- Author
-
Guevara, David R., Yong-Mei Bi, and Rothstein, Steven J.
- Subjects
GENETIC engineering of crops ,CROP genetics ,CROP yields ,CULTIVARS ,NITROGEN in soils ,NITROGEN fertilizers - Abstract
Copyright of Canadian Journal of Plant Science is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2014
- Full Text
- View/download PDF
48. High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation.
- Author
-
Yong-Mei Bi, Meyer, Ann, Downs, Gregory S., Xuejiang Shi, El-kereamy, Ashraf, Lukens, Lewis, and Rothstein, Steven J.
- Subjects
- *
NUCLEOTIDE sequence , *CULTIVARS , *EFFECT of nitrogen on plants , *NITROGEN metabolism ,CORN genetics - Abstract
Background Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation. Results A different set of genes were found to be N-responsive in the three genotypes. Many biological processes important for N metabolism such as the cellular nitrogen compound metabolic process and the cellular amino acid metabolic process were enriched in the Nresponsive gene list from the hybrid shoots but not from the parental lines' shoots. Coupled to this, sugar, carbohydrate, monosaccharide, glucose, and sorbitol transport pathways were all up-regulated in the hybrid, but not in the parents under N limitation. Expression patterns also differed between shoots and roots, such as the up-regulation of the cytokinin degradation pathway in the shoots of the hybrid and down-regulation of that pathway in the roots. The change of gene expression under N limitation in the hybrid resembled the parent with the higher NUE trait. The transcript abundances of alleles derived from each parent were estimated using polymorphic sites in mapped reads in the hybrid. While there were allele abundance differences, there was no correlation between these and the expression differences seen between the hybrid and the two parents. Conclusions Gene expression in two parental inbreds and the corresponding hybrid line in response to N limitation was surveyed using the mRNA-Seq technology. The data showed that the three genotypes respond very differently to N-limiting conditions, and the hybrid clearly has a unique expression pattern compared to its parents. Our results expand our current understanding of N responses and will help move us forward towards effective strategies to improve NUE and enhance crop production. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
49. Structural and Transcriptional Comparative Analysis of the S Locus Regions in Two Self-Incompatible Brassica napus Lines
- Author
-
Steven J. Rothstein, Lisa Jackman, Yong-Mei Bi, Yuhai Cui, and Norbert Brugière
- Subjects
Transposable element ,Transcription, Genetic ,Molecular Sequence Data ,Brassica ,Plant Science ,Biology ,Genome ,Open Reading Frames ,Sequence Homology, Nucleic Acid ,Animals ,Amino Acid Sequence ,Gene ,Crosses, Genetic ,Glycoproteins ,Plant Proteins ,Genetics ,Contig ,Base Sequence ,Sequence Homology, Amino Acid ,Haplotype ,food and beverages ,Chromosome Mapping ,Cell Biology ,Fosmid ,CDNA Subtraction ,DNA Transposable Elements ,Pollen ,Protein Kinases ,Sequence Alignment ,Recombination ,Genome, Plant ,Research Article - Abstract
Self-incompatibility (SI) in Brassica is controlled by a single locus, termed the S locus. There is evidence that two of the S locus genes, SLG , which encodes a secreted glycoprotein, and SRK , which encodes a putative receptor kinase, are required for SI on the stigma side. The current model postulates that a pollen ligand recognizing the SLG/SRK receptors is encoded in the genomic region defined by the SLG and SRK genes. A fosmid contig of ∼65 kb spanning the SLG-910 and SRK-910 genes was isolated from the Brassica napus W1 line. A new gene, SLL3 , was identified using a novel approach combining cDNA subtraction and direct selection. This gene encodes a putative secreted small peptide and exists as multiple copies in the Brassica genome. Sequencing analysis of the 65-kb contig revealed seven additional genes and a transposon. None of these seven genes exhibited features expected of S genes on the pollen side. An ∼88-kb contig of the A14 S region also was isolated from the B. napus T2 line and sequenced. Comparison of the two S regions revealed that (1) the gene organization downstream of SLG in both S haplotypes is highly colinear; (2) the distance between SLG-A14 and SRK-A14 genes is much larger than that between SLG-910 and SRK-910 , with the intervening region filled with retroelements and haplotype-specific genes; and (3) the gene organization downstream of SRK in the two haplotypes is divergent. These observations lead us to propose that the SLG downstream region might be one border of the S locus and that the accumulation of heteromorphic sequences, such as retroelements as well as haplotype-unique genes, may act as a mechanism to suppress recombination between SLG and SRK.
- Published
- 1999
50. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs.
- Author
-
Liseron-Monfils, Christophe, Yong-Mei Bi, Downs, Gregory S., Wenqing Wu, Signorelli, Tara, Guangwen Lu, Xi Chen, Bondo, Eddie, Tong Zhu, Lukens, Lewis N., Colasanti, Joseph, Rothstein, Steven J., and Raizada, Manish N.
- Published
- 2013
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.