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1.
Emerg Top Life Sci ; 5(2): 317-324, 2021 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-33599739

RESUMO

Plant growth-promoting microbes can affect the plant microbiome, improving different properties of the plant such as yield and health. Many companies are commercializing these microbes as products called biologicals. Defining the product concept is one of the first and most important steps in making a biological product. Companies can use phenotyping and genotyping approaches to identify the microbe to make into a live bacterial product. Screening usually begins in the laboratory and often moves from high-throughput methods to more time and resource-intensive methods culminating in large scale field testing. Once the microbe is chosen, the fermentation process grows the bacteria to the necessary amounts, while the formulation process ensures a stable product in the desired form such as a liquid or powder. The products must show yield increases in the field over several seasons and conditions, but also must be easy to use and cost-effective to be adopted by farmers and other customers. Tying all these data together from the selection process to test results gives a customer a 'reason to believe' for the marketing and launch of a successful product.


Assuntos
Indústrias , Desenvolvimento Vegetal , Bactérias/genética , Marketing , Plantas
2.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33526654

RESUMO

Gene expression is reconfigured rapidly during the cell cycle to execute the cellular functions specific to each phase. Studies conducted with synchronized plant cell suspension cultures have identified hundreds of genes with periodic expression patterns across the phases of the cell cycle, but these results may differ from expression occurring in the context of intact organs. Here, we describe the use of fluorescence-activated cell sorting to analyze the gene expression profile of G2/M cells in the growing root. To this end, we isolated cells expressing the early mitosis cell cycle marker CYCLINB1;1-GFP from Arabidopsis root tips. Transcriptome analysis of these cells allowed identification of hundreds of genes whose expression is reduced or enriched in G2/M cells, including many not previously reported from cell suspension cultures. From this dataset, we identified SCL28, a transcription factor belonging to the GRAS family, whose messenger RNA accumulates to the highest levels in G2/M and is regulated by MYB3R transcription factors. Functional analysis indicates that SCL28 promotes progression through G2/M and modulates the selection of cell division planes.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/citologia , Mitose , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Meristema/metabolismo , Mitose/genética , Organogênese , Fatores de Transcrição/metabolismo , Transcriptoma/genética
3.
Nature ; 543(7646): 513-518, 2017 03 23.
Artigo em Inglês | MEDLINE | ID: mdl-28297714

RESUMO

Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions. We define a molecular mechanism regulating coordination between nutrition and defence in the presence of a synthetic bacterial community. We further demonstrate that the master transcriptional regulators of phosphate stress response in Arabidopsis thaliana also directly repress defence, consistent with plant prioritization of nutritional stress over defence. Our work will further efforts to define and deploy useful microbes to enhance plant performance.


Assuntos
Arabidopsis/imunologia , Arabidopsis/microbiologia , Microbiota/fisiologia , Fosfatos/metabolismo , Imunidade Vegetal , Raízes de Plantas/metabolismo , Raízes de Plantas/microbiologia , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Microbiota/imunologia , Mutação , Imunidade Vegetal/genética , Fatores de Transcrição/deficiência , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
4.
Nat Plants ; 2(5): 16058, 2016 04 29.
Artigo em Inglês | MEDLINE | ID: mdl-27243651

RESUMO

DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base-resolution whole-genome DNA methylomes, mRNA transcriptomes and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell-type-specific patterns of DNA methylation, especially in the CHH sequence context, where H is A, C or T. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized so far. It is hypermethylated within transposable elements (TEs), accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24-nt small RNAs (smRNAs). The absence of the nucleosome remodeller DECREASED DNA METHYLATION 1 (DDM1), required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests that a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing an excess of 24-nt smRNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types.


Assuntos
Arabidopsis/genética , Metilação de DNA , Proteínas de Plantas/genética , Raízes de Plantas/metabolismo , Transcriptoma , Arabidopsis/metabolismo , Epigênese Genética , Meristema/metabolismo , Proteínas de Plantas/metabolismo
5.
Plant Cell ; 27(12): 3354-66, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26645252

RESUMO

To ensure an adequate organ mass, the daughters of stem cells progress through a transit-amplifying phase displaying rapid cell division cycles before differentiating. Here, we show that Arabidopsis thaliana microRNA miR396 regulates the transition of root stem cells into transit-amplifying cells by interacting with GROWTH-REGULATING FACTORs (GRFs). The GRFs are expressed in transit-amplifying cells but are excluded from the stem cells through inhibition by miR396. Inactivation of the GRFs increases the meristem size and induces periclinal formative divisions in transit-amplifying cells. The GRFs repress PLETHORA (PLT) genes, regulating their spatial expression gradient. Conversely, PLT activates MIR396 in the stem cells to repress the GRFs. We identified a pathway regulated by GRF transcription factors that represses stem cell-promoting genes in actively proliferating cells, which is essential for the progression of the cell cycle and the orientation of the cell division plane. If unchecked, the expression of the GRFs in the stem cell niche suppresses formative cell divisions and distorts the organization of the quiescent center. We propose that the interactions identified here between miR396 and GRF and PLT transcription factors are necessary to establish the boundary between the stem cell niche and the transit-amplifying region.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , MicroRNAs/genética , Arabidopsis/citologia , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Divisão Celular , Meristema/citologia , Meristema/genética , Meristema/crescimento & desenvolvimento , Raízes de Plantas/citologia , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Plantas Geneticamente Modificadas , Nicho de Células-Tronco/genética , Células-Tronco , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
6.
Science ; 349(6250): 860-4, 2015 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-26184915

RESUMO

Immune systems distinguish "self" from "nonself" to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.


Assuntos
Microbiota/fisiologia , Reguladores de Crescimento de Plantas/fisiologia , Raízes de Plantas/imunologia , Raízes de Plantas/microbiologia , Ácido Salicílico/metabolismo , Microbiologia do Solo , Arabidopsis/genética , Arabidopsis/imunologia , Arabidopsis/microbiologia , Bactérias/classificação , Bactérias/isolamento & purificação , Fenômenos Fisiológicos Bacterianos , Microbiota/efeitos dos fármacos , Reguladores de Crescimento de Plantas/genética , Reguladores de Crescimento de Plantas/farmacologia , Raízes de Plantas/genética , Ácido Salicílico/farmacologia
7.
Proc Natl Acad Sci U S A ; 109(18): 6811-8, 2012 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-22447775

RESUMO

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Arabidopsis/anatomia & histologia , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Sequência de Bases , Cromatografia Líquida , Primers do DNA/genética , Perfilação da Expressão Gênica , Raízes de Plantas/anatomia & histologia , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Plantas Geneticamente Modificadas , Análise Serial de Proteínas , Mapeamento de Interação de Proteínas , Proteoma/genética , Proteoma/metabolismo , Proteômica , RNA de Plantas/genética , RNA de Plantas/metabolismo , Espectrometria de Massas em Tandem
8.
Genome Res ; 22(1): 163-76, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21940835

RESUMO

Small non-coding RNAs (ncRNAs) are key regulators of plant development through modulation of the processing, stability, and translation of larger RNAs. We present small RNA data sets comprising more than 200 million aligned Illumina sequence reads covering all major cell types of the root as well as four distinct developmental zones. MicroRNAs (miRNAs) constitute a class of small ncRNAs that are particularly important for development. Of the 243 known miRNAs, 133 were found to be expressed in the root, and most showed tissue- or zone-specific expression patterns. We identified 66 new high-confidence miRNAs using a computational pipeline, PIPmiR, specifically developed for the identification of plant miRNAs. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance.


Assuntos
Arabidopsis/fisiologia , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/fisiologia , MicroRNAs/biossíntese , Modelos Biológicos , RNA de Plantas/biossíntese , MicroRNAs/genética , Especificidade de Órgãos/fisiologia , RNA de Plantas/genética
9.
Plant Cell ; 23(3): 855-64, 2011 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21386031

RESUMO

Multicellular organisms depend on cell-to-cell communication to coordinate both development and environmental responses across diverse cell types. Intercellular signaling is particularly critical in plants because development is primarily postembryonic and continuous over a plant's life span. Additionally, development is impacted by restrictions imposed by a sessile lifestyle and limitations on relative cell positions. Many non-cell-autonomous signaling mechanisms are known to function in plant development, including those involving receptor kinases, small peptides, and mobile transcription factors. In this review, we focus on recent findings that highlight novel mechanisms in intercellular signaling during development. New details of small RNA movement, including microRNA movement, are discussed, as well as protein movement and distribution of reactive oxygen species (ROS) in ROS signaling. Finally, a novel temporal mechanism for lateral root positioning and the implications for intercellular signaling are considered.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Comunicação Celular , Raízes de Plantas/metabolismo , Transdução de Sinais , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/fisiologia , Relógios Biológicos , Transporte Biológico , Proteínas de Membrana/metabolismo , MicroRNAs/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/fisiologia , Proteínas Quinases/metabolismo , RNA de Plantas/metabolismo , RNA Interferente Pequeno/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Fatores de Transcrição/metabolismo
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