Biomedical subjects

Joanne Chory

Publications and source records attributed to Joanne Chory.

At least 19 recordsLinked to original sources

PubMed2006

Brassinosteroid signaling pathway.

Plant growth is regulated by an intricate network of hormonal signaling pathways. These small-molecule hormones cause changes in gene expression that are associated with cell expansion and division and changes in development. Paradoxically, six of these hormones appear to have largely overlapping functions, yet the loss of response to any one hormone cannot be compensated by the action of another plant hormone. Among these hormones are the brassinosteroids (BRs), the polyhydroxylated steroid hormones of plants. The emerging picture of BR signal transduction diverges radically from the paradigms of animal steroid signaling, which generally involve the action of members of the nuclear receptor superfamily. BRs bind the extracellular domain of a small family of leucine-rich-repeat receptor kinases to activate intracellular signal transduction cascades that regulate the expression of hundreds of genes. The signaling pathway involves a cell surface receptor complex, a glycogen synthase kinase 3, a kelch-containing serine/threonine phosphatase, and a novel family of basic helix-loop-helix and Myc-like plant specific transcription factors. The receptor and each of the signaling components were identified in Arabidopsis thaliana, and knowledge of their sequences allowed identification of orthologs in rice, tomato, barley, and pea.

Arabidopsis Proteins↗

PubMed2006

Arabidopsis brassinosteroid signaling pathway.

Plants control their size through the action of several phytohormones. One class of growth-promoting hormones is the brassinosteroids (BRs), the polyhydroxylated steroid hormones of plants. Here, we present the Arabidopsis-specific proteins that are the founding members of key BR signaling pathway components found in all plants. The genetic studies that identified these components are unique to Arabidopsis owing to its rapid generation time, sophisticated genetics, and facile transformation protocols, thereby highlighting the importance of a reference plant for understanding fundamental processes in all land plants.

Arabidopsis↗

PubMed2006

Brassinosteroid signaling: a paradigm for steroid hormone signaling from the cell surface.

Plants use the coordinated action of several small-molecule hormones to grow and develop optimally in response to a changing environment. Among these hormones are the brassinosteroids (BRs), the polyhydroxylated steroid hormones of plants. BRs bind a small family of leucine-rich repeat receptor kinases at the cell surface, thereby initiating an intracellular signal transduction cascade that results in the altered expression of hundreds of genes.

Arabidopsis↗

PubMed2006

An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development.

The ATP-dependent Clp protease has been well-characterized in Escherichia coli, but knowledge of its function in higher plants is limited. In bacteria, this two-component protease consists of a Ser-type endopeptidase ClpP, which relies on the ATP-dependent unfolding activity from an Hsp100 molecular chaperone to initiate protein degradation. In the chloroplasts of higher plants, multiple isoforms of the proteolytic subunit exist, with Arabidopsis having five ClpPs and four ClpP-like proteins termed ClpR predicted in its genome. In this work we characterized an Arabidopsis mutant impaired in one subunit of the chloroplast-localized Clp protease core, ClpR1. clpR1-1, a virescent mutant, carries a pre-mature stop codon in the clpR1 gene, resulting in no detectable ClpR1 protein. The accumulation of several chloroplast proteins, as well as most of the chloroplast-localized Clp protease subunits, is inhibited in clpR1-1. Unexpectedly, some plastid-encoded proteins do not accumulate, although their transcripts accumulate to wild-type levels. Maturation of 23S and 4.5S chloroplast ribosomal RNA (cp-rRNA) is delayed in clpR1-1, and both RNAs accumulate as higher molecular weight precursors. Also, chloroplasts in clpR1-1 are smaller than in wild type and have fewer thylakoid membranes with smaller grana stacks. We propose that a ClpR1-containing activity is required for chloroplast development and differentiation and in its absence both are delayed.

Arabidopsis↗

PubMed2006

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.

UNLABELLED: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004) FEBS Lett., 573, 83-92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. AVAILABILITY: RankProd is available at Bioconductor http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd

Computational Biology↗

PubMed2006

Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses.

Small-molecule hormones govern every aspect of the biology of plants. Many processes, such as growth, are regulated in similar ways by multiple hormones, and recent studies have revealed extensive crosstalk among different hormonal signaling pathways. These results have led to the proposal that a common set of signaling components may integrate inputs from multiple hormones to regulate growth. In this study, we tested this proposal by asking whether different hormones converge on a common set of transcriptional targets in Arabidopsis seedlings. Using publicly available microarray data, we analyzed the transcriptional effects of seven hormones, including abscisic acid, gibberellin, auxin, ethylene, cytokinin, brassinosteroid, and jasmonate. A high-sensitivity analysis revealed a surprisingly low number of common target genes. Instead, different hormones appear to regulate distinct members of protein families. We conclude that there is not a core transcriptional growth-regulatory module in young Arabidopsis seedlings.

Abscisic Acid↗

PubMed2006

Brassinosteroids regulate dissociation of BKI1, a negative regulator of BRI1 signaling, from the plasma membrane.

Brassinosteroids, the steroid hormones of plants, are perceived at the plasma membrane by a leucine-rich repeat receptor serine/threonine kinase called BRI1. We report a BRI1-interacting protein, BKI1, which is a negative regulator of brassinosteroid signaling. Brassinosteroids cause the rapid dissociation of BKI1-yellow fluorescent protein from the plasma membrane in a process that is dependent on BRI1-kinase. BKI1 is a substrate of BRI1 kinase and limits the interaction of BRI1 with its proposed coreceptor, BAK1, suggesting that BKI1 prevents the activation of BRI1.

Amino Acid Sequence↗

PubMed2006

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.

Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA, a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant P values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response.

Arabidopsis↗

PubMed2006

Downstream nuclear events in brassinosteroid signalling.

Brassinosteroids (BRs) are steroid hormones that control many aspects of plant growth and development. BRs bind to the plasma membrane receptor kinase BRI1, and act through a signalling pathway that involves a glycogen synthase kinase-3-like kinase (BIN2) and a serine/threonine phosphatase (BSU1). Previous models proposed that BIN2 negatively regulates BR signalling by controlling the stability and subcellular localization of the related transcription factors BES1 and BZR1 by phosphorylation, in a manner reminiscent of the canonical Wnt signalling pathway of metazoans. Here we present strong evidence for a different mode of regulation of BR signalling. We show that BES1 is localized constitutively to the nucleus, where its activity is modulated by nuclear-localized BIN2 kinase. BIN2-mediated phosphorylation of BES1 inhibits its DNA-binding activity on BR-responsive target promoters and its transcriptional activity through impaired multimerization. Our observations demonstrate that phosphorylation-dependent inhibition of DNA binding and trans-activation is the key primary mechanism of BES1 regulation.

Arabidopsis↗

PubMed2006

Plastid-to-nucleus retrograde signaling.

Plant cells store genetic information in the genomes of three organelles: the nucleus, plastid, and mitochondrion. The nucleus controls most aspects of organelle gene expression, development, and function. In return, organelles send signals to the nucleus to control nuclear gene expression, a process called retrograde signaling. This review summarizes our current understanding of plastid-to-nucleus retrograde signaling, which involves multiple, partially redundant signaling pathways. The best studied is a pathway that is triggered by buildup of Mg-ProtoporphyrinIX, the first intermediate in the chlorophyll branch of the tetrapyrrole biosynthetic pathway. In addition, there is evidence for a plastid gene expression-dependent pathway, as well as a third pathway that is dependent on the redox state of photosynthetic electron transport components. Although genetic studies have identified several players involved in signal generation, very little is known of the signaling components or transcription factors that regulate the expression of hundreds of nuclear genes.

Cell Nucleus↗

PubMed2005

The Arabidopsis PEX12 gene is required for peroxisome biogenesis and is essential for development.

Peroxisomes perform diverse and vital functions in eukaryotes, and abnormalities in peroxisomal function lead to severe developmental disorders in humans. Peroxisomes are also involved in a wide array of physiological and metabolic functions unique to plants, yet many aspects of this important organelle are poorly understood. In yeast and mammals, various steps in peroxisome biogenesis require the function of peroxin (PEX) proteins, among which PEX12 is a RING finger peroxisomal membrane protein involved in the import of matrix proteins. To investigate the role of PEX12 in plants, we identified a T-DNA knockout allele of PEX12 and generated partial loss-of-function pex12 mutants using RNA interference. We show that pex12 null mutants are developmentally arrested during early embryogenesis, and that the embryo-lethal phenotype can be rescued by overexpression of the PEX12-cyan fluorescent protein fusion protein, which targets to the peroxisome. Using virus-induced gene-silencing techniques, we demonstrate that peroxisomal number and fluorescence of the yellow fluorescent protein-peroxisome targeting signal type 1 protein are greatly reduced when PEX12 is silenced. RNA interference plants with partial reduction of the PEX12 transcript exhibit impaired peroxisome biogenesis and function, inhibition of plant growth, and reduced fertility. Our work provides evidence that the Arabidopsis (Arabidopsis thaliana) PEX12 protein is required for peroxisome biogenesis and plays an essential role throughout plant development.

Amino Acid Sequence↗

PubMed2005

Phytochrome control of the Arabidopsis transcriptome anticipates seedling exposure to light.

Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here, we show that a subset of genes is upregulated in phytochrome B (phyB) mutants even before dark-grown Arabidopsis thaliana seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE3 (ABI3), and the phyB mutation also enhances ABI3 expression. These changes in transcriptome have physiological consequences, because seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, whereas ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream transdevelopmental phase signal that preconditions the seedling to its most likely environment.

Arabidopsis↗

PubMed2005

A new FronTIR in targeted protein degradation and plant development.

Three papers, two in a recent issue of Nature and one in the July issue of Developmental Cell, identify a family of F box proteins as the long-sought receptors for the plant growth hormone auxin. The new studies reveal that auxin, a small molecule, regulates F box proteins, which are involved in ubiquitin-mediated protein degradation. This finding has profound implications for understanding plant physiology and development and for defining new modes of regulation of SCF ubiquitin ligase complexes.

Arabidopsis Proteins↗

PubMed2005

FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions.

FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) are two genes that, unless plants are vernalized, greatly delay flowering time in Arabidopsis thaliana. Natural loss-of-function mutations in FRI cause the early flowering growth habits of many A. thaliana accessions. To quantify the variation among wild accessions due to FRI, and to identify additional genetic loci in wild accessions that influence flowering time, we surveyed the flowering times of 145 accessions in long-day photoperiods, with and without a 30-day vernalization treatment, and genotyped them for two common natural lesions in FRI. FRI is disrupted in at least 84 of the accessions, accounting for only approximately 40% of the flowering-time variation in long days. During efforts to dissect the causes for variation that are independent of known dysfunctional FRI alleles, we found new loss-of-function alleles in FLC, as well as late-flowering alleles that do not map to FRI or FLC. An FLC nonsense mutation was found in the early flowering Van-0 accession, which has otherwise functional FRI. In contrast, Lz-0 flowers late because of high levels of FLC expression, even though it has a deletion in FRI. Finally, eXtreme array mapping identified genomic regions linked to the vernalization-independent, late-flowering habit of Bur-0, which has an alternatively spliced FLC allele that behaves as a null allele.

Alternative Splicing↗

PubMed2005

Structure of the Mg-chelatase cofactor GUN4 reveals a novel hand-shaped fold for porphyrin binding.

In plants, the accumulation of the chlorophyll precursor Mg-protoporphyrin IX (Mg-Proto) in the plastid regulates the expression of a number of nuclear genes with functions related to photosynthesis. Analysis of the plastid-to-nucleus signaling activity of Mg-Proto in Arabidopsis thaliana led to the discovery of GUN4, a novel porphyrin-binding protein that also dramatically enhances the activity of Mg-chelatase, the enzyme that synthesizes Mg-Proto. GUN4 may also play a role in both photoprotection and the cellular shuttling of tetrapyrroles. Here we report a 1.78-A resolution crystal structure of Synechocystis GUN4, in which the porphyrin-binding domain adopts a unique three dimensional fold with a "cupped hand" shape. Biophysical and biochemical analyses revealed the specific site of interaction between GUN4 and Mg-Proto and the energetic determinants for the GUN4.Mg-Proto interaction. Our data support a novel protective function for GUN4 in tetrapyrrole trafficking. The combined structural and energetic analyses presented herein form the physical-chemical basis for understanding GUN4 biological activity, including its role in the stimulation of Mg-chelatase activity, as well as in Mg-Proto retrograde signaling.

Arabidopsis↗

PubMed2005

Regulation of phytochrome B nuclear localization through light-dependent unmasking of nuclear-localization signals.

Phytochromes are red and far-red photoreceptors that regulate plant growth and development in response to environmental light cues. Phytochromes exist in two photo-interconvertible conformational states: an inactive Pr form and an active Pfr form. The alteration of phytochromes' subcellular location functions as a major regulatory mechanism of their biological activities. Whereas phytochromes in the Pr form localize in the cytoplasm, phytochromes in the Pfr form accumulate in the nucleus, where they interact with transcription factors to regulate gene expression. The molecular details of the regulation of phytochrome translocation by light are poorly understood. Using Arabidopsis phyB as a model, we demonstrate that the C-terminal PAS-related domain (PRD) is both necessary and sufficient for phyB nuclear import and that the entire C terminus is required for nuclear-body (NB) localization. We also show that phyB's N-terminal bilin lyase domain (BLD) and PHY domain interact directly with the PRD in a light-dependent manner. In vivo localization studies indicate that BLD-PHY is sufficient to regulate phyB's nuclear accumulation. For phyB nuclear localization, our results suggest a molecular mechanism in which the nuclear-localization signal in the PRD is masked by interactions with phyB's chromophore-attachment domains and unmasked by light-dependent conformational changes.

Arabidopsis↗

PubMed2005

Quantitative trait locus mapping and DNA array hybridization identify an FLM deletion as a cause for natural flowering-time variation.

Much of the flowering time variation in wild strains of Arabidopsis thaliana is due to allelic variation at two epistatically acting loci, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FLC encodes a MADS (MCM1/AGAMOUS/DEFICIENS/SRF1) domain transcription factor that directly represses a series of flowering-promoting genes. FRI and FLC, however, do not explain all of the observed variation, especially when plants are grown in short days. To identify loci that act in addition to FRI and FLC in controlling flowering of natural accessions, we have analyzed a recombinant inbred line population derived from crosses of accession Niederzenz (Nd) to Columbia, both of which contain natural FRI lesions. Quantitative trait locus mapping and genomic DNA analysis by microarray hybridization were used to identify candidate genes affecting variation in flowering behavior. In both long and short days, the quantitative trait locus of largest effect, termed FLOWERING 1 (FLW1), was found to be associated with a Nd-specific deletion of FLOWERING LOCUS M (FLM), which encodes a floral repressor closely related to FLC. Analysis of near isogenic lines and quantitative transgenic complementation experiments confirmed that the FLM deletion is, in large part, responsible for the early flowering of the Nd accession.

Alleles↗

PubMed2005

A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis.

Brassinosteroids (BRs) signal through a plasma membrane-localized receptor kinase to regulate plant growth and development. We showed previously that a novel protein, BES1, accumulates in the nucleus in response to BRs, where it plays a role in BR-regulated gene expression; however, the mechanism by which BES1 regulates gene expression is unknown. In this study, we dissect BES1 subdomains and establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo. BES1 interacts with a basic helix-loop-helix protein, BIM1, to synergistically bind to E box (CANNTG) sequences present in many BR-induced promoters. Loss-of-function and gain-of-function mutants of BIM1 and its close family members display BR response phenotypes. Thus, BES1 defines a new class of plant-specific transcription factors that cooperate with transcription factors such as BIM1 to regulate BR-induced genes.

Amino Acid Sequence↗