Tropic-stimulus induced changes in gene expression
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana Brassica oleracea
PROVIDER: GSE3847 | GEO | 2006/01/09
SECONDARY ACCESSION(S): PRJNA94071
REPOSITORIES: GEO
Similar Datasets
Project description:Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny-Went theory Went, F.W. & Thimann, K.V. Phytohormones (1937) (Macmillan, New York) predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet, the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced (TSI) genes in Brassica oleracea that are responsive to an auxin gradient, and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny-Went theory, and suggest that morphologically-graded transcription represents an important mechanism for interpreting tropically-stimulated gradients of auxin. Intriguingly, two of the TSI genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are upregulated prior to curvature in the flank that will elongate. This observation suggests that morphologically-graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures. Experiment Overall Design: A 15° ophthalmic scalpel (Feather, Osaka, Japan) was used to isolate tissue flanks (~1 cm in length, see Fig. 1A) from etiolated B. oleracea seedlings that had received one of three treatments: 1) a mock stimulation; 2) a 2 h phototropic stimulation; or 3) a 2 h gravitropic stimulation. Only the outer third of the hypocotyl was collected for each flank section, and opposing flanks were collected into separate pools. Hence there were five distinct tissue samples (two flanks for each of two tropic stimulations plus one set of control flanks) with each sample being generated and collected in triplicate for a total of fifteen biological samples. Tissue flanks were immediately quick frozen in liquid N2 and stored at â80°C until RNAs were isolated. Total RNA was extracted from frozen tissue using the RNeasy kit (Qiagen, Valencia, CA), followed by cRNA synthesis (ENZO Diagnostics, Farmingdale, NY). cRNA probe generation, as well as microarray hybridization, washing and scanning were performed as described by manufacturer protocols (Affymetrix, Santa Clara, CA).
2007-07-10 | E-GEOD-3847 | biostudies-arrayexpress
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the full model described in the article.
2024-09-02 | BIOMD0000000413 | BioModels
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the simplified model described in the article. It is assumed that, on the timescale of DII-VENUS degradation, the concentrations of auxin, TIR1/AFB, and their complexes can be approximated by quasi-steady-state expressions. This reduced the full model to a single ODE that describes how the DII-VENUS dynamics depend on the auxin influx and four parameter groupings.
2024-09-02 | BIOMD0000000414 | BioModels
Project description:Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of temporal regulation of the movement of flowers we used a whole genome microarray as a discovery platform to identify genes differentially expressed in a RNAi knockdown line silenced in the expression of the circadian clock component ZEITLUPE (irZTL-314).
2019-06-30 | GSE116648 | GEO
Project description:Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of the movement of flowers we used a whole genome microarray as a discovery platform to identify genes differentially expressed in adaxial and abaxial sides of the floral peduncle at different stages of the movement.
2020-01-31 | GSE117235 | GEO
Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved.
2013-05-01 | GSE40621 | GEO
Project description:Mutations in the CINCINNATA gene in Antirrhinum and its orthologues in Arabidopsis cause negative surface curvature in leaves due to excess marginal growth. CIN-like genes code for TCP transcription factors and are expressed in a broad zone of a growing leaf somewhat distal to the proliferation zone. Although a few TCP targets are known, the role of CIN-like TCP genes in regulating leaf curvature has remained unclear. We have compared the global transcription profile of wild type and cincinnata mutant to identify its targets. By combining DNA-protein interaction, chromatin immunoprecipitation and RNA in situ hybridization, we show that CIN maintains surface flatness by regulating signaling or level of major plant hormones. CIN promotes cytokinin signaling directly and GA level indirectly, in accelerating maturity in leaf cells along the tip-to-base direction. In addition, CIN suppresses auxin signaling more at the margin than centre by establishing a margin-to-medial expression gradient of a homologue of the auxin suppressor IAA3. Our results uncover an underlying mechanism in a developing leaf that controls maturity of leaf and its surface curvature. Considering the conservation of CIN-like genes and their function in leaf morphogenesis in multiple plant species, it is likely that such mechanism is evolutionarily conserved. Two color Experiment, Organism: Arabidopsis thaliana and Antirrhinum. Arrays Used: 1. Agilent Arabidopsis thaliana Gene expression Microarray 22k (AMADID: 013324) 2. Agilent Custom Arabidopsis thaliana 4x44k Gene Expression (AMADID: 015226) 3. Agilent custom Antirrhinum 4x44k Gene expression (AMADID: 016341) designed by Genotypic Technology Private Limited.
2013-05-01 | E-GEOD-40621 | biostudies-arrayexpress
Project description:The endosperm is a reproductive tissue supporting embryo development. In most flowering plants, the initial divisions of endosperm nuclei are not succeeded by cellularization; this process occurs only after a specific number of mitotic cycles have taken place. The timing of cellularization significantly influences seed viability and size. Previous research implicated auxin as a key factor in initiating nuclear divisions and determining the timing of cellularization. Here we uncover the involvement of a family of clustered auxin response factors (cARFs) as dosage-sensitive regulators of endosperm cellularization. cARFs, maternally expressed and paternally silenced, are shown to induce cellularization, thereby restricting seed growth. Our findings align with the predictions of the parental conflict theory, suggesting that cARFs represent major molecular targets in this conflict. We further demonstrate a recurring amplification of cARFs in the Brassicaceae, suggesting an evolutionary response to parental conflict by reinforcing maternal control over endosperm cellularization. Our study highlights that antagonistic parental control on endosperm cellularization converges on auxin biosynthesis and signalling.
2024-03-22 | GSE232803 | GEO
Project description:The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) functions as an agronomic weed control herbicide. High concentrations of 2,4-D induce plant growth defects, particularly leaf epinasty and stem curvature. Although the 2,4-D phenotype is associated with ROS production, little is known about ROS-dependent signalling. In this study, by using T-DNA Arabidopsis mutants to silence peroxisomal acyl CoA oxidase 1 (acx1-2), we identified ACX1 as one of the main sources of ROS production and as partly the cause of the epinasty phenotype following the application of 2,4-D. Transcriptomic analyses of WT plants after treatment with 2,4-D revealed a ROS-related peroxisomal footprint in early plant responses, while other organelles, such as mitochondria and chloroplasts, are involved in later responses. Interestingly, a group of ACX1-dependent transcripts in plant responses to 2,4-D, previously associated with epinasty, is related to auxin biosynthesis, metabolism and signalling. We found that protein AUXIN SIGNALING F-BOX 3 (AFB3), a component of SCF (ASK-cullin-F-box) E3 ubiquitin ligase complexes, which functions as an auxin receptor and mediates Aux/IAA proteasomal degradation, acts downstream of ACX1 and is involved in the epinasty phenotype induced by 2,4-D. We also found that protein degradation associated with ubiquitin E3-RING and E3-SCF-FBOX in ACX1-dependent signalling in plant responses to 2,4-D is significantly regulated over longer treatment periods.
2021-12-01 | GSE179303 | GEO
Project description:Investigation of whole genome gene expression level changes in Arabidopsis roots by the effect of light. Plant growth is sustained by a continuous cell division in meristems followed by cell differentiation and elongation. We have found that in Arabidopsis thaliana roots, flavonols play a key role in regulating the transition from cell division to differentiation. Using an engineered device to grow roots in darkness, but shoot in light cycle, coupled with transcriptomic and metabolomics analysis, we deciphered that flavonols accumulation regulates proliferation-promoting levels of auxin-PLETHORA and superoxide anion (O2-). High flavonols levels restrict auxin transport and the PLETHORA gradient but also superoxide radical content, promoting an accelerated cell differentiation. Furthermore, cytokinin-SHY2 and H2O2-UPB1 pathways, which promote differentiation and, respectively, antagonize auxin and O2- activity, increase flavonols biosynthesis establishing mutual interactions among these pathways. Flavonols function as positional signals integrating hormonal and ROS pathways to determine final organ growth. This work analyze the effect of root illumination in gene transcription. Details of how plants and roots are grown are described in Silva et al. (submitted)
2016-04-01 | GSE68093 | GEO