Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Brassica oleracea seedlings subjected to phototropic or gravitropic stimuli

ABSTRACT: 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 15Â° 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 â80Â°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).

ORGANISM(S): Brassica oleracea

SUBMITTER: Emmanuel Liscum

PROVIDER: E-GEOD-3847 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A gradient of auxin and auxin-dependent transcription precedes tropic growth responses.

Esmon C Alex CA Tinsley Amanda G AG Ljung Karin K Sandberg Goran G Hearne Leonard B LB Liscum Emmanuel E

Proceedings of the National Academy of Sciences of the United States of America 20051221 1

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. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment ...[more]

PMID: 16371470

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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.

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).

Dataset Information

Transcription profiling of Brassica oleracea seedlings subjected to phototropic or gravitropic stimuli

Publications

A gradient of auxin and auxin-dependent transcription precedes tropic growth responses.

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