Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation

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https://doi.org/10.1105/tpc.106.042200
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Keywords

Arabidopsis, Arabidopsis Proteins, Cotyledon, DNA, Bacterial, Gene Expression Profiling, Gene Expression Regulation, Plant, Hypocotyl, Light, Mutagenesis, Insertional, Mutation, Phytochrome, Signal Transduction, Transcription Factors

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Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. / Khanna, Rajnish; Shen, Yu; Toledo-Ortiz, Gabriela et al.
In: Plant Cell, Vol. 18, No. 9, 09.2006, p. 2157-2171.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Bibtex

@article{e3cada4711814e4f95009c7458629d4d,

title = "Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation",

abstract = "In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.",

keywords = "Arabidopsis, Arabidopsis Proteins, Cotyledon, DNA, Bacterial, Gene Expression Profiling, Gene Expression Regulation, Plant, Hypocotyl, Light, Mutagenesis, Insertional, Mutation, Phytochrome, Signal Transduction, Transcription Factors",

author = "Rajnish Khanna and Yu Shen and Gabriela Toledo-Ortiz and Kikis, {Elise A.} and Henrik Johannesson and Yong-Sic Hwang and Quail, {Peter H.}",

year = "2006",

month = sep,

doi = "10.1105/tpc.106.042200",

language = "English",

volume = "18",

pages = "2157--2171",

journal = "Plant Cell",

issn = "1040-4651",

publisher = "American Society of Plant Biologists",

number = "9",

}

RIS

TY - JOUR

T1 - Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation

AU - Khanna, Rajnish

AU - Shen, Yu

AU - Toledo-Ortiz, Gabriela

AU - Kikis, Elise A.

AU - Johannesson, Henrik

AU - Hwang, Yong-Sic

AU - Quail, Peter H.

PY - 2006/9

Y1 - 2006/9

N2 - In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.

AB - In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.

KW - Arabidopsis

KW - Arabidopsis Proteins

KW - Cotyledon

KW - DNA, Bacterial

KW - Gene Expression Profiling

KW - Gene Expression Regulation, Plant

KW - Hypocotyl

KW - Light

KW - Mutagenesis, Insertional

KW - Mutation

KW - Phytochrome

KW - Signal Transduction

KW - Transcription Factors

U2 - 10.1105/tpc.106.042200

DO - 10.1105/tpc.106.042200

M3 - Journal article

C2 - 16891401

VL - 18

SP - 2157

EP - 2171

JO - Plant Cell

JF - Plant Cell

SN - 1040-4651

IS - 9

ER -

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