A Genomic Analysis of the Shade Avoidance Response in Arabidopsis
Open accessAbstract
Plants respond to the proximity of neighboring vegetation by elongating to prevent shading. Red-depleted light reflected from neighboring vegetation triggers a shade avoidance response leading to a dramatic change in plant architecture. These changes in light quality are detected by the phytochrome family of photoreceptors. We analyzed global changes in gene expression over time in wild-type, phyB mutant, and phyA phyB double mutant seedlings of Arabidopsis in response to simulated shade. Using pattern fitting software, we identified 301 genes as shade responsive with patterns of expression corresponding to one of various physiological response modes. A requirement for a consistent pattern of expression across 12 chips in this way allowed more subtle changes in gene expression to be considered meaningful. A number of previously characterized genes involved in light and hormone signaling were identified as shade responsive, as well as several putative, novel shade-specific signal transduction factors. In addition, changes in expression of genes in a range of pathways associated with elongation growth and stress responses were observed. The majority of shade-responsive genes demonstrated antagonistic regulation by phyA and phyB in response to shade following the pattern of many physiological responses. An analysis of promoter elements of genes regulated in this way identified conserved promoter motifs potentially important in shade regulation.
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Phytochromes can regulate other auxin transporters such as PIN1, PIN3, PIN7 and PID.
“Phytochromes can also regulate other auxin transporters such as PIN1, PIN3, PIN7 and PID”
From The action of enhancing weak light capture via phototropic growth and chloroplast movement in plants (2022) · cites this paper as Devlin et al., 2003
The Discussion (page unavailable) reports that PIN3 and PIN7 transcripts fit a pattern of shade-responsive expression under antagonistic phyA and phyB regulation. The paper does not report the claimed regulation of PIN1 or PID, and its evidence concerns transcript levels rather than direct regulation of transporter activity. (LLM, conf=0.88)
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The action of enhancing weak light capture via phototropic growth and chloroplast movement in plants
Xin, G.-Y., Li, L.-P., Wang, P.-T., Li, X.-Y., Han, Y.-J., & Zhao, X. (2022) · Stress Biology · doi:10.1007/s44154-022-00066-x · Cited by 17 · see citing works
“(2014) demonstrated that PINOID kinase (PID) can regulate the phosphorylation state of PINs and affect their localization.”
BackgroundInfluentialTonello, L., Gashi, B., Scuotto, A., Cappello, G., Cocchi, M., Gabrielli, F., & Tuszynski, J. A. (2018) · Journal of Integrative Neuroscience · doi:10.3233/jin-170048 · Cited by 3 · see citing works
- Authors
- Devlin, P. F., Yanovsky, M. J., & Kay, S. A.
- Affiliations
- Scripps Research Institute (US)
- Venue
- Plant Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-12-01
- Volume
- 133
- Issue
- 4
- Pages
- 1617-1629
- ISSN
- 0032-0889 (ISSN-L)
- 1532-2548
- PMC
- PMC300718
- OpenAlex
- W2158813927
- Cited by
- 275
- References
- 51
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 5 · 2023: 5 · 2022: 8 · 2021: 7 · 2020: 21 · 2019: 8 · 2018: 4 · 2017: 17 · 2016: 6 · 2015: 15 · 2014: 13 · 2013: 19 · 2012: 21
- FWCI
- 12.58
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- PLANT PHYSIOLOGY (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM 56006, R01GM056006)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Light effects on plants
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Parasitism and Resistance
- Keywords
- shade avoidance response, Arabidopsis thaliana, phytochrome, phyA, phytochrome B, gene expression profiling, plant architecture, promoter elements, light signaling, hormone signaling, elongation growth, stress response
- MeSH terms
- Base Sequence, Darkness, Light, Nucleic Acid Hybridization, Promoter Regions, Genetic, Arabidopsis, Gene Expression Regulation, Plant, Phototropism, Genome, Plant, Oligonucleotide Array Sequence Analysis
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