Genomic and phenomic screens for flower related RING type ubiquitin E3 ligases in Arabidopsis

Research output: Contribution to journalArticleScientificpeer-review

Abstract

Flowering time control integrates endogenous as well as environmental signals to promote flower
development. The pathways and molecular networks involved are complex and integrate many
modes of signal transduction. In plants ubiquitin mediated protein degradation pathway has been
proposed to be as important mode of signaling as phosphorylation and transcription. To
systematically study the role of ubiquitin signaling in the molecular regulation of flowering we
have taken a genomic approach to identify flower related Ubiquitin Proteasome System
components. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosen
as targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligases
were retrieved and verified in the Arabidopsis genome v11. Their differential expression was used
for their categorization into flower organs or developmental stages. Known regulators of flowering
time or floral organ development were identified in these categories through literature search and
representative mutants for each category were purchased for functional characterization by growth
and morphological phenotyping. To this end, a workflow was developed for high throughput
phenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsis
plants in one experimental round.
Original languageEnglish
Article number416
JournalFrontiers in plant science
Volume8
Number of pages17
ISSN1664-462X
DOIs
Publication statusPublished - 28 Mar 2017
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 414 Agricultural biotechnology
  • Arabidopsis
  • flower
  • RING E3 ligase
  • ubiquitin
  • high throughput
  • image based phenotyping
  • phenomics data analysis
  • ZINC-FINGER PROTEIN
  • PROTEASOME SYSTEM
  • GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
  • CONSTANS EXPRESSION
  • GENE-EXPRESSION
  • GABI-KAT
  • THALIANA
  • plant
  • time
  • information

Cite this

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title = "Genomic and phenomic screens for flower related RING type ubiquitin E3 ligases in Arabidopsis",
abstract = "Flowering time control integrates endogenous as well as environmental signals to promote flowerdevelopment. The pathways and molecular networks involved are complex and integrate manymodes of signal transduction. In plants ubiquitin mediated protein degradation pathway has beenproposed to be as important mode of signaling as phosphorylation and transcription. Tosystematically study the role of ubiquitin signaling in the molecular regulation of flowering wehave taken a genomic approach to identify flower related Ubiquitin Proteasome Systemcomponents. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosenas targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligaseswere retrieved and verified in the Arabidopsis genome v11. Their differential expression was usedfor their categorization into flower organs or developmental stages. Known regulators of floweringtime or floral organ development were identified in these categories through literature search andrepresentative mutants for each category were purchased for functional characterization by growthand morphological phenotyping. To this end, a workflow was developed for high throughputphenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsisplants in one experimental round.",
keywords = "414 Agricultural biotechnology, Arabidopsis, flower, RING E3 ligase, ubiquitin, high throughput, image based phenotyping, phenomics data analysis, ZINC-FINGER PROTEIN, PROTEASOME SYSTEM, GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, CONSTANS EXPRESSION, GENE-EXPRESSION, GABI-KAT, THALIANA, plant, time, information",
author = "Mirko Pavicic and Katriina Mouhu and Feng Wang and Bilicka, {Marcelina Marta} and Erik Chovanček and Himanen, {Kristiina Irma Helena}",
year = "2017",
month = "3",
day = "28",
doi = "10.3389/fpls.2017.00416",
language = "English",
volume = "8",
journal = "Frontiers in plant science",
issn = "1664-462X",
publisher = "Frontiers Media",

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TY - JOUR

T1 - Genomic and phenomic screens for flower related RING type ubiquitin E3 ligases in Arabidopsis

AU - Pavicic, Mirko

AU - Mouhu, Katriina

AU - Wang, Feng

AU - Bilicka, Marcelina Marta

AU - Chovanček, Erik

AU - Himanen, Kristiina Irma Helena

PY - 2017/3/28

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N2 - Flowering time control integrates endogenous as well as environmental signals to promote flowerdevelopment. The pathways and molecular networks involved are complex and integrate manymodes of signal transduction. In plants ubiquitin mediated protein degradation pathway has beenproposed to be as important mode of signaling as phosphorylation and transcription. Tosystematically study the role of ubiquitin signaling in the molecular regulation of flowering wehave taken a genomic approach to identify flower related Ubiquitin Proteasome Systemcomponents. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosenas targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligaseswere retrieved and verified in the Arabidopsis genome v11. Their differential expression was usedfor their categorization into flower organs or developmental stages. Known regulators of floweringtime or floral organ development were identified in these categories through literature search andrepresentative mutants for each category were purchased for functional characterization by growthand morphological phenotyping. To this end, a workflow was developed for high throughputphenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsisplants in one experimental round.

AB - Flowering time control integrates endogenous as well as environmental signals to promote flowerdevelopment. The pathways and molecular networks involved are complex and integrate manymodes of signal transduction. In plants ubiquitin mediated protein degradation pathway has beenproposed to be as important mode of signaling as phosphorylation and transcription. Tosystematically study the role of ubiquitin signaling in the molecular regulation of flowering wehave taken a genomic approach to identify flower related Ubiquitin Proteasome Systemcomponents. As a large and versatile gene family the RING type ubiquitin E3 ligases were chosenas targets of the genomic screen. To this end the complete list of Arabidopsis RING E3 ligaseswere retrieved and verified in the Arabidopsis genome v11. Their differential expression was usedfor their categorization into flower organs or developmental stages. Known regulators of floweringtime or floral organ development were identified in these categories through literature search andrepresentative mutants for each category were purchased for functional characterization by growthand morphological phenotyping. To this end, a workflow was developed for high throughputphenotypic screening of growth, morphology and flowering of nearly a thousand Arabidopsisplants in one experimental round.

KW - 414 Agricultural biotechnology

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KW - flower

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KW - ubiquitin

KW - high throughput

KW - image based phenotyping

KW - phenomics data analysis

KW - ZINC-FINGER PROTEIN

KW - PROTEASOME SYSTEM

KW - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

KW - CONSTANS EXPRESSION

KW - GENE-EXPRESSION

KW - GABI-KAT

KW - THALIANA

KW - plant

KW - time

KW - information

U2 - 10.3389/fpls.2017.00416

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