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Arabidopsis SLOMO-Decoy line AP-MS

ABSTRACT: SLOMO is an F-box protein, but little is known about its function and interactors as an F-box protein. we used a SLOMO-decoy approach here. The SLOMO-decoy protein, which lacks the F-box domain, is still able to bind to substrates but lacks the ability to recruit E2 conjugating enzymes to mediate substrate ubiquitination and degradation. We generated a stable Arabidopsis line expressing 35S::GFP:SLOMO-Decoy, and performed immunoprecipitation mass spectrometry (IP-MS) analyses on GFP:SLOMO-decoy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Root, Shoot

SUBMITTER: Shanshuo Zhu

LAB HEAD: Ive De Smet

PROVIDER: PXD028319 | Pride | 2025-05-26

REPOSITORIES: Pride

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			Action	DRS
	E21461_u_1p_PSB-204_1.7z	Other
	E21463_u_1p_PSB-204_2.7z	Other
	E21465_u_1p_PSB-204_3.7z	Other
	E21467_u_1p_PSB-204_4.7z	Other
	E21469_u_1p_PSB-204_5.7z	Other

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1 - 5 of 14

Publications

Phosphoproteome analyses pinpoint the F-box protein SLOW MOTION as a regulator of warm temperature-mediated hypocotyl growth in Arabidopsis.

Zhu Shanshuo S Pan Lixia L Vu Lam Dai LD Xu Xiangyu X Orosa-Puente Beatriz B Zhu Tingting T Neyt Pia P van de Cotte Brigitte B Jacobs Thomas B TB Gendron Joshua M JM Spoel Steven H SH Gevaert Kris K De Smet Ive I

The New phytologist 20231110 2

Hypocotyl elongation is controlled by several signals and is a major characteristic of plants growing in darkness or under warm temperature. While already several molecular mechanisms associated with this process are known, protein degradation and associated E3 ligases have hardly been studied in the context of warm temperature. In a time-course phosphoproteome analysis on Arabidopsis seedlings exposed to control or warm ambient temperature, we observed reduced levels of diverse proteins over ti ...[more]

PMID: 37950543

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A conserved signaling complex controls warm temperature-mediated plant growth

Project description:The model plant Arabidopsis thaliana responds to mild high temperature by increased elongation growth of organs to enhance cooling capacity, in a process called thermomorphogenesis. Our understanding of the genetic regulation of thermomorphogenesis has increased in recent years. However, hardly anything is known about molecular mechanisms outside A. thaliana and cellular signaling pathways have been underexplored. Therefore, we mapped changes in protein phosphorylation in A. thaliana and crops exposed to warm temperature. Based on these results, we identified and characterized a novel, functionally conserved signaling complex of MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASEs (MAP4KS) in warm temperature-mediated growth regulation in plants. This contributes to our understanding of warm temperature signaling, and can help guarantee food security under a changing climate

2021-03-25 | PXD015483 | Pride

Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor

Project description:The F-box protein MORE AXILLARY GROWTH 2 (MAX2) is a central component in the signaling cascade of strigolactones (SLs) as well as of the smoke derived karrikins (KARs) and the so far unknown endogenous KAI2 ligand (KL). The two groups of molecules are involved in overlapping and unique developmental processes, and signal-specific outcomes are attributed to perception by the paralogous α/β-hydrolases DWARF14 (D14) for SL and KARRIKIN INSENSITIVE 2/ HYPOSENSITIVE TO LIGHT (KAI2/HTL) for KAR/KL. Additionally, depending on which receptor is activated, specific members of the SUPPRESSOR OF MAX2 1 (SMAX1) – LIKE (SMXL) 6, 7, 8 clade control KAR/KL and SL responses respectively. As proteins that function in the same signal transduction pathway often occur in large protein complexes, we aimed at discovering new players of the MAX2, D14 and KAI2 protein network by tandem affinity purification using Arabidopsis cell cultures. When using MAX2 as a bait, various proteins were co-purified among which general components of the Skp1-Cullin-F-box complex and members of the CONSTITUTIVE PHOTOMORPHOGENIC 9 signalosome. Here, we report the identification of a novel interactor of MAX2, a type 5 serine/threonine protein phosphatase, designated PHYTOCHROME-ASSOCIATED PROTEIN PHOSPHATASE 5 (PAPP5). Quantitative affinity purification pointed at PAPP5 as being more present in KAI2 rather than D14 protein complexes. In agreement, mutant analysis suggests that PAPP5 modulates KAR/KL-dependent seed germination in suboptimal conditions and seedling development. Additionally, PAPP5 was found to dephosphorylate MAX2 in vivo independent of the synthetic strigolactone analog, rac-GR24. Together, by analyzing the protein complexes to which MAX2, D14 and KAI2 belong, we revealed a new MAX2 interactor that might act through dephosphorylating MAX2 to control mainly KAR/KL signaling.

2021-01-06 | PXD015657 | Pride

Nucleo-cytoplasmic distribution of SAP18 reveals its dual function in splicing and thermotolerance in Arabidopsis

Project description:The dynamic shuttling of proteins between the nucleus and cytoplasm orchestrates vital functions in eukaryotes. Here, we unveil multifaceted functions of Arabidopsis Sin3-associated protein 18 kDa (SAP18) in regulating development and stress tolerance. As a crucial component of the Apoptosis- and Splicing-Associated Protein (ASAP) complex in the nucleus, SAP18 plays an integral role in the precise splicing of genes associated with leaf development, decoding its significance in post-transcriptional regulatory networks. Under heat shock conditions, SAP18 relocates to cytoplasmic stress granules and processing bodies, suggesting a novel thermoprotective role. This dual localization highlights SAP18 versatility in coordinating cellular responses, encompassing both nuclear splicing regulation and cytoplasmic stress granule dynamics. Our findings significantly expand the understanding of the intricate involvement of SAP18 in plant growth, and pave the way for future exploration of its diverse functions in thermotolerance mechanisms.

2024-11-04 | PXD050985 | Pride

Chip-chip from HepG2 cells and HepG2 cells with slug overexpression

Project description:The transcription factor slug represses genes with E-box and then activates cancer stem cell related pathway: Wnt, Notch and Hedgehog pathway. Chromatin immunoprecipitation (ChIP) of slug by ChIP-on-chip analysis demonstrated that slug indirectly activates cancer stem cell related pathway and thus promotes vasculogenic mimicry formation. Comparison of HepG2-control in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel.

2012-09-21 | E-GEOD-41027 | biostudies-arrayexpress

LZY-interacting proteins in Arabidopsis

Project description:In many plant species, roots maintain specific growth angles relative to the direction of gravity, known as gravitropic set point angles (GSA). These contribute to the efficient acquisition of water and nutrients. AtLAZY1/LAZY1-LIKE (LZY) genes are involved in GSA control by regulating auxin flow toward the direction of gravity in Arabidopsis. LZYs are plant-specific unknown proteins with no domain for which the function is inferable. To clarify the molecular function of LZYs, we identified the proteins that interact with them by immunoprecipitation coupled with mass spectrometry.

2020-01-09 | PXD016219 | Pride

The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum

Project description:In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. Here, we demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.

2024-04-30 | PXD051782 | Pride

Analysis of RIP-seq of Ded1 and eIF4A(Tif1) with and without glucose depletion

Project description:The aim of this experiment was to look at RNAs which associate with DEAD-box RNA helicases with and without 10 minutes of glucose starvation.

2021-09-30 | E-MTAB-9095 | biostudies-arrayexpress

SMAX1/SMXL2 interacting proteins in Arabidopsis seedling through IP-MS

Project description:Karrikins (KARs) are a class of butenolide molecules found in smoke. KARs regulate many aspects of plant development and environmental responses, including Seed germination, hypocotyl elongation, leaf shape, root development, and resistance to drought, salt, and heat stress. The transcriptional repressor proteins SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-like2 (SMXL2) integrate karrikin signaling by repressing gene expression through direct binding to promoters or through inhibiting activities of transcription factors. To elucidate the mechanism by which SMAX1 and SMXL2 mediate KAR signaling, we performed immunoprecipitation followed by mass spectrometry (IP-MS) analysis and identified peptides in transgenic seedlings that overexpress GFP, SMAX1-GFP, and SMXL2-GFP, respectively.

2024-06-22 | PXD052400 | Pride

Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells

Project description:DDX6 is an abundant cytoplasmic DEAD-box RNA helicase which is involved in disparate aspects of mRNA stability and translation, leading to a confused understanding of its global function. We carried out a large-scale study of total and polysomial mRNA after DDX6 depletion to get an accurate picture of its roles in human cells.

2017-09-28 | E-MTAB-4091 | biostudies-arrayexpress

ChIP-Seq of fly Schneider S2 cells to investigate CID islands

Project description:The centromere-specific Histone H3-variant CENH3 (also known as CENP-A) is considered to be an epigenetic mark for establishment and propagation of centromere identity. Pulse-induction of CENH3 (Drosophila CID) in Schneider S2 cells incorporates into noncentromeric regions and generates CID islands that resist clearing from chromosome arms for multiple cell generations. We demonstrate that CID islands represent functional ectopic kinetochores, which are non-randomly distributed on the chromosome and display a preferential localization near telomeres and pericentric heterochromatin in transcriptionally silent, intergenic chromatin domains. Although overexpression of heterochromatin protein 1 (HP1) or increasing Histone acetylation interferes with CID islands formation on a global scale, induction of a locally defined region of synthetic heterochromatin by targeting HP1-LacI fusions to stably integrated Lac Operator arrays produces a proximal hotspot for CID islands formation. These data suggest that the characteristics of regions bordering heterochromatin promote de novo kinetochore assembly and thereby contribute to centromere identity.

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