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Arabidopsis thaliana PSS1 TurboID C-teminal fusion

ABSTRACT: Arabidopsis, PSS1, miniTurbo, proximity labeling, nonhost resistance, Phytophthora sojae, protein interactome, mass spectrometry

INSTRUMENT(S):

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

TISSUE(S): Seedling

SUBMITTER: Christian Montes Serey

LAB HEAD: Madan K. Bhattacharyya

PROVIDER: PXD065664 | Pride | 2026-06-11

REPOSITORIES: Pride

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	0116_CMS_240301-OA-TMTp_FAIMS-TbID_C-4x1000ng_OE480-01.raw	Raw
	0116_CMS_240301-OA-TMTp_FAIMS-TbID_C-4x1000ng_OE480-02.raw	Raw
	0116_CMS_240301-OA-TMTp_FAIMS-TbID_C-4x1000ng_OE480-03.raw	Raw
	0116_CMS_240301-OA-TMTp_FAIMS-TbID_C-4x1000ng_OE480-04.raw	Raw
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Publications

Proximity labelling suggests association of the nonhost receptor PSS1 protein with enzymes of multiple defense pathways in Arabidopsis.

Akintayo Oluwatoyosi F OF Montes Serey Christian C Walley Justin W JW Bhattacharyya Madan K MK

Frontiers in plant science 20260305

<h4>Introduction</h4><i>PSS1</i> encoding a glycine-rich integral plasma membrane protein plays a pivotal role in nonhost resistance of Arabidopsis against the soybean pathogens, <i>Phytophthora sojae</i> and <i>Fusarium virguliforme</i>. Notably, <i>P. sojae</i> fails to penetrate the wildtype Col-0 ecotype but not the pss1 mutant. To elucidate the molecular basis of <i>PSS1</i>-mediated nonhost immunity, we employed a miniTurbo-based proximity labeling approach.<h4>Methods</h4>The miniTurbo fu ...[more]

PMID: 41869043

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Arabidopsis thaliana PSS1 TurboID N-teminal fusion

Project description:The Arabidopsis PSS1 gene, which encodes a glycine-rich protein, plays a pivotal role in nonhost resistance to the soybean oomycete Phytophthora sojae and the fungal pathogen Fusarium virguliforme. To elucidate the molecular basis of PSS1-mediated immunity, we employed miniTurbo-based proximity labeling in stable transgenic Arabidopsis lines expressing miniTurbo fused to either wild-type PSS1 or its nonfunctional mutant variant, PSS1G119D. Seedlings were challenged with or without P. sojae, and biotinylated proteins were isolated and analyzed by mass spectrometry. The resulting PSS1 interactomes revealed several candidate proteins predominantly localized in the plastid and cytosol. Notably, proteins such as LIN2, ATPMEPCRA, and TGG1 were specifically enriched in wild-type PSS1 lines under P. sojae infection, suggesting their potential involvement in PSS1-mediated nonhost resistance. Our findings offer novel insights into immune protein networks and provide a foundational resource for dissecting nonhost immunity mechanisms in plants

2026-06-11 | PXD065660 | Pride

SRSF12 is a primate-specific splicing factor that induces a tissue-specific gene expression program

Project description:Alternative splicing expands proteomic diversity and is tightly regulated by splicing factors, including the serine/arginine-rich (SR) protein family. Here, we analyze the poorly characterized protein SRSF12. Although SRSF12 is conserved across vertebrates, it is poorly expressed in most mammals, and we find that SRSF12 knockouts in mice do not result in overt physiological or transcriptomic alterations. In contrast, SRSF12 is more highly expressed in primates where it is predominantly expressed during meiosis and in the brain. SRSF12 localizes to splicing speckles in cultured human cells and interacts with the core splicing factors. Strikingly, ectopic expression of SRSF12 in human cells induces widespread transcriptional changes, activating testis- and brain-specific gene expression programs. SRSF12 overexpression also leads to mitotic arrest and cell death, phenotypes that require both its structured RNA recognition motif and intrinsically disordered arginine/serine-rich C-terminal domain. Together, our results suggest that SRSF12 has evolved primate-specific expression to regulate testis- and brain-specific genes.

2026-01-05 | PXD066334 | Pride

TEAD1 condensates are transcriptionally inactive storage sites on the pericentromeric heterochromatin

Project description:TEA domain transcription factor 1 (TEAD1), a Hippo pathway transcription factor important in cellular homeostasis and development, is increasingly implicated in cancer biology. Here, we reveal a novel role for TEAD1 in organizing nuclear condensates, independent of active transcription. Using high-resolution imaging, ChIP-seq, RNA-seq and proximity-based proteomics, we demonstrate that in patient-derived renal cell carcinoma cells, TEAD1 forms micron-sized foci by binding to the heterochromatic pericentromeric regions using its DNA-binding domain. These TEAD1 foci do not mediate transcription but instead serve as depots for excess TEAD 1. This contrasts with TEAD1 organization in other genomic regions of both RCC and normal kidney cells, where TEAD1 associates with markers of active transcription. Our findings provide a mechanistic framework for TEAD1’s dual regulatory roles, offering new insights into its contribution to transcriptional dysregulation and tumor progression.

2026-04-27 | PXD072858 | Pride

Comprehensive retinal characterization of myopic guinea pigs after PI3K/AKT inhibition via data-independent acquisition on an Orbitrap Exploris 480 mass spectrometer.

Project description:Myopia progression is driven by abnormal signaling pathways, particularly the PI3K/AKT pathway. Using a lens-induced myopia model in guinea pigs, we administered the PI3K/AKT inhibitor LY294002 via intravitreal injection and performed quantitative proteomic analysis with data-independent acquisition mass spectrometry. This study provides retinal proteomic data from normal, myopic, and drug-treated guinea pigs. It also establishes the first comprehensive retinal proteome database for guinea pig myopia, offering insights into myopia development and the role of the PI3K/AKT pathway in its progression.

2026-03-23 | PXD074201 | Pride

A genome-wide screen for essentiality upon telomerase inhibition identifies a novel p53 regulator, C16ORF72/TAPR1

Project description:Telomere erosion contributes to age-associated tissue dysfunction and senescence, and p53 plays a crucial role in this response. We undertook a genome-wide screen to identify gene deletions that sensitized p53-positive human cells to loss of telomere integrity, and uncovered a previously unannotated gene, C16ORF72, which we term Telomere Attrition and p53 Response 1: TAPR1. CRISPR-Cas9 mediated deletion of TAPR1 led to elevated p53 and induction of p53 transcriptional targets. TAPR1-disrupted cells exhibited a synthetic-sick relationship with the loss of telomerase, or treatment with the topoisomerase II inhibitor doxorubicin. Stabilization of p53 with nutlin-3a further decreased cell fitness in cells lacking TAPR1 or telomerase, whereas deletion of TP53 rescued the decreased fitness of TAPR1-deleted cells. We propose that TAPR1 regulates p53 turnover, thereby tapering the p53-dependent response to telomere erosion. We discuss the possible implications of such a mechanism in the preservation of genome integrity during senescence or aging.

2021-03-04 | PXD022128 | Pride

Proteomic analysis of LysoIP from HeLa untagged, Control and ASAH1-/-

Project description:This quantitative proteomic analysis of lysosome-enriched fractions isolated by immunoprecipitation (LysoIP) from HeLa cells expressing TMEM192-3xHA, untagged controls, and ASAH1 knockout lines. Triplicate biological replicates were processed using TMTpro 18-plex labeling and high-resolution Orbitrap mass spectrometry with FAIMS. Data were searched against the human proteome with stringent FDR filtering and reporter ion quantification, enabling comparative profiling of lysosomal protein composition and changes associated with ASAH1 deficiency.

2025-08-12 | PXD067219 | Pride

CRISPR activation of the ribosome-associated quality control factor ASCC3 ameliorates fragile X syndrome phenotypes in mice

Project description:Loss of fragile X messenger ribonucleoprotein (FMRP) causes fragile X syndrome (FXS), an inherited neurodevelopmental disorder resulting in intellectual disability and autism-spectrum disorder. Despite the prevalence of the FXS, the molecular function of FMRP remains uncertain. Here, we showed that FMRP regulates collided ribosomes. Activating signal cointegrator 1 complex subunit 3 (ASCC3), an early-acting ribosome-associated quality control (RQC) factor, was identified as an FMRP-interacting protein. Mechanistically, FMRP recruits ASCC3 to collided ribosomes and either positively or negatively regulates translation, depending on transcript context. Disease-associated ASCC3 variants that perturbed ASCC3-FMRP interaction were defective in ribosome association and handling of collided ribosomes. In FXS patient cells and mouse models of FXS, ASCC3 abundance was reduced, and Clustered Regularly Interspaced Short Palindromic Repeats-mediated activation (CRISPRa) of ASCC3 overcame challenges to conventional gene delivery approaches presented by the sheer size of ASCC3 and rescued synaptic defects and behavioral deficits. In conclusion, these data implicated FMRP in the handling of collided ribosomes to maintain protein homeostasis during neurodevelopment and synaptogenesis and showed. Proof-of-concept that targeting RQC may offer alternative treatment strategies for FXS.

2026-04-20 | PXD067852 | Pride

Transcription profiling of Arabidopsis overexpressers and mutants of TFs-gene LBD37 and LBD38 under different nitrogen regimes

Project description:Nitrogen (N) and nitrate (NO3-) per se regulate many aspects of plant metabolism, growth and development. N/NO3- also suppresses parts of secondary metabolism including anthocyanin synthesis. Molecular components for this repression are unknown. We report that three N/NO3--induced members of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family of transcription factors (LBD37, LBD38 and LBD39) act as negative regulators of anthocyanin biosynthesis in Arabidopsis (Arabidopsis thaliana). Over-expression of each of the three genes in the absence of N/NO3- strongly suppresses the key regulators of anthocyanin synthesis PAP1 and PAP2, genes in the anthocyanin-specific part of flavonoid synthesis, as well as cyanidin- but not quercetin- or kaempferol-glycoside production. Conversely, lbd37, lbd38 or lbd39 T-DNA insertion mutants accumulate anthocyanins when grown in N/NO3--sufficient conditions and show constitutive expression of anthocyanin biosynthetic genes. The LBD genes also repress many other known N-responsive genes including key genes required for NO3- uptake and assimilation, resulting in altered NO3- content, nitrate reductase activity/activation, protein, amino acid and starch levels, and N-related growth phenotypes. The results identify LBD37 and its two close homologs as novel repressers of anthocyanin biosynthesis and N-availability signals in general. They also show that besides being developmental regulators LBD genes fulfill roles in metabolic regulation. We used microarrays to test whether LBD37 and LBD38 have a more widespread role in NO3-/N-regulation. Experiment Overall Design: 9-day old Arabidopsis seedlings were harvested for RNA extraction and hybridization on Affymetrix microarrays. Total RNA was prepared separately from three biological replicates of N-limited LBD37OX, LBD38OX and WT seedlings, and N-replete lbd37-1 mutant, lbd38 mutant and WT seedlings (18 samples).

2009-11-28 | E-GEOD-18818 | biostudies-arrayexpress

Dynamic proximity based interactome of the transcription factor RELA to identify gene-regulatory networks revealed

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2024-11-04 | PXD045888 | Pride

Mesoscale regulation of microtubule-organising centres by the E3 ligase TRIM37

Project description:Centrosomes ensure accurate chromosome segregation during cell division. Although the regulation of centrosome number is well-established, less is known about the suppression of non-centrosomal Microtubule-Organising Centres (ncMTOCs). The E3 ligase TRIM37, implicated in Mulibrey nanism and 17q23-amplified cancers, has emerged as a key regulator of both centrosomes and ncMTOCs. Yet, the mechanism by which TRIM37 achieves enzymatic activation to target these mesoscale structures had thus far remained unknown. Here, we elucidate the activation process of TRIM37, unveiling a process that initiates with TRAF domain-directed substrate recognition, followed by B-box domain-mediated oligomerisation, and culminates in RING domain dimerisation. Using optogenetics, we demonstrate that the E3 activity of TRIM37 is directly coupled to the assembly state of its substrates, being activated only when centrosomal proteins cluster into higher-order assemblies resembling MTOCs. This regulatory framework provides a mechanistic basis for understanding TRIM37-driven pathologies and echoes the restriction of the HIV capsid by TRIM5, thus unveiling a conserved activation blueprint among TRIM proteins to control turnover of complexes assembled at the mesoscale level.

2025-03-18 | PXD061083 | Pride

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