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Transcriptome analysis of mutations in plant novel nuclear basket protein GBPL3 pnet2_abc mutants

ABSTRACT: Transcriptome analysis of mutations in plant novel nuclear basket protein GBPL3 pnet2_abc mutants

PROVIDER: PRJNA821100 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18516930_1.fastq.gz	Fastqsanger.gz
	SRR18516930_2.fastq.gz	Fastqsanger.gz
	SRR18516931_1.fastq.gz	Fastqsanger.gz
	SRR18516931_2.fastq.gz	Fastqsanger.gz
	SRR18516932_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of mutations in plant novel nuclear basket protein GBPL3 pnet2_abc mutants

Project description:Purpose: To understand the molecular mechanism underlying the phenotype caused by mutation in the plant novel nuclear basket protein GBPL3, we performed the whole genome transcriptome analysis on 7-day-old seedlings of WT, gbpl3 mutant using RNA-seq. Conclusions: PNET2 negatively regulates immune response and positively regulates auxin signal and microtuble activity.

2022-03-30 | GSE199667 | GEO

GBPL3 is a novel component of the nuclear pore complex and functionally connects the nuclear basket with the nucleoskeleton in plants

Project description:The nuclear basket (NB) is an essential structure of the nuclear pore complex (NPC). It serves as a dynamic and multi-functional platform that participates in various critical nuclear processes, including cargo transport, molecular docking, and gene expression regulation. However, the compositional and functional mechanisms are not completely understood, particularly in plants. Here, we identified a guanylate-binding protein (GBP)-like GTPase (GBPL3) as a novel NPC basket component in Arabidopsis. Using fluorescence and immunoelectron microscopy, we found that GBPL3 is enriched in the nuclear rim and localizes to the nuclear pore. Proximity labeling proteomics and protein-protein interaction assays revealed that GBPL3 is predominantly distributed at the NPC basket and physically associated with NB nucleoporins as well as many chromatin remodelers, transcription apparatus, and regulators, and the RNA splicing and processing machinery, suggesting a conserved function of the nuclear basket in transcription regulation as reported in yeasts and animals. Moreover, we found that GBPL3 physically interacts with the nucleoskeleton via its disordered coiled-coil regions. Simultaneous loss of GBPL3 with any one of all the four Arabidopsis nucleoskeleton genes CRWNs led to distinct development- and stress-related phenotypes, ranging from seedling lethality to leaf lesions, concomitant aberrant transcription of stress-related genes. Our results indicate that GBPL3 is a bona fide component of the plant NPC and physically and functionally connects the nuclear basket with different components of the nucleoskeleton, which is required for the coordination of plant development and stress responses.

2022-08-25 | PXD032906 | Pride

Meiotic Nuclear Pore Complex Modularity Provides Key Insights into Nuclear Basket Organization

Project description:Using phosphoproteomics and time-lapse fluorescence microscopy, we report that NPCs nuclear pore complexes (NPCs) undergo two distinct modularity events for the nucleoporins Nup60 and Nup2 during budding yeast meiosis: partial and full nuclear basket detachment.

2022-12-08 | PXD033245 | Pride

Docking a flexible basket onto the core of the nuclear pore complex

Project description:The nuclear basket attaches to the nucleoplasmic side of the nuclear pore complex (NPC), coupling transcription to mRNA quality control and export. The basket expands the functional repertoire of a subset of NPCs in S. cerevisiae by drawing a unique RNA/protein interactome. Yet, how the basket docks onto the NPC core remains unknown. By integrating AlphaFold-powered interaction screens, electron microscopy and membrane-templated reconstitution, we uncovered a membrane-anchored tripartite junction between basket and NPC core. The basket subunit Nup60 harbours three adjacent short linear motifs (SLiMs) which connect Mlp1, a parallel homodimer consisting of coiled-coil segments interrupted by flexible hinges, and the Nup85 subunit of the Y-complex. We reconstituted the Y-complex•Nup60•Mlp1 assembly on a synthetic membrane and validated the protein interfaces in vivo. Our study explains how a SLiM-based protein junction can substantially reshape NPC structure and function, advancing our understanding of compositional and conformational NPC heterogeneity.

2024-07-11 | PXD052015 | Pride

Distinct Basket Nucleoporins roles in Nuclear Pore Function and Gene Expression

Project description:Nuclear pore complexes (NPCs) are important for cellular functions beyond nucleocytoplasmic trafficking, including genome organization and gene expression. This multi-faceted nature and the slow turnover of NPC components complicates investigations of how individual nucleoporins act in these diverse processes. To address this question, we used an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins Nup153, Nup50 and Tpr. Here, we provide MS data for the Nuclear Pore-enriched fraction of human DLD-1 cells, expressing CRISPR-engeneered degron, fused with the endogenous locus of corresponding basket NUPs, in the absence or presence of Auxin.

2020-06-30 | PXD020075 | Pride

Transcriptome analysis of mutations in plant nuclear membrane proteins PNET2A/B/C

Project description:Purpose: To understand the molecular mechanism underlying the severe phenotype caused by mutations in the plant nuclear membrane proteins PNET2_A/B/C, we performed the whole genome transcriptome analysis on 7-day-old seedlings of WT, pnet2_ac and pnet2_bc double mutant, and pnet2_abc triple mutant using RNA-seq.

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Project description:Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance

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The canonical helixes of Nup50c drive its interaction with Nup82 at nuclear basket in plants

Project description:The nuclear basket (NB) as essential peripheral parts of nuclear pore complex (NPC), plays crucial roles in mRNA surveillance and transport, chromatin organization, and regulation of gene expression. However, the architectural and functional understanding of plant NB remains largely unknown. Using proximity labeling technology we identified a novel paralog of plant Nup50, designated Nup50c. Nup50c is predominantly located at the NB and interacts with plant-specific NB component Nup82. The C terminal region of Nup82 is responsible for the interaction with the canonical helixes of Nup50c and tethering it to the NPC.

2024-10-14 | PXD056763 |

Exome sequencing identified mutations in clpex mouse mutants

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The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores.

Project description:Transcription hinders replication fork progression and stability, and the Mec1/ATR checkpoint protects fork integrity. Examining checkpoint-dependent mechanisms controlling fork stability, we find that fork reversal or dormant origin firing owing to checkpoint defects are rescued in checkpoint mutants lacking THO, TREX-2 or inner basket nucleoporins. Gene gating tethers transcribed genes to the nuclear periphery and is counteracted by checkpoint kinases through phosphorylation of nucleoporins such as Mlp1. Checkpoint mutants fail to detach transcribed genes from nuclear pores, thus generating topological impediments for incoming forks. Releasing this topological complexity by introducing a double-strand break between a fork and a transcribed unit prevents fork collapse. Mlp1 mutants mimicking constitutive checkpoint-dependent phosphorylation also alleviate checkpoint defects. We propose that the checkpoint assists fork progression and stability at transcribed genes by phosphorylating key nucleoporins and counteracting gene gating, thus neutralizing the topological tension generated at nuclear pore gated genes.

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