Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Conserved Nuclear Membrane Protein As an Essential Component of Plant Nuclear Lamina Is Required for Proper Genome Organization and Activity

ABSTRACT: Plant conserved nuclear membrane protein PNET2 was identified to associate with nucleoskeleton protein CRWN and KAKU4, nucleosome histone H2. As an essential component of nuclear lamina, PNET2 is required for global transcriptional reprogramming and chromasomal packing, thus to control plant survival.

INSTRUMENT(S): LTQ Orbitrap Elite

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

TISSUE(S): Plant Cell, Seedling

SUBMITTER: Yu Tang

LAB HEAD: Yangnan Gu

PROVIDER: PXD026924 | Pride | 2023-03-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MS181575_PNET2_A-3.msf	Msf
	MS181575_PNET2_A-3_1.raw	Raw
	MS181575_PNET2_A-3_2.raw	Raw
	MS181575_PNET2_A-3_3.raw	Raw
	MS181575_PNET2_A-3_4.raw	Raw

Items per page:

1 - 5 of 127

Publications

GBPL3 localizes to the nuclear pore complex and functionally connects the nuclear basket with the nucleoskeleton in plants.

Tang Yu Y Ho Man Ip MI Kang Byung-Ho BH Gu Yangnan Y

PLoS biology 20221021 10

The nuclear basket (NB) is an essential structure of the nuclear pore complex (NPC) and serves as a dynamic and multifunctional platform that participates in various critical nuclear processes, including cargo transport, molecular docking, and gene expression regulation. However, the underlying molecular 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 ...[more]

PMID: 36269771

Similar Datasets

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

A plant-specific mitochondria outer membrane protein regulates mitochondrial fusion

Project description:Mitochondria are essential organelles in eukaryotes for energy production and are composed by a double-layered membrane structure that contains a smooth mitochondrial outer membrane (MOM) and a highly invaginated mitochondrial inner membrane (MIM). Mitochondria are dynamic with the ability to fuse and divide, constantly forming changing tubular networks in most eukaryotic cells. However, how mitochondria fusion occurs and functions in plants remains unclear. Here, we identified SAV as an outer membrane mitochondrial component mediates mitochondria fusion and is involved in plant development in Arabidopsis.

2024-09-05 | PXD039252 | Pride

Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice

Project description:Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Despite hundreds of stress-related genes being identified, only a few have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, a hub stress regulator that integrates the regulations of both drought and heat tolerance in rice. ONAC023 positively regulates drought and heat tolerance at both seedling and reproductive stages. Notably, the functioning of ONAC023 is obliterated without stress treatment and can be triggered by drought and heat stresses at two layers. Besides the stress-induced expression, ONAC023 also exhibits cytoplasm-nucleus transport via a remorin-importin-α-assisted pathway regulated by the stress-dependent dephosphorylation of OsREM1.5. Under drought or heat stress, the nuclear ONAC023 can target and promote the expression of diverse genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various processes including water transport, reactive oxygen species homeostasis, and alternative splicing. These results manifest that ONAC023 is fine-tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.

2024-06-13 | PXD046729 | Pride

TurboID-mediated proximity labeling for screening interacting proteins of FIP37 in Arabidopsis

Project description:Proximity labeling (PL) was recently developed to detect protein–protein interactions (PPIs) and members of subcellular multiprotein structures in living cells. Proximity labeling is conducted by fusing an engineered enzyme with catalytic activity, such as biotin ligase, to a protein of interest (bait protein) to biotinylate adjacent proteins. The biotinylated protein can be purified by strep-tavidin beads, and identified by mass spectrometry (MS). TurboID is an engineered biotin ligase with high catalytic efficiency, which is used for proximity labeling. Although TurboID-based proximity labeling technology has been successfully established in mammals, its application in plant systems is limited. Here, we report the usage of TurboID for proximity labeling of FIP37, a core member of m6A methyltransferase complex, to identify FIP37 interacting proteins in Ara-bidopsis thaliana. By analyzing the MS data, we found 214 proteins biotinylated by GFP-TurboID-FIP37 fusion, including five components of m6A methyltransferase complex that have been previously confirmed. Therefore, the identified proteins may include potential proteins directly involved in the m6A pathway or functionally related to m6A-coupled mRNA processing due to spatial proximity. Moreover, we demonstrated the feasibility of proximity labeling tech-nology in plant epitranscriptomics studies, thereby expanding the application of this technology to more subjects of plant research.

2024-01-26 | PXD043041 | Pride

Nitric oxide synthase interactome

Project description:Identify the proteins interacting with human nitric oxide synthases

2023-06-01 | PXD040726 | Pride

Pathogen protein modularity enables mimicry of a host phosphatase

Project description:Pathogens rely on a diverse complement of effector proteins to manipulate host cellular processes. The devastating plant pathogen Phytophthora produces numerous effectors that consist of tandem repeats of the “(L)WY” motif. Here, we discovered a specific (L)WY-LWY combination that enables efficient recruitment of the Serine/Threonine protein phosphatase 2A (PP2A) core enzyme in plant hosts. Structural characterization of an effector-PP2A complex and biochemical analyses demonstrate multiple effectors adopt this module at the amino terminus to form functional PP2A holoenzymes but have divergent C-terminal LWY units. Our results discovered a virulence strategy widely employed by Phytophthora in which an essential phosphatase complex of the host is appropriated to promote disease and highlight how diversification in an effector repertoire is promoted by protein modularity.

2024-10-01 | PXD034179 | Pride

The inner nuclear membrane-associated degradation system in plants

Project description:The homeostasis of the inner nuclear membrane (INM) proteins plays a critical role in regulating the nuclear structure, genome integrity, and signal transduction. However, little is known about the turnover of INM proteins in higher eukaryotes. Here we demonstrated that the conserved INM protein SUN1 undergoes proteasome-dependent degradation in Arabidopsis. Using in vivo proximity labeling-coupled mass spectrometry, we showed that SUN1 associates with the CDC48 complex, which mediates membrane protein extraction and proteolysis. Moreover, we discovered a specific subclade of plant ubiquitin regulatory X (UBX) domain-containing proteins (PUXs), including PUX3, PUX4, and PXU5, that negatively regulate this process. The three PUX proteins associate with the nucleoskeleton to target the INM, where they physically interact with CDC48, likely directly regulating the activity or substrate specificity of CDC48. Our findings provide direct evidence for the existence of plant INM-associated degradation pathway and uncover a nucleoskeleton-associated regulatory mechanism for it.

2020-03-11 | PXD015920 |

Function of plant oncogenes(1)

Project description:The rolB plant oncogene exerts its oncogenic properties by modulating the abundance of chaperones

2018-02-09 | PXD005889 | Pride

Nuclear RNA forms an interconnected network of transcription-dependent and tunable microgels

Project description:The human cell nucleus is comprised of proteins, chromatin and RNA, yet how they interact to form supramolecular structures and drive key biological processes remains unknown. Conflicting models have proposed either a fluid-like or solid-like nature for the intranuclear microenvironment. To reconcile this discrepancy, we investigated the 3D structure and properties of the nuclear interior using experiments and computer simulations. We reveal a novel mechanism where newly synthesized RNA interacts with SAF-A (scaffold attachment factor A, or HNRNPU), forming interconnected microgels degraded by the exonuclease XRN2, leading to dynamic cycles of gelation and fluidization. This emergent microgel network depends on transcription, and is disrupted by SAF- A depletion. It also decreases protein mobility and regulates chromatin compaction by modulating microphase separation, thereby opening transcriptionally active regions. This tunable intranuclear network exhibits scale-dependent fluid- and solid-like features, that we suggest may regulate transcription by controlling access to regulatory proteins and polymerases.

2024-06-18 | PXD053208 | Pride

iTRAQ-based proteomic analysis reveals genome-wide protein expression patterns in allohexaploid bread wheat in adaptation to potassium deficiency and an important role of jasmonic acid

Project description:Two-week old bread wheat seedlings hydroponically grown Hoagland solution were transferred to potassium (K+)-free conditions for 8 d, their root and leaf proteome profiles were assessed using iTRAQ proteome method, and NCBInr database combined with the recently published bread wheat genome information were used to analyze the identified protein species. Over 4,000 unique proteins were identified, 818 K+-responsive protein species showed significant abundance regulation. The most majority of the identified K+-responsive protein species had exact gene loci, and showed no global but tissue- and chromosome- dependent genome distributions. The identified protein species were associated with diverse functions and exhibited organ-specific differences. Most of identified protein species associated with hormone synthesis were the enzymes involved in the synthesis of jasmonic acid (JA). Allene oxide synthase (AOS), a key JA synthesis-related enzyme, was significantly induced in both root and leaf organs of K+-deficient wheat seedlings, and its overexpression in rice enhanced the tolerance to low K+ or K+ deficiency, increased contents of K+ and JA and transcription levels of some K+-responsive genes. However, rice AOS T-DNA inserted mutant (osaos) exhibited more sensitivity to K+ deficiency. K+ deficiency significantly increased abundance of a high affinity K+ transporter (TaAHAK1), TaAHAK1 transgenic rice seedlings markedly alleviated sensitivity to K+ deficiency, and K+ deficiency also upregulated expression of homologous OsHAK1 gene in TaAOS transgenic rice plants. These results suggested an essential role of JA in K+ deficiency and gave molecular insight into the responses of plant to K+ deficiency.

2017-10-09 | PXD003570 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data