Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics studies of the The GT1 domain of RNase J in Arabidopsis

ABSTRACT: This study investigates the function of the C-terminal GT1 domain of chloroplast RNase J in Arabidopsis thaliana, focusing on its role in RNA quality control and double-stranded RNA (dsRNA) metabolism. To characterize the molecular effects of GT1 domain disruption, comparative proteomic analyses were performed on transgenic Arabidopsis seedlings expressing FLAG-tagged RNase J variants: wild type (WTc), GT1 domain deletion (ΔGT), and GT1 tryptophan-mutated (mGT) forms that are deficient in nucleic acid binding.The resulting proteomic dataset supports the conclusion that loss or mutation of the GT1 domain does not markedly alter chloroplast protein accumulation, despite significant effects on chloroplast dsRNA levels and transcriptome organization. These findings establish a link between RNase J’s GT1 domain, dsRNA recognition, and plastid RNA quality control.

INSTRUMENT(S):

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

SUBMITTER: Oded Kleifeld

LAB HEAD: Gadi Schuster

PROVIDER: PXD069635 | Pride | 2026-01-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2025-01-06-decoys-contam-UP000006548.fas	Other
	Results.zip	Other
	Seq87402_480Ex2.raw	Raw
	Seq87403_480Ex2.raw	Raw
	Seq87404_480Ex2.raw	Raw

Items per page:

1 - 5 of 11

Similar Datasets

Small RNAs generated in vitro by budding-yeast Dicer

Project description:The Dicer ribonuclease III (RNase III) enzymes process long double-stranded RNA (dsRNA) into the small interfering RNAs (siRNAs) that direct RNA interference. Here, we describe the structure and activity of a catalytically active fragment of Kluyveromyces polysporus Dcr1, which represents the noncanonical Dicers found in budding yeast. The crystal structure reveals a homodimer that resembles bacterial RNase III but includes a novel N-terminal domain and newly identified catalytic residues conserved throughout eukaryotic RNase III enzymes. Biochemical analyses show that Dcr1 dimers bind cooperatively along the dsRNA substrate and cleave at precise intervals based on the distance between consecutive active sites. Thus, unlike canonical Dicers, which successively remove siRNA duplexes from the dsRNA termini, Dcr1 initiates processing in the interior and works outward. The distinct mechanism of budding-yeast Dicers establishes a novel paradigm for natural protein-based molecular rulers and imparts substrate preferences with ramifications for biological function.

2011-05-11 | GSE29168 | GEO

Small RNAs generated in vitro by budding-yeast Dicer

2011-05-11 | E-GEOD-29168 | biostudies-arrayexpress

Whole cell proteomic changes in high-light tolerant alga from the desert

Project description:Non-photochemical quenching (NPQ) mechanisms are crucial for protecting photosynthesis from photoinhibition in plants, algae, and cyanobacteria. Modulating these mechanisms has long been a goal for improving photosynthesis and crop yields. The current work demonstrates that Chlorella ohadii, a green micro-alga thriving in the desert under high light intensities that are fatal to many photosynthetic organisms, neither performs nor requires NPQ to protect photosynthesis under constant high light. This dataset includes the whole-cell proteomic changes that occur in Chlorella ohadii cultures grown under high light compared to those grown under low light, with a particular focus on changes in protein oxidative damage, as indicated by the oxidation of tryptophan residues.

2025-05-07 | PXD053918 | Pride

Rnase L reprograms translation by widespread mRNA turnover escaped by antiviral mRNAs

Project description:In response to foreign and endogenous double-stranded RNA (dsRNA), protein kinase R (PKR) and ribonuclease L (RNase L) reprogram translation in mammalian cells. PKR inhibits translation initiation through eIF2 phosphorylation, which triggers stress granule (SG) formation and promotes translation of stress responsive mRNAs. The mechanisms of RNase L-driven translation repression, its contribution to SG assembly, and its regulation of dsRNA stress-induced mRNAs are unknown. We demonstrate that RNase L drives translational shut-off in response to dsRNA by promoting widespread turnover of mRNAs. This alters stress granule assembly and reprograms translation by only allowing for the translation of mRNAs resistant to RNase L degradation, including numerous antiviral mRNAs such as IFN- . Individual cells differentially activate dsRNA responses revealing variation that can affect cellular outcomes. This identifies bulk mRNA degradation and the resistance of antiviral mRNAs as the mechanism by which RNaseL reprograms translation in response to dsRNA.

2019-07-10 | GSE124144 | GEO

RtcB RNAseq to map cyclic phosphate-bearing RNA fragments during poly I:C treatment

Project description:RNase L is activated by 2-5A, which is synthesized specifically upon dsRNA sensing. Activated RNase L cleaves cellular RNAs, generating fragments that bear 2'-3' cylic phosphate and/or 5'-OH. Here we perform cyclic-phosphate capture and RNA-seq to map the precise sites at which cleavage is induced during dsRNA stress.

2019-05-14 | GSE131130 | GEO

Structural insights into dsRNA processing by Drosophila Dicer-2/Loqs-PD

Project description:Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA silencing mechanism in many eukaryotes. In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), plays major role in generating 21 base-pair (bp) siRNA duplexes from long double-stranded RNAs (dsRNAs). The ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes. Here we report the cryo-EM structures of Dcr-2/Loqs-PD in the apo state and in multiple processing states of a 50-bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and significant conformational changes of Dcr-2 during a dsRNA processing cycle. The N-terminal helicase and DUF283 domains undergo conformational change upon initial dsRNA binding, forming an ATP binding pocket and a 5’-phosphate binding pocket. The overall conformation of Dcr-2/Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, while the interaction between DUF283 and RIIIDb domains prevents non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active center. Additional ATP-dependent conformational changes are required to form an active-dicing state and precisely cleave the dsRNA into 21-bp siRNA duplex confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full-cycle of ATP-dependent dsRNA processing by Dcr-2/Loqs-PD.

2022-04-21 | PXD033365 |

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:The RNA editing enzyme ADAR1, is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon inducible, is predominately cytoplasmic. Using three different approaches, co-IP with endogenous ADAR1, and Strep-tag co-IP and BioID with individual ADAR1 isoforms, a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors and editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a dsRNA-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with HMW poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.

2024-12-08 | PXD056080 | Pride

Determination of RNA Secondary Structure By RNA-Sequencing of HEK293T Cells

Project description:RNA molecule fold into three dimensional structures in order to fill important roles in the cell such as translation and post-transcriptional regulation. These three dimensional structures, in turn, depend on the pattern of hydrogen bonds between ribonucleotides. We employ a technique based on high throughput RNA Sequencing (RNA-Seq) to uncover this patter on a transcriptome wide scale. We take advantage of two ribonucleases that have structure specific activity. RNAse S1 specifically digests single stranded RNA while RNAse V1 is specific to double stranded RNA. We aliquot each of our sample into to reactions. One is thoroughly treated with RNAse S1, digesting away single stranded RNA and leaving behind dsRNA. The other is treated with RNAse V1, which has the inverse effect. The surviving dsRNA and ssRNA molecules are then subject to high throughput sequencing. The resulting reads are used to generate a structure score, revelaing which regions of each transcript are involved in base pairing and which are unpaired.

2016-05-17 | E-GEOD-72681 | biostudies-arrayexpress

Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response

Project description:During viral infection, several dsRNA sensors are activated in the cell and trigger changes in gene expression. One of these sensors activates a generic endonuclease, RNase L, that cleaves many types of RNA in the cell. However, how the resultant widespread RNA decay affects gene expression is not fully understood. Here we found that gene expression changes caused by activating dsRNA sensing pathways are tuned by RNase L activation, pointing to an intricate antiviral response where multiple inputs are integrated to create an optimized output. We show that RNA fragmentation induces the activation of the Ribotoxic Stress Response, potentially through ribosome collisions. The p38 and JNK pathways that are actuated as part of this response promote outcomes that likely inhibit the virus, such as programmed cell death. We also show that RNase L appears to limit the translation of genes that are regulated by another dsRNA-induced pathway, the Integrated Stress Response. Intriguingly, we found the activity of another generic endonuclease, RNase A, recapitulates many of the same molecular phenotypes as activated RNase L, demonstrating how widespread RNA cleavage events can directly evoke an antiviral program.

2024-04-30 | GSE244125 | GEO

Endonucleolytic RNA cleavage drives changes in gene expression during the innate immune response [ribosome profiling]

2024-04-30 | GSE244176 | GEO