Browse
Submit Data
Databases
API
Help

Dataset Information

395 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of exogenous auxin on the Arabidopsis thaliana root proteome

ABSTRACT: This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.

INSTRUMENT(S): Synapt MS

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

TISSUE(S): Plant Cell, Root

SUBMITTER: Keith Ray

LAB HEAD: Richard F. Helm

PROVIDER: PXD001400 | Pride | 2017-07-18

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	130626_C12A_2_25_mM.raw.zip	Raw
	130626_C12A_2_75_mM.raw.zip	Raw
	130626_C12A_3_150_mM.raw.zip	Raw
	130626_C24A_2_350_mM.raw.zip	Raw
	130626_C24B_2_75_mM.raw.zip	Raw

Items per page:

1 - 5 of 164

Publications

Exogenous Auxin Elicits Changes in the Arabidopsis thaliana Root Proteome in a Time-Dependent Manner.

Slade William O WO Ray W Keith WK Hildreth Sherry B SB Winkel Brenda S J BSJ Helm Richard F RF

Proteomes 20170710 3

Auxin is involved in many aspects of root development and physiology, including the formation of lateral roots. Improving our understanding of how the auxin response is mediated at the protein level over time can aid in developing a more complete molecular framework of the process. This study evaluates the effects of exogenous auxin treatment on the <i>Arabidopsis</i> root proteome after exposure of young seedlings to auxin for 8, 12, and 24 h, a timeframe permitting the initiation and full matu ...[more]

PMID: 28698516

Similar Datasets

The Adult Aedes aegypti Midgut Peritrophic Matrix Proteome

Project description:This study was undertaken to characterize the proteome of the midgut peritrophic matrix of Aedes aegypti.

2018-04-05 | PXD007627 | Pride

Cyclic ion mobility for hydrogen/deuterium exchange-mass spectrometry applications

Project description:Hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has emerged as a powerful tool to probe protein dynamics. As a bottom-up technique, HDX-MS provides information at peptide-level resolution, allowing structural localisation of dynamic changes. Consequently, HDX-MS data quality is largely determined by the number of peptides that are identified and monitored after deuteration. Integration of ion mobility (IM) into HDX-MS workflows has been shown to increase data quality by providing an orthogonal mode of peptide ion separation in the gas-phase. This is of critical importance for challenging targets such as integral membrane proteins (IMPs), which often suffer from low sequence coverage and/or redundancy in HDX-MS analyses. The increasing complexity of samples being investigated by HDX-MS, such as membrane mimetic reconstituted and in vivo IMPs, has generated need for instrumentation with greater resolving power. Recently, Giles et al. developed cyclic ion mobility (cIM), an IM device with racetrack geometry that enables scalable, multi-pass IM separations. Using 1-pass and multi-pass cIM routines, we use the recently commercialised SELECT SERIES™ Cyclic™ IM spectrometer for HDX-MS analyses of 4 detergent solubilised IMP samples and report its enhanced performance. Furthermore, we develop a novel processing strategy capable of better handling multi-pass cIM data. Interestingly, use of 1-pass and multi-pass cIM routines produced unique peptide populations, with their combined peptide output being 31 to 222% higher than previous generation SYNAPT G2-Si instrumentation. Thus, we propose a novel HDX-MS workflow with integrated cIM which has the potential to enable the analysis of more complex systems with greater accuracy and speed.

2024-04-08 | PXD048293 | Pride

Ensured auxin sensing by degron flexibility

Project description:Using a structural proteomics approach via chemical cross-linking combined with mass spectrometry (XL-MS), we have resolved SCFTIR auxin·AUX/IAA complex overall topology, and established the power of IDRs modulating auxin receptor assemblies.

2020-05-11 | PXD015285 | Pride

Distinct mechanistic, conformational and substrate selectivity profiles emerging in the evolution of high catalytic activity enzymes via parallel trajectories

Project description:Recent laboratory evolution studies have demonstrated that parallel evolutionary trajectories can lead to genetically distinct enzymes with high activity towards a non-preferred substrate. However, it is unknown whether such genetically distinct enzymes have convergent conformational dynamics and mechanistic features. To address this question, we used as a model the Homo sapiens kynureninase (HsKYNase), which is of great interest for cancer immunotherapy. Earlier, we reported on a highly unusual evolutionary trajectory that led to the isolation of HsKYNase_66, having a 410-fold increase in the kcat/KM for kynurenine (KYN) and reverse substrate selectivity relative to the parental wild-type enzyme. Here, by following a completely different evolutionary trajectory we generated a genetically distinct variant, HsKYNase_93D9, that exhibits KYN catalytic activity comparable to that of HsKYNase_66, but instead it is a “generalist” that accepts 3’-hydroxykynurenine (OH-KYN) with the same proficiency. Pre-steady-state kinetic analysis revealed that whereas the evolution of HsKYNase_66 was accompanied by a change in the rate-determining step of the reaction, HsKYNase_93D9 retained the same catalytic mechanism as the parental OH-KYN-preferring human enzyme. HDX-MS revealed that the conformational dynamics of the two enzymes during catalysis are markedly different and distinct from ortholog procaryotic enzymes with high KYN activity. Our work provides a mechanistic framework for understanding the relationship betweenevolutionary mechanisms and phenotypic traits of evolved generalist and specialist enzyme species.

2024-07-29 | PXD053893 | Pride

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS: Preparation of more than 4000 native protein maps

Project description:Soluble proteins of human bronchial smooth muscle cells (HBSMC) were separated by nondenaturing micro 2DE and a 30 mm X 40 mm area of the CBB-stained slab gel (1.0 mm thick) was cut into 1.1 mm X 1.1 mm squares, then the proteins in the 972 gel pieces (squares) were applied to quantitative LC-MS/MS. Grid-cutting of the gel was employed to; (i) ensure the total analysis of the proteins in the area, (ii) standardize the conditions of analysis by LC-MS/MS, (iii) reconstruct the protein distribution patterns from the quantity data [Jin, et al. Electrophoresis 2014, 35, 2055-2064, PRIDE Project PXD000852]. Totally 4323 proteins were identified in successfully analyzed 967 squares and the quantity distribution of each was reconstructed as a color density pattern (a native protein map). The quantity of the proteins distributed from 3.6 % to 1 X 10-5 % of the total protein quantity in the grid area. Each protein map was characterized by many features, such as the position of quantity peak square, number of detected squares, degree of concentration (focused or dispersed), etc. About 4 percent of the proteins were detected in 100 or more squares, suggesting that they might be ubiquitous and interacting with other proteins. In contrast, many proteins showed more concentrated quantity distribution and the quantity peak positions of 565 proteins with defined degree of concentration were summarized into a quantity peak map. These results for the first time visualized the distribution patterns of cellular proteins on a nondenaturing 2DE gel, which would further provide information on their interactions.

2015-08-10 | PXD001471 | Pride

mRNA-Seq of primary MEFs untreated or treated with auxin for OGT degradation

Project description:Primary mouse embryonic fibroblasts (MEFs) were derived from E12.5 embryos from the breeding of male mice which are homozygous for the insertion of the OsTIR1 transgene and females which are heterozygous for the AID knock-in at the endogenous Ogt locus (OgtAID/WT). The resulting MEFs clones were genotyped for sex and presence of the insertions and three pairs of OsTIR1-het;OgtAID/Y and control OsTIR1-het;OgtWT/Y male clones were used for the experiment, each pair coming from a different litter. The experiment consisted in treating each clone with auxin (IAA) for 24 hours, 48 hours or 96 hours and collecting them for single-end mRNA-Seq. One plate per clone was left untreated and also collected for mRNA-Seq.

2024-08-15 | E-MTAB-13298 | biostudies-arrayexpress

Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 vs Dro1-NIL

Project description:Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type) We used two rice varieties, IR64 and near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL). We performed comprehensive microarray analysis of rice root tips with auxin treatment (3h) and pre-treatment (0h) in IR64 and Dro1-NIL. Seedling root tips of IR64 and Dro1-NIL were treated with 10 M-BM-5M 2,4-D. n = 3 biological repeats (15 seedlings per repeat).

2013-05-07 | E-GEOD-46255 | biostudies-arrayexpress

Variation in auxin sensing guides AUX/IAA repressor ubiquitylation and destruction

Project description:Auxin is a drug-like small molecule and morphogen that triggers the formation of SCFTIR1/AFB-AUX/IAA co-receptor complexes leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors in plants. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. TIR1-IAA19 and TIR1-IAA6 interactions form co-receptors with different affinities, which specify ubiquitylation and turnover rate of the AUX/IAA. We demonstrate lysine ubiquitylation in IAA6/IAA19 and propose this ubiquitylation signature to be a consequence of auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologs, that contributes differentially to auxin sensing. We postulate that AUX/IAAs have emerged as a versatility toolbox for auxin-modulated transcriptional control, as the gamut of AUX/IAA destruction kinetics enables fine-tuning of transcriptional auxin response and contributes to the complexity of hormone signaling.

2017-06-14 | PXD004027 | Pride

Hydrogen-deuterium exchange mass spectrometry of wt Mtr4 with various RNA substrates

Project description:Mtr4 is a eukaryotic RNA helicase required for RNA decay by the nuclear exosome. Previous studies have shown how RNA enroute to the exosome threads through the highly conserved helicase core of Mtr4. Mtr4 also contains an arch domain, although details of potential interactions between the arch and RNA have been elusive. To understand the interaction of Saccharomyces cerevisiae Mtr4 with various RNAs, we have characterized RNA binding in solution using hydrogen-deuterium exchange mass spectrometry, and affinity and unwinding assays. We have identified RNA interactions within the helicase core that are consistent with existing structures and do not vary between tRNA, single-stranded RNA, and double-stranded RNA constructs. We have also identified novel RNA interactions with a region of the arch known as the fist or KOW. These interactions are important for RNA unwinding and vary in strength depending on RNA structure and length. They account for Mtr4 discrimination between different RNAs. These interactions further drive Mtr4 to adopt a closed conformation characterized by reduced dynamics of the arch arm and intra-domain contacts between the fist and helicase core.

2022-03-07 | PXD031962 | Pride

Zhang-arabidopsis-auxin vs NPA

Project description:transcription profiling of different development stage and different treatment

2012-02-22 | E-MEXP-3127 | biostudies-arrayexpress