Proteomics dataset containing proteins that obscure identification of TOPLESS interactors in Arabidopsis.
Ontology highlight
ABSTRACT:
SUBMITTER: Collins J
PROVIDER: S-EPMC6138984 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Datasets were generated from Tandem Affinity Purification of the TOPLESS co-repressor from Arabidopsis.
2018-06-18 | MSV000082477 | MassIVE
Project description:Consistent with its proposed status as an early branching eukaryote, Giardia has the most divergent actin of any eukaryote and lacks core actin regulators. Although conserved actin-binding proteins are missing from Giardia, its actin is utilized similarly to that of other eukaryotes and functions in core cellular processes such as cellular organization, endocytosis, and cytokinesis. We set out to identify actin-binding proteins in Giardia using affinity purification coupled with mass spectroscopy (multidimensional protein identification technology [MudPIT]) and have identified >80 putative actin-binding proteins. Several of these have homology to conserved proteins known to complex with actin for functions in the nucleus and flagella. We validated localization and interaction for seven of these proteins, including 14-3-3, a known cytoskeletal regulator with a controversial relationship to actin. Our results indicate that although Giardia lacks canonical actin-binding proteins, there is a conserved set of actin-interacting proteins that are evolutionarily indispensable and perhaps represent some of the earliest functions of the actin cytoskeleton.
| S-EPMC4054273 | biostudies-literature
Project description:BACKGROUND: FYVE domains have emerged as membrane-targeting domains highly specific for phosphatidylinositol 3-phosphate (PtdIns(3)P). They are predominantly found in proteins involved in various trafficking pathways. Although FYVE domains may function as individual modules, dimers or in partnership with other proteins, structurally, all FYVE domains share a fold comprising two small characteristic double-stranded beta-sheets, and a C-terminal alpha-helix, which houses eight conserved Zn2+ ion-binding cysteines. To date, the structural, biochemical, and biophysical mechanisms for subcellular targeting of FYVE domains for proteins from various model organisms have been worked out but plant FYVE domains remain noticeably under-investigated. RESULTS: We carried out an extensive examination of all Arabidopsis FYVE domains, including their identification, classification, molecular modeling and biophysical characterization using computational approaches. Our classification of fifteen Arabidopsis FYVE proteins at the outset reveals unique domain architectures for FYVE containing proteins, which are not paralleled in other organisms. Detailed sequence analysis and biophysical characterization of the structural models are used to predict membrane interaction mechanisms previously described for other FYVE domains and their subtle variations as well as novel mechanisms that seem to be specific to plants. CONCLUSIONS: Our study contributes to the understanding of the molecular basis of FYVE-based membrane targeting in plants on a genomic scale. The results show that FYVE domain containing proteins in plants have evolved to incorporate significant differences from those in other organisms implying that they play a unique role in plant signaling pathways and/or play similar/parallel roles in signaling to other organisms but use different protein players/signaling mechanisms.
| S-EPMC3017826 | biostudies-literature
Project description:Interactors of the plant natriuretic peptide present in Arabidopsis thaliana, termed AtPNP-A, were affinity-based isolated from A. thaliana (Col-0) leaf mesophyll cell protoplasts by incubating the protoplasts with biologically active biotinylated peptide corresponding to amino acid sequence of the active site of AtPNP-A (pAtPNP-A), either in the presence or absence of a cross-linking agent, 3,3'-dithiobis(sulfosuccinimidyl propionate) (DTSSP), or with equimolar amount of biotin with DTSSP (negative control). Upon biotin/streptavidin-based isolation of proteins bound to the pAtPNP-A or biotin, the proteins were separated by sodium dodecyl sulphate - polyacrylamide gel electrophoresis (SDS-PAGE), digested with trypsin and subjected to identification with liquid chromatography tandem mass spectrometry (LC-MS/MS). Label-free quantification of identified proteins allowed identification of binding partners of AtPNP-A, paving the way for pinpointing novel signal transduction pathways AtPNP-A is involved in. The raw and processed LC-MS/MS data reported in this article have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD017925.
| S-EPMC7210391 | biostudies-literature
Project description:MicroRNAs (miRNAs) are important for regulating gene expression in muticellular organisms. MiRNA processing is a two-step process. In animal cells, the first step is nuclear and the second step cytoplasmic, whereas in plant cells, both steps occur in the nucleus via the enzyme Dicer-like1 (DCL1) and other proteins including the zinc-finger-domain protein Serrate (SE) and a double-stranded RNA (dsRNA) binding-domain protein, Hyponastic Leaves1 (HYL1). Furthermore, plant miRNAs are methylated by Hua Enhancer (HEN1) at their 3' ends and loaded onto Argonaute1 (AGO1). However, little is known about the cellular basis of miRNA biogenesis. Using live-cell imaging, we show here that DCL1 and HYL1 colocalize in discrete nuclear bodies in addition to being present in a low-level diffuse nucleoplasmic distribution. These bodies, which we refer to as nuclear dicing bodies (D-bodies), differ from Cajal bodies. A mutated DCL1 with impaired function in miRNA processing fails to target to D-bodies, and an introduced primary (pri)-miRNA transcript is recruited to D-bodies. Furthermore, bimolecular fluorescence complementation (BiFC) shows that DCL1, HYL1, and SE interact in D-bodies. On the basis of these data, we propose that D-bodies are crucial for orchestrating pri-miRNA processing and/or storage/assembly of miRNA-processing complexes in the nuclei of plant cells.
| S-EPMC1950788 | biostudies-literature
Project description:Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, we analyzed all the proteins of Arabidopsis thaliana. Three-dimensional structures at the level of the domain are assigned by fold recognition and threading based on a novel fold library that extends common domain classifications. iGAP is being applied to proteins from all available proteomes as part of a comparative proteomics resource. The database is accessible from the web.
| S-EPMC193643 | biostudies-literature
Project description:Trichomes are highly specialized uni- or multicellular outgrowths of epidermal cells of plant organs that, in the case of leaves, contribute to plant resistance against abiotic and biotic stress. The model plant Arabidopsis thaliana features single-celled non-glandular rosette leaf trichomes that are dispensable under laboratory conditions. Trichomes have therefore become a successful model to identify plant genes involved in cellular differentiation and cell wall development. We have recently devised an improved method for the enrichment of plant leaf trichomes that relies on the biochemical weakening of the trichome-leaf junctions and a magnetic stirrer-based mechanical stimulus for trichome release followed by density gradient purification of trichomes. Here we provide detailed information on a label-free quantitative (LFQ) shotgun proteomics dataset collected at four stages while applying this protocol to isolate trichomes from rosette leaves of A. thaliana, from (i) whole seedlings before enrichment, from (ii) trichome-depleted material after separation, from (iii) detached trichomes, and from (iv) enriched trichomes after sucrose density gradient centrifugation. Proteins were extracted, digested with trypsin and the resulting peptides identified by nanoflow-chromatography coupled to tandem mass spectrometry. This dataset informs on proteins and biochemical processes present and/or enriched in A. thaliana rosette leaf trichomes, complementing recent large-scale proteome maps. The data further enables comparative analysis with trichome proteomic data from other plant species, may be reanalyzed using different software packages or search settings, and may serve as a reference benchmark for future method refinement.
| S-EPMC9936375 | biostudies-literature
Project description:BackgroundIn plants, calcium (Ca2+) has emerged as an important messenger mediating the action of many hormonal and environmental signals, including biotic and abiotic stresses. Many different signals raise cytosolic calcium concentration ([Ca2+]cyt), which in turn is thought to regulate cellular and developmental processes via Ca2+-binding proteins. Three out of the four classes of Ca2+-binding proteins in plants contain Ca2+-binding EF-hand motif(s). This motif is a conserved helix-loop-helix structure that can bind a single Ca2+ ion. To identify all EF-hand-containing proteins in Arabidopsis, we analyzed its completed genome sequence for genes encoding EF-hand-containing proteins.ResultsA maximum of 250 proteins possibly having EF-hands were identified. Diverse proteins, including enzymes, proteins involved in transcription and translation, protein- and nucleic-acid-binding proteins and a large number of unknown proteins, have one or more putative EF-hands. Phylogenetic analysis identified six major groups that contain some families of proteins.ConclusionsThe presence of EF-hand motif(s) in a diversity of proteins is consistent with the involvement of Ca2+ in regulating many cellular and developmental processes. Thus far, only 47 of the possible 250 EF-hand proteins have been reported in the literature. Various domains that we identified in many of the uncharacterized EF-hand-containing proteins should help in elucidating their cellular role(s). Our analyses suggest that the Ca2+ messenger system is widely used in plants and that EF-hand-containing proteins are likely to be the key transducers mediating Ca2+ action.
| S-EPMC134623 | biostudies-literature
Project description:Evolutionarily conserved DEK domain-containing proteins have been implicated in multiple chromatin-related processes, mRNA splicing and transcriptional regulation in eukaryotes. Here, we show that two DEK proteins, DEK3 and DEK4, control the floral transition in Arabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors, FLOWERING LOCUS C (FLC), and its two homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, to promote their expression. The binding of DEK3 and DEK4 to a histone octamer in vivo affects histone modifications at FLC, MAF4 and MAF5 loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II with FLC, MAF4 and MAF5 chromatin to promote their expression. Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering in Arabidopsis.
| S-EPMC8985477 | biostudies-literature
Project description:The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli are poorly understood. Previously, we had used the N-terminus of Arabidopsis thaliana TPL to enable repression of a synthetic auxin response circuit in Saccharomyces cerevisiae (yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle module subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.
| S-EPMC8203292 | biostudies-literature