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Protein complex identification in Arabidopsis thaliana root membranes through SEC-MS

ABSTRACT: With the information gathered through mass-shift- and correlation-analysis, we predict PPi on a proteomic scale and describe the results in form of a network. This experiment was done with 3 week old Arabidopsis thaliana wt seedlings grown in hydroponic culture (1/2 MS-Medium)

INSTRUMENT(S): Q Exactive

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

TISSUE(S): Root

SUBMITTER: Max Gilbert

LAB HEAD: Waltraud Schulze

PROVIDER: PXD009511 | Pride | 2018-11-04

REPOSITORIES: Pride

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Publications

Global Identification of Protein Complexes within the Membrane Proteome of Arabidopsis Roots Using a SEC-MS Approach.

Gilbert Max M Schulze Waltraud X WX

Journal of proteome research 20181113 1

Biological processes consist of several consecutive and interacting steps as, for example, in signal transduction cascades or metabolic reaction chains. These processes are regulated by protein-protein interactions and the formation of larger protein complexes, which also occur within biological membranes. To gain a large-scale overview of complex-forming proteins and the composition of such complexes within the cellular membranes of Arabidopsis roots, we use the combination of size-exclusion ch ...[more]

PMID: 30370772

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Protein-protein interaction network dynamics induced by nitrogen starvation in Arabidopsis root membranes

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2021-06-18 | PXD015841 | Pride

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SEC

Project description:SEC Raw sequence reads

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A regulatory role for Sec tRNA[Ser]Sec in selenoprotein synthesis.

Project description:Selenium is biologically active through the functions of selenoproteins that contain the amino acid selenocysteine. This amino acid is translated in response to in-frame UGA codons in mRNAs that include a SECIS element in its 3' untranslated region, and this process requires a unique tRNA, referred to as tRNA([Ser]Sec). The translation of UGA as selenocysteine, rather than its use as a termination signal, is a candidate restriction point for the regulation of selenoprotein synthesis by selenium. A specialized reporter construct was used that permits the evaluation of SECIS-directed UGA translation to examine mechanisms of the regulation of selenoprotein translation. Using SECIS elements from five different selenoprotein mRNAs, UGA translation was quantified in response to selenium supplementation and alterations in tRNA([Ser]Sec) levels and isoform distributions. Although each of the evaluated SECIS elements exhibited differences in their baseline activities, each was stimulated to a similar extent by increased selenium or tRNA([Ser]Sec) levels and was inhibited by diminished levels of the methylated isoform of tRNA([Ser]Sec) achieved using a dominant-negative acting mutant tRNA([Ser]Sec). tRNA([Ser]Sec) was found to be limiting for UGA translation under conditions of high selenoprotein mRNA in both a transient reporter assay and in cells with elevated GPx-1 mRNA. This and data indicating increased amounts of the methylated isoform of tRNA([Ser]Sec) during selenoprotein translation indicate that it is this isoform that is translationally active and that selenium-induced tRNA methylation is a mechanism of regulation of the synthesis of selenoproteins.

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Rsp5/Nedd4 is the major ubiquitin ligase that targets cytosolic misfolded proteins upon heat-stress

Project description:The heat-shock response is a complex cellular program that induces major changes in protein translation, folding and degradation to alleviate toxicity caused by protein misfolding. While heat-shock has been widely used to study proteostasis, it remained unclear how misfolded proteins are targeted for proteolysis in these conditions. We found that Rsp5 and its mammalian homologue Nedd4 are the main E3-ligases responsible for the increased ubiquitination induced by heat-stress. We determined that Rsp5 ubiquitinates cytosolic misfolded proteins upon heat-shock for proteasome degradation. We found that ubiquitination of heat-induced substrates requires the Hsp40 co-chaperone Ydj1 that is further associated with Rsp5 upon heat-shock. Additionally, ubiquitination is also promoted by PY Rsp5-binding motifs found primarily in the structured regions of stress-induced substrates, which can act as heat-induced degrons. Our results support a bipartite recognition mechanism combining direct and chaperone-dependent ubiquitination of misfolded cytosolic proteins by Rsp5.

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