Quantitative proteomic analysis of ethylene-regulated post-translational modification and protein-protein interaction in arabidopsis

2018 ◽  
Author(s):  
Shichang Liu
Keyword(s):  
Protein Interaction ◽  
Proteomic Analysis ◽  
Post Translational Modification ◽  
Quantitative Proteomic Analysis ◽  
Protein Protein Interaction

scholarly journals Split-TurboID enables contact-dependent proximity labeling in cells

2020 ◽  
Author(s):  
Kelvin F. Cho ◽  
Tess C. Branon ◽  
Sanjana Rajeev ◽  
Tanya Svinkina ◽  
Namrata D. Udeshi ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Interaction ◽  
Proteomic Analysis ◽  
Protein Protein Interaction ◽  
Conventional Fractionation ◽  
Contact Sites ◽  
Biochemical Fractionation ◽  
Versatile Tool ◽  
Endogenous Proteins ◽  
In Cells

AbstractProximity labeling (PL) catalyzed by promiscuous enzymes such as TurboID have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein-protein interaction or membrane-membrane apposition. At endoplasmic reticulum (ER)-mitochondria contact sites, reconstituted TurboID catalyzed spatially-restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to ER-mitochondria contacts. We validated eight novel candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially-specific proximity labeling in cells.

scholarly journals Protein-protein-interaction Network Organization of the Hypusine Modification System

2012 ◽  
Vol 11 (11) ◽  
pp. 1289-1305 ◽  
Author(s):  
Henning Sievert ◽  
Simone Venz ◽  
Oscar Platas-Barradas ◽  
Vishnu M. Dhople ◽  
Martin Schaletzky ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Large Scale ◽  
Affinity Purification ◽  
Interaction Network ◽  
Initiation Factor ◽  
Post Translational Modification ◽  
Comprehensive Overview ◽  
Data Set ◽  
Modification System ◽  
Protein Protein Interaction

Hypusine modification of eukaryotic initiation factor 5A (eIF-5A) represents a unique and highly specific post-translational modification with regulatory functions in cancer, diabetes, and infectious diseases. However, the specific cellular pathways that are influenced by the hypusine modification remain largely unknown. To globally characterize eIF-5A and hypusine-dependent pathways, we used an approach that combines large-scale bioreactor cell culture with tandem affinity purification and mass spectrometry: “bioreactor-TAP-MS/MS.” By applying this approach systematically to all four components of the hypusine modification system (eIF-5A1, eIF-5A2, DHS, and DOHH), we identified 248 interacting proteins as components of the cellular hypusine network, with diverse functions including regulation of translation, mRNA processing, DNA replication, and cell cycle regulation. Network analysis of this data set enabled us to provide a comprehensive overview of the protein-protein interaction landscape of the hypusine modification system. In addition, we validated the interaction of eIF-5A with some of the newly identified associated proteins in more detail. Our analysis has revealed numerous novel interactions, and thus provides a valuable resource for understanding how this crucial homeostatic signaling pathway affects different cellular functions.

Envisioning the immune interactome in Arabidopsis

2020 ◽  
Vol 47 (6) ◽  
pp. 486
Author(s):  
Rashmi Maurya ◽  
Deepti Srivastava ◽  
Munna Singh ◽  
Samir V. Sawant
Keyword(s):  
Protein Interaction ◽  
Plant Pathogen ◽  
Post Translational Modification ◽  
Kinase Substrate ◽  
Protein Protein Interaction ◽  
Signal Perception ◽  
Substrate Protein ◽  
Molecular Machinery ◽  
Plant Pathogen Interaction ◽  
Plant Pathogenesis

During plant–pathogen interaction, immune targets were regulated by protein–protein interaction events such as ligand-receptor/co-receptor, kinase-substrate, protein sequestration, activation or repression via post-translational modification and homo/oligo/hetro-dimerisation of proteins. A judicious use of molecular machinery requires coordinated protein interaction among defence components. Immune signalling in Arabidopsis can be broadly represented in successive or simultaneous steps; pathogen recognition at cell surface, Ca2+ and reactive oxygen species signalling, MAPK signalling, post-translational modification, transcriptional regulation and phyto-hormone signalling. Proteome wide interaction studies have shown the existence of interaction hubs associated with physiological function. So far, a number of protein interaction events regulating immune targets have been identified, but their understanding in an interactome view is lacking. We focussed specifically on the integration of protein interaction signalling in context to plant–pathogenesis and identified the key targets. The present review focuses towards a comprehensive view of the plant immune interactome including signal perception, progression, integration and physiological response during plant pathogen interaction.

scholarly journals MetOSite: an integrated resource for the study of methionine residues sulfoxidation

2019 ◽  
Vol 35 (22) ◽  
pp. 4849-4850 ◽  
Author(s):  
Héctor Valverde ◽  
Francisco R Cantón ◽  
Juan Carlos Aledo
Keyword(s):  
Protein Interaction ◽  
Protein Function ◽  
Redox Regulation ◽  
Homo Sapiens ◽  
Methionine Sulfoxide ◽  
Subcellular Location ◽  
Biological Properties ◽  
Post Translational Modification ◽  
Protein Protein Interaction ◽  
Methionine Residues

Abstract Motivation The oxidation of protein-bound methionine to form methionine sulfoxide has traditionally been regarded as an oxidative damage. However, growing evidences support the view of this reversible reaction also as a regulatory post-translational modification. Thus, the oxidation of methionine residues has been reported to have multiple and varied implications for protein function. However, despite the importance of this modification and the abundance of reports, all these data are scattered in the literature. No database/resource on methionine sulfoxidation exists currently. Since this information is useful to gain further insights into the redox regulation of cellular proteins, we have created a primary database of experimentally confirmed sulfoxidation sites. Results MetOSite currently contains 7242 methionine sulfoxide sites found in 3562 different proteins from 23 species, with Homo sapiens, Arabidopsis thaliana and Bacillus cereus as the main contributors. Each collected site has been classified according to the effect of its sulfoxidation on the biological properties of the modified protein. Thus, MetOSite documents cases where the sulfoxidation of methionine leads to (i) gain of activity, (ii) loss of activity, (iii) increased protein–protein interaction susceptibility, (iv) decreased protein–protein interaction susceptibility, (v) changes in protein stability and (vi) changes in subcellular location. Availability and implementation MetOSite is available at https://metosite.uma.es.

iTRAQ-based quantitative proteomic analysis of two transgenic soybean lines and the corresponding non-genetically modified isogenic variety

2019 ◽  
Vol 167 (1) ◽  
pp. 67-78
Author(s):  
Weixiao Liu ◽  
Zhe Zhang ◽  
Xuri Liu ◽  
Wujun Jin
Keyword(s):  
Proteomic Analysis ◽  
Interaction Analysis ◽  
Genetically Modified ◽  
Unintended Effects ◽  
Post Translational Modification ◽  
Absolute Quantitation ◽  
Protein Protein Interaction ◽  
Transduction Mechanisms ◽  
Isobaric Tags ◽  
Gm Soybean

Abstract To investigate the unintended effects of genetically modified (GM) crops, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed with seed cotyledons of two GM soybean lines, MON87705 and MON87701×MON89788, and the corresponding non-transgenic isogenic variety A3525. Thirty-five differentially abundant proteins (DAPs) were identified in MON87705/A3525, 27 of which were upregulated and 8 downregulated. Thirty-eight DAPs were identified from the MON87701×MON89788/A3525 sample, including 29 upregulated proteins and 9 downregulated proteins. Pathway analysis showed that most of these DAPs participate in protein processing in endoplasmic reticulum and in metabolic pathways. Protein–protein interaction analysis of these DAPs demonstrated that the main interacting proteins are associated with post-translational modification, protein turnover, chaperones and signal transduction mechanisms. Nevertheless, these DAPs were not identified as new unintended toxins or allergens and only showed changes in abundance. All these results suggest that the seed cotyledon proteomic profiles of the two GM soybean lines studied were not dramatically altered compared with that of their natural isogenic control.

scholarly journals Split-TurboID enables contact-dependent proximity labeling in cells

2020 ◽  
Vol 117 (22) ◽  
pp. 12143-12154 ◽  
Author(s):  
Kelvin F. Cho ◽  
Tess C. Branon ◽  
Sanjana Rajeev ◽  
Tanya Svinkina ◽  
Namrata D. Udeshi ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Interaction ◽  
Proteomic Analysis ◽  
Protein Protein Interaction ◽  
Conventional Fractionation ◽  
Contact Sites ◽  
Biochemical Fractionation ◽  
Versatile Tool ◽  
Endogenous Proteins ◽  
In Cells

Proximity labeling catalyzed by promiscuous enzymes, such as TurboID, have enabled the proteomic analysis of subcellular regions difficult or impossible to access by conventional fractionation-based approaches. Yet some cellular regions, such as organelle contact sites, remain out of reach for current PL methods. To address this limitation, we split the enzyme TurboID into two inactive fragments that recombine when driven together by a protein–protein interaction or membrane–membrane apposition. At endoplasmic reticulum–mitochondria contact sites, reconstituted TurboID catalyzed spatially restricted biotinylation, enabling the enrichment and identification of >100 endogenous proteins, including many not previously linked to endoplasmic reticulum–mitochondria contacts. We validated eight candidates by biochemical fractionation and overexpression imaging. Overall, split-TurboID is a versatile tool for conditional and spatially specific proximity labeling in cells.

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