Dataset Information

An integrated global analysis of compartmentalized HRAS signaling - Phosphoproteomics

ABSTRACT: Modern omics technologies allow us obtaining global information on different types of biological networks. However, integrating these different types of analyzes into a coherent framework for a comprehensive biological interpretation remains challenging. Here, we present a conceptual framework that integrates protein interaction, phosphoproteomics and transcriptomics data. Applying this method to analyze HRAS signaling from different subcellular compartments shows that spatially-defined networks contribute specific functions to HRAS signaling. Changes in HRAS protein interactions at different sites lead to different kinase activation patterns that differentially regulate gene transcription. HRAS mediated signaling is the strongest from the plasma membrane, but it regulates the largest number of genes from the endoplasmic reticulum. The integrated networks provide a topologically and functionally resolved view of HRAS signaling. They reveal new HRAS functions including the control of cell migration from the endoplasmic reticulum and p53 dependent cell survival when signaling from the Golgi apparatus.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Hela Cell

DISEASE(S): Cervix Carcinoma

SUBMITTER: David Matallanas

LAB HEAD: David Gomez

PROVIDER: PXD012506 | Pride | 2019-03-08

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	MaxQuantOutput.tar.gz	Other
	OR9_20130905_TT_JG_10B.raw	Raw
	OR9_20130905_TT_JG_10C.raw	Raw
	OR9_20130905_TT_JG_11B.raw	Raw
	OR9_20130905_TT_JG_11C.raw	Raw

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Publications

An Integrated Global Analysis of Compartmentalized HRAS Signaling.

Santra Tapesh T Herrero Ana A Rodriguez Javier J von Kriegsheim Alex A Iglesias-Martinez Luis F LF Schwarzl Thomas T Higgins Des D Aye Thin-Thin TT Heck Albert J R AJR Calvo Fernando F Agudo-Ibáñez Lorena L Crespo Piero P Matallanas David D Kolch Walter W

Cell reports 20190301 11

Modern omics technologies allow us to obtain global information on different types of biological networks. However, integrating these different types of analyses into a coherent framework for a comprehensive biological interpretation remains challenging. Here, we present a conceptual framework that integrates protein interaction, phosphoproteomics, and transcriptomics data. Applying this method to analyze HRAS signaling from different subcellular compartments shows that spatially defined network ...[more]

PMID: 30865897

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Project description:The honeybee brain is comprised of a nervous system that sufficiently regulates this life transition. Knowledge about how protein phosphorylation functions in regards to the neurobiological activities in the honeybee brain to drive the age-specific labor division is still lacking. Protein phosphorylation, the most common post-translational modification (PTM), is a key switch for rapid on-off control of signaling cascades that regulate cell differentiation and development, enzyme activity and metabolic maintenance in living cells. A fundamental mechanism for regulating signaling network and protein activity is the covalent PTM of serine (Ser), threonine (Thr), and tyrosine (Tyr) residues with phosphate. Fortunately, because of advances in phosphopeptide enrichment and improvements in mass spectrometry (MS) instrumentation and methods, phosphoproteomics has enabled large-scale identification of protein phosphorylation sites and phosphorylation networks in biological samples. Although the proteome has been mapped in the brain of nurse and forager bees, knowledge about age-specific effects of phosphorylation regulation on proteins in the honeybee brain is still lacking. Moreover, information in regards to the honeybee phosphoproteome is also very limited. Only very recently, in-depth phosphoproteomics analyses of protein phosphorylation networks in the hypopharyngealgland of the honeybee have been reported. Although the phosphoproteome analyses during the development of brood and salivary glands has been reported, only very limited proteins were phosphorylated and phosphorylation sites of those phosphoproteins were not assigned. Therefore, a comprehensive characterization of phosphoproteomics and changes in the brains of nurse and forager bees is key to understand the phosphorylation events underlying age-specific physiology to achieve the completion of biological missions in this well-organized social community of the honeybee. Honeybee (A. m. ligustica) colonies used for sampling were raised at the apiary of the Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing. Newly emerged (<12 h after emergence) worker bees were marked on their thoraxes and placed back into the colonies to develop and then the marked nurse and forager bees were collected on days 10 and 20, respectively. There were 150 bees sampled from each of the five colonies which have queens at the same age. In brief, for each time point, worker bees were sampled from five colonies, and pooled all samples for further analysis. This procedure was repeated three times, so that we finally ended up with three independent biological replicates per time point, each consisting of 150 honeybees. Then their brains were dissected, and the brain samples were pooled and stored at −80 °C for further analysis. All the colonies were managed with almost identical population, food, and brood during the nectar flow of chaste berry (Vitexnegundo L.) in June.