Publications related to Protein catabolism

Coordination of protein synthesis and degradation in mammalian cells

The cellular protein levels are determined by protein synthesis and turnover rates. Two processes are involved in the proteome's turnover in proliferating cells: protein degradation and dilution. In theory, maintaining the cellular proteome concentration, ...

EPFL2023

Metabolic dependencies of metastasis-initiating cells in breast cancer

Candice Megan T Young

Metastasis is the process by which cancer cells from the primary tumor travel through the blood stream to generate a secondary tumor site in a distant organ. Although very few cells are able to make this journey, the resulting effects are dire since most c ...

EPFL2023

FIB-milled plasmonic nanoapertures allow for long trapping times of individual proteins

Wayne Yang Wen Wei

We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling ...

CELL PRESS2021

In vivo detection of d-amino acid oxidase with hyperpolarized d-[1-C-13]alanine

Rolf Gruetter, Hikari Ananda Infinity Yoshihara, Alice Radaelli

d-amino acid oxidase (DAO) is a peroxisomal enzyme that catalyzes the oxidative deamination of several neutral and basic d-amino acids to their corresponding alpha-keto acids. In most mammalian species studied, high DAO activity is found in the kidney, liv ...

2020

Augmented mitochondrial energy metabolism is an early response to chronic glucose stress in human pancreatic beta cells

Loïc Dayon, Andreas Wiederkehr, Sofia Moco, Isabelle Chareyron

Aims/hypothesis In islets from individuals with type 2 diabetes and in islets exposed to chronic elevated glucose, mitochondrial energy metabolism is impaired. Here, we studied early metabolic changes and mitochondrial adaptations in human beta cells durin ...

2020

Alterations of Brain Energy Metabolism in Type 2 Diabetic Goto-Kakizaki Rats Measured In Vivo by (13)C Magnetic Resonance Spectroscopy

Rolf Gruetter, João Miguel das Neves Duarte, Sarah Catherine Sonnay, Freya-Merret Girault

Type 2 diabetes (T2D) is associated with deterioration of brain structure and function. Here, we tested the hypothesis that T2D induces a reorganization of the brain metabolic networks that support brain function. For that, alterations of neuronal and glia ...

2019

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

Felix Naef, David Michael Suter, Andrea Brigitta Alber, Eric Paquet, Martina Biserni

Cells need to reliably control their proteome composition to maintain homeostasis and regulate growth. How protein synthesis and degradation interplay to control protein expression levels remains unclear. Here, we combined a tandem fluorescent timer and pu ...

CELL PRESS2018

Astrocytic and neuronal oxidative metabolism are coupled to the rate of glutamate-glutamine cycle in the tree shrew visual cortex

Rolf Gruetter, Nathalie Just, Sarah Catherine Sonnay, Gregor Rainer, João Miguel das Neves Duarte, Anne Catherine Clerc

Astrocytes play an important role in glutamatergic neurotransmission, namely by clearing synaptic glutamate and converting it into glutamine that is transferred back to neurons. The rate of this glutamate–glutamine cycle (VNT) has been proposed to couple t ...

Wiley-Blackwell2018

The cold denaturation of IscU highlights structure–function dualism in marginally stable proteins

Paolo De Los Rios

Proteins undergo both cold and heat denaturation, but often cold denaturation cannot be detected because it occurs at temperatures below water freezing. Proteins undergoing detectable cold as well as heat denaturation yield a reliable curve of protein stab ...

2018

Ultra high magnetic field for glial contribution into brain metabolism studied by MR spectroscopy and CEST methods for molecular imaging of glycogen

Elise Marie Catherine Vinckenbosch

Magnetic resonance at ultra-high field increases signal and spectral dispersion. In this thesis, I use those characteristics to investigate three different subjects in 13C spectroscopy, hyperpolarized methods and chemical exchange saturation transfer (CEST ...

EPFL2018

Energy metabolism in the rat cortex under thiopental anaesthesia measured

Rolf Gruetter, Nathalie Just, João Miguel das Neves Duarte, Sarah Catherine Sonnay

Barbiturates, commonly used as general anaesthetics, depress neuronal activity and thus cerebral metabolism. Moreover, they are likely to disrupt the metabolic support of astrocytes to neurons, as well as the uptake of nutrients from circulation. By employ ...

Wiley-Blackwell2017

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

Joana Raquel Pinto Vieira

Systems biology is a multidisciplinary field that weaves together all the basic sciences through the use of computational and bioinformatics tools, to provide a more integrative view of the complex molecular interactions taking place within and among cells ...

EPFL2017

Cytosolic Proteostasis Networks of the Mitochondrial Stress Response

Johan Auwerx, Davide D'Amico, Vincenzo Sorrentino

Mitochondrial stress requires timely intervention to prevent mitochondria' and cellular dysfunction. Re-establishing the correct protein homeostasis is crucial for coping with mitochondria' stress and maintaining cellular homeostasis. The best-characterize ...

Elsevier Science London2017

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Vassily Hatzimanikatis, Meriç Ataman

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional ...

2017

Expression proteomics study to determine metallodrug targets and optimal drug combinations

Paul Joseph Dyson, Kai Johnsson, David Hacker, Claire Samantha Allardyce

The emerging technique termed functional identification of target by expression proteomics (FITExP) has been shown to identify the key protein targets of anti-cancer drugs. Here, we use this approach to elucidate the proteins involved in the mechanism of a ...

Nature Research2017

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria

Matteo Dal Peraro, John McKinney, Florence Pojer, Giulia Fonti, Paul Murima, Tarun Chopra

Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux bifurcation between the oxidative TCA cycle and the glyoxylate shunt. In Escher ...

Nature Publishing Group2016

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Stefano Andreozzi

Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of om ...

Elsevier2016

Mitochondrial unfolded protein response, its molecular mechanism and physiological impact

Virginija Jovaisaite

Mitochondria are the main producers of ATP, the energy currency of the cell, and they perform a wide array of other fundamental functions. These organelles are essential not only for cellular metabolism, but also for organismal physiology and lifespan. A r ...

EPFL2016

Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

Andrej Benjak

Background: Nitrogen is essential for microbial growth and its importance is demonstrated by the complex regulatory systems used to control the transport, assimilation and metabolism of nitrogen. Recent studies are beginning to shed light on how mycobacter ...

BioMed Central2015

Direct noninvasive estimation of myocardial tricarboxylic acid cycle flux in vivo using hyperpolarized 13C magnetic resonance

Rolf Gruetter, Tian Cheng, Arnaud Comment, Hongxia Lei, Josefina Adriana Maria Bastiaansen

BACKGROUND: The heart relies on continuous energy production and imbalances herein impair cardiac function directly. The tricarboxylic acid (TCA) cycle is the primary means of energy generation in the healthy myocardium, but direct noninvasive quantificati ...

Elsevier2015