Concept

Essential gene

Related publications (23)

GCN2 adapts protein synthesis to scavenging-dependent growth

Pancreatic cancer cells with limited access to free amino acids can grow by scavenging extracellular protein. In a murine model of pancreatic cancer, we performed a genome-wide CRISPR screen for genes required for scavenging-dependent growth. The screen id ...

2022

Characterization of the electron-accepting part of the organohalide respiration chain of Dehalobacter and Desulfitobacterium

Lorenzo Cimmino

Organohalide respiration (OHR) is a bacterial anaerobic process that use halogenated compounds, e.g. tetrachloroethene (PCE), as terminal electron acceptors. D. restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and D. hafniense strain TCE1, a ba ...

EPFL2022

High-throughput Microfluidic Platforms for S. cerevisiae Single Cell Studies

Hon Ming Andrew Yip

Cells consume extra-cellular nutrients and resources to maintain cellular fitness. Extra-cellular conditions vary over time. Cellular programs encoded in genes adjust to adapt to the environments. Gene regulatory networks (GRNs) have evolved to be responsi ...

EPFL2022

Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA

Gabriela Garcia Rodriguez

The rnlAB toxin-antitoxin operon from Escherichia co/ifunctions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the tox ...

OXFORD UNIV PRESS2021

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Pierre Guy Rémy Salvy, Mohammadomid Oftadeh

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Nature Portfolio2021

The functional proteome landscape of Escherichia coli

Camille Véronique Bernadette Goemans

Recent developments in high-throughput reverse genetics1,2 have revolutionized our ability to map gene function and interactions3,4,5,6. The power of these approaches depends on their ability to identify functionally associated genes, which elicit similar ...

2020

Overexpression of transcription factor Foxa1 and target genes remediate therapeutic protein production bottlenecks in Chinese hamster ovary cells

Nicolas Mermod, Audrey Véronique Berger

Despite extensive research conducted to increase protein production from Chinese hamster ovary (CHO) cells, cellular bottlenecks often remain, hindering high yields. In this study, a transcriptomic analysis led to the identification of 32 genes that are co ...

WILEY2020

Disruption of the SucT acyltransferase in Mycobacterium smegmatis abrogates succinylation of cell envelope polysaccharides

Haig Alexander Eskandarian

Similar to other prokaryotes, mycobacteria decorate their major cell envelope glycans with minor covalent substituents whose biological significance remains largely unknown. We report on the discovery of a mycobacterial enzyme, named here SucT, that adds s ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2019

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

Paolo De Los Rios, Alessandro Barducci, Salvatore Assenza, Alberto Stefano Sassi

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the struct ...

2019

Systems Phytohormone Responses to Mitochondrial Proteotoxic Stress

Johan Auwerx, Xu Wang

Mitochondrial function is controlled by two separate genomes. This feature makes mitochondria prone to proteotoxic stress when a stoichiometric imbalance occurs in the protein complexes that perform oxidative phosphorylation, which consist of both nucleara ...

Cell Press2017

Thermodynamic bounds on the ultra- and infra-affinity of Hsp70 for its substrates

Paolo De Los Rios

The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting proteins against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into organelles. These f ...

2017

Therapeutic Proteins Engineered for Super-Affinity to the Extracellular Matrix in Regenerative Medicine

Priscilla Suhasna Maithili Briquez

Regenerative medicine aims to repair body tissues when natural mechanisms fail. Growth factors (GFs) are essential proteins that promote tissue regeneration upon injury, and as such, are very promising therapeutic drugs in regenerative medicine. Due to the ...

EPFL2016

Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform

Johannes Becker

Genome-wide manipulations and measurements have made huge progress over the last decades. In Saccharomyces cerevisiae, a well-studied eukaryotic model organism, homologous recombination allows for systematic deletion or alteration of a majority of its gene ...

EPFL2015

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Vassily Hatzimanikatis, Stepan Tymoshenko

Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstr ...

Public Library Science2015

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

Targeting Bacterial Central Metabolism for Drug Development

John McKinney, Paul Murima

Current antibiotics, derived mainly from natural sources, inhibit a narrow spectrum of cellular processes, namely DNA replication, protein synthesis, and cell wall biosynthesis. With the worldwide explosion of drug resistance, there is renewed interest in ...

Elsevier2014

Quantitative Mass Spectrometry Reveals Plasticity of Metabolic Networks in Mycobacterium smegmatis

John McKinney, Marc Moniatte, Romain Hamelin, Florence Armand, Diego Chiappe, Tarun Chopra

Mycobacterium tuberculosis has a remarkable ability to persist within the human host as a clinically inapparent or chronically active infection. Fatty acids are thought to be an important carbon source used by the bacteria during long term infection. Catab ...

Amer Soc Biochemistry Molecular Biology Inc2014

Adaptive Response of Group B Streptococcus to High Glucose Conditions: New Insights on the CovRS Regulation Network

Isabella Santi

Although the contribution of carbohydrate catabolism to bacterial colonization and infection is well recognized, the transcriptional changes during these processes are still unknown. In this study, we have performed comparative global gene expression analy ...

Public Library of Science2013

An acetylation rheostat for the control of muscle energy homeostasis

Johan Auwerx, Keir Joe Menzies

In recent years, the role of acetylation has gained ground as an essential modulator of intermediary metabolism in skeletal muscle. Imbalance in energy homeostasis or chronic cellular stress, due to diet, aging, or disease, translate into alterations in th ...

Society for Endocrinology2013

Gene expression profiling of R6/2 transgenic mice with different CAG repeat lengths reveals genes associated with disease onset and progression in Huntington's disease

R6/2 transgenic mice with expanded CAG repeats (> 300) have a surprisingly prolonged disease progression and longer lifespan than prototypical parent R6/2 mice (carrying 150 CAGs); however, the mechanism of this phenotype amelioration is unknown. We compar ...

Elsevier2011