Publications related to Ribosome

Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction

Camille Véronique Bernadette Goemans, Christian Eugen Zimmerli, Martin Beck

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative b ...

Nature Research2024

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

Advancing Cell-Free Synthetic Biology: From sustained PURE protein synthesis to an isothermal one-pot DNA replication system

Laura Sophie Grasemann

One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

EPFL2024

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity

Benjamin Marcel Daniel Rothé

Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic inte ...

Nature Research2021

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Nagammal Neelagandan

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) pr ...

National Academy of Sciences2020

Label-free Bacteria Quantification in Blood Plasma by a Bioprinted Microarray Based Interferometric Point-of-Care Device

Hatice Altug, Filiz Yesilköy, Alexander Belushkin

Existing clinical methods for bacteria detection lack speed, sensitivity, and, importantly, point-of-care (PoC) applicability. Thus, finding ways to push the sensitivity of clinical PoC biosensing technologies is crucial. Here we report a portable PoC devi ...

AMER CHEMICAL SOC2019

Cell-specific image-guided transcriptomics identifies complex injuries caused by ischemic acute kidney injury in mice

Elena Goun, Pavlo Khodakivskyi

The kidney's inherent complexity has made identifying cell-specific pathways challenging, particularly when temporally associating them with the dynamic pathophysiology of acute kidney injury (AKI). Here, we combine renal cell-specific luciferase reporter ...

Springer2019

Distribution of the ribosome associated endonuclease Rae1 and the potential role of conserved amino acids in codon recognition

Jérémie Piton

We recently identified a novel ribonuclease in Bacillus subtilis called Rae1 that cleaves mRNAs in a translation-dependent manner. Rae1 is a member of the NYN/PIN family of ribonucleases and is highly conserved in the Firmicutes, the Cyanobacteria and the ...

TAYLOR & FRANCIS INC2018

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

Cédric Gobet

Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...

EPFL2018

Diurnal Oscillations in Liver Mass and Cell Size Accompany Ribosome Assembly Cycles

Frédéric Bruno Martin Gachon, Daniel Alain Dominique Marie Mauvoisin, Jingkui Wang

The liver plays a pivotal role in metabolism and xenobiotic detoxification, processes that must be particularly efficient when animals are active and feed. A major question is how the liver adapts to these diurnal changes in physiology. Here, we show that, ...

Cell Press2017

Placeholder factors in ribosome biogenesis: please, pave my way

The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and ...

Shared Science Publishers OG2017

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

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Felix Naef, Loïc Dayon, Jingkui Wang, Frédéric Bruno Martin Gachon, Martin Kussmann, Daniel Alain Dominique Marie Mauvoisin, Florian Atger, Federico Sizzano

Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulatio ...

Cell Press2017

Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells

Diego Chiappe

Lysine acetylation is a widespread posttranslational modification affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make i ...

Amer Soc Biochemistry Molecular Biology Inc2017

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

Vassily Hatzimanikatis, Julien Racle, Joana Raquel Pinto Vieira

Understanding the mechanisms behind translation and its rate-limiting steps is crucial for both the development of drug targets and improvement of heterologous protein production with many biotechnological applications, such as in pharmaceutical and biofue ...

Elsevier2016

Mercury tissue residue approach in Chironomus riparius: Involvement of toxicokinetics and comparison of subcellular fractionation methods

Along with the growing body of evidence that total internal concentration is not a good indicator of toxicity, the Critical Body Residue (CBR) approach recently evolved into the Tissue Residue Approach (TRA) which considers the biologically active portion ...

Elsevier Science Bv2016

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

Vassily Hatzimanikatis, Julien Racle, Adam Stefaniuk

Noise in genetic networks has been the subject of extensive experimental and computational studies. However, very few of these studies have considered noise properties using mechanistic models that account for the discrete movement of ribosomes and RNA pol ...

Amer Inst Physics2015

Mechanistically Consistent Reduced Models of Synthetic Gene Networks

Vassily Hatzimanikatis

Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by syst ...

Cell Press2013

Mitonuclear protein imbalance as a conserved longevity mechanism

Johan Auwerx, Graham Knott, Laurent Mouchiroud, Richardus Houtkooper, Dongryeol Ryu, Elena Katsyuba, Norman Lionel Moullan

Longevity is regulated by a network of closely linked metabolic systems. We used a combination of mouse population genetics and RNA interference in Caenorhabditis elegans to identify mitochondrial ribosomal protein S5 (Mrps5) and other mitochondrial riboso ...

Nature Publishing Group2013