Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

Isolation of an archaeon at the prokaryote–eukaryote interface

(2020) Hiroyuki Imachi et al.   NATURE

Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes

(2019) Jeremy Weaver et al.   mBio

Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

(2019) Sezen Meydan et al.   MOLECULAR CELL

High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress

(2019) Colin Chih-Chien Wu et al.   MOLECULAR CELL

Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core

(2019) Emmanuelle Schmitt et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

(2019) Fuad Mohammad et al.   eLife

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

(2019) Anja Spang et al.   Nature Microbiology

Ribosome pausing, a dangerous necessity for co-translational events

(2019) Martine A Collart et al.   NUCLEIC ACIDS RESEARCH

The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label‐Free Mass Spectrometry

(2019) Živojin Jevtić et al.   PROTEOMICS

Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry

(2018) Jean-Benoît Lalanne et al.   CELL

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

(2018) Diego Rivera Gelsinger et al.   JOURNAL OF BACTERIOLOGY

A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation

(2018) Yan Zhang et al.   MOLECULAR CELL

Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells

(2018) Alicia M. Darnell et al.   MOLECULAR CELL

Translation in Prokaryotes

(2018) Marina V. Rodnina   Cold Spring Harbor Perspectives in Biology

Ribosome Profiling: Global Views of Translation

(2018) Nicholas T. Ingolia et al.   Cold Spring Harbor Perspectives in Biology

mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii

(2018) Leander Wyss et al.   Scientific Reports

Ribosome Profiling of Synechocystis Reveals Altered Ribosome Allocation at Carbon Starvation

(2018) Jan Karlsen et al.   mSystems

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Archaea and the origin of eukaryotes

(2017) Laura Eme et al.   NATURE REVIEWS MICROBIOLOGY

Ribosome pausing, arrest and rescue in bacteria and eukaryotes

(2017) Allen R. Buskirk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

(2016) Julia Babski et al.   BMC GENOMICS

Ribonuclease selection for ribosome profiling

(2016) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)

(2016) Yujin Jeong et al.   Nature Communications

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

Four translation initiation pathways employed by the leaderless mRNA in eukaryotes

(2016) Kseniya A. Akulich et al.   Scientific Reports

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

History of the ribosome and the origin of translation

(2015) Anton S. Petrov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The awesome power of ribosome profiling

(2015) Richard Jackson et al.   RNA

Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape

(2015) Scarlet S. Shell et al.   PLoS Genetics

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast

(2015) Jeffrey A. Hussmann et al.   PLoS Genetics

De novo assembly of bacterial transcriptomes from RNA-seq data

(2015) Brian Tjaden   GENOME BIOLOGY

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo

(2015) Kenji Nakahigashi et al.   BMC GENOMICS

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

(2014) Audrey M Michel et al.   BMC BIOINFORMATICS

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Translation inhibitors cause abnormalities in ribosome profiling experiments

(2014) Maxim V. Gerashchenko et al.   NUCLEIC ACIDS RESEARCH

Haloferax volcanii, a Prokaryotic Species that Does Not Use the Shine Dalgarno Mechanism for Translation Initiation at 5′-UTRs

(2014) Piet Kramer et al.   PLoS One

Macrolide antibiotics allosterically predispose the ribosome for translation arrest

(2014) Shanmugapriya Sothiselvam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

eIF5A Promotes Translation of Polyproline Motifs

(2013) Erik Gutierrez et al.   MOLECULAR CELL

Small open reading frames associated with morphogenesis are hidden in plant genomes

(2013) K. Hanada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes

(2013) Aharon Oren   Frontiers in Microbiology

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance

(2012) E. C. Hobbs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translation initiation in Archaea: conserved and domain-specific features

(2011) Dario Benelli et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

Regulation of Translation in Haloarchaea: 5′- and 3′-UTRs Are Essential and Have to Functionally Interact In Vivo

(2009) Mariam Brenneis et al.   PLoS One

Altering Chemosensitivity by Modulating Translation Elongation

(2009) Francis Robert et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Polarity in Archaeal Operon Transcription in Thermococcus kodakaraensis

(2008) T. J. Santangelo et al.   JOURNAL OF BACTERIOLOGY

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY