The ribosome in action: Tuning of translational efficiency and protein folding

Redefining the Translational Status of 80S Monosomes

(2016) Erin E. Heyer et al.   CELL

Translation regulation via nascent polypeptide-mediated ribosome stalling

(2016) Daniel N Wilson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding

(2016) Ajeet K. Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

(2016) Yuichiro Mishima et al.   MOLECULAR CELL

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

Digital Quantification of Proteins and mRNA in Single Mammalian Cells

(2016) Cem Albayrak et al.   MOLECULAR CELL

Codon influence on protein expression in E. coli correlates with mRNA levels

(2016) Grégory Boël et al.   NATURE

Nascent peptide assists the ribosome in recognizing chemically distinct small molecules

(2016) Pulkit Gupta et al.   Nature Chemical Biology

Choreography of molecular movements during ribosome progression along mRNA

(2016) Riccardo Belardinelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding

(2016) Lisa D Cabrita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor

(2016) Annika Deckert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding

(2016) Daniel A. Nissley et al.   Nature Communications

Choreography of molecular movements during ribosome progression along mRNA

(2016) Riccardo Belardinelli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding

(2016) Lisa D Cabrita et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

(2016) David E. Weinberg et al.   Cell Reports

Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling

(2016) Fuad Mohammad et al.   Cell Reports

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

(2016) Spyros Darmanis et al.   Cell Reports

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

Signalling to eIF4E in cancer

(2015) N. Siddiqui et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

Translation Initiation Factor 3 Regulates Switching between Different Modes of Ribosomal Subunit Joining

(2015) Daniel D. MacDougall et al.   JOURNAL OF MOLECULAR BIOLOGY

Determinants of the Rate of mRNA Translocation in Bacterial Protein Synthesis

(2015) Anneli Borg et al.   JOURNAL OF MOLECULAR BIOLOGY

Entropic Contribution of Elongation Factor P to Proline Positioning at the Catalytic Center of the Ribosome

(2015) Lili K. Doerfel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

(2015) Chien-Hung Yu et al.   MOLECULAR CELL

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Charge-driven dynamics of nascent-chain movement through the SecYEG translocon

(2015) Nurzian Ismail et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

(2015) Thomas E. Gorochowski et al.   NUCLEIC ACIDS RESEARCH

Directional transition from initiation to elongation in bacterial translation

(2015) Akanksha Goyal et al.   NUCLEIC ACIDS RESEARCH

Operon structure and cotranslational subunit association direct protein assembly in bacteria

(2015) Y.-W. Shieh et al.   SCIENCE

Translational tuning optimizes nascent protein folding in cells

(2015) S. J. Kim et al.   SCIENCE

Cotranslational protein folding on the ribosome monitored in real time

(2015) W. Holtkamp et al.   SCIENCE

Structural insights into the translational infidelity mechanism

(2015) Alexey Rozov et al.   Nature Communications

Charge-driven dynamics of nascent-chain movement through the SecYEG translocon

(2015) Nurzian Ismail et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranslational Protein Folding inside the Ribosome Exit Tunnel

(2015) Ola B. Nilsson et al.   Cell Reports

High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP

(2015) Christopher J. Woolstenhulme et al.   Cell Reports

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

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

Ribosomes slide on lysine-encoding homopolymeric A stretches

(2015) Kristin S Koutmou et al.   eLife

Translational control by lysine-encoding A-rich sequences

(2015) L. L. Arthur et al.   Science Advances

Understanding the Influence of Codon Translation Rates on Cotranslational Protein Folding

(2014) Edward P. O’Brien et al.   ACCOUNTS OF CHEMICAL RESEARCH

The Scanning Mechanism of Eukaryotic Translation Initiation

(2014) Alan G. Hinnebusch   Annual Review of Biochemistry

Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA

(2014) Barbara Gorgoni et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Programmed –1 Frameshifting by Kinetic Partitioning during Impeded Translocation

(2014) Neva Caliskan et al.   CELL

An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation

(2014) Arvind R. Subramaniam et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Expanding Anfinsen’s Principle: Contributions of Synonymous Codon Selection to Rational Protein Design

(2014) Ian M. Sander et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

(2014) C. Pop et al.   Molecular Systems Biology

Dynamic pathways of −1 translational frameshifting

(2014) Jin Chen et al.   NATURE

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

(2014) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

(2014) Joao C. Guimaraes et al.   NUCLEIC ACIDS RESEARCH

Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site

(2014) Agata L. Starosta et al.   NUCLEIC ACIDS RESEARCH

The effect of tRNA levels on decoding times of mRNA codons

(2014) Alexandra Dana et al.   NUCLEIC ACIDS RESEARCH

A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

(2014) H.-K. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Exposing synonymous mutations

(2014) Ryan C. Hunt et al.   TRENDS IN GENETICS

The Effects of Codon Context on In Vivo Translation Speed

(2014) Fabienne F. V. Chevance et al.   PLoS Genetics

Measurement of average decoding rates of the 61 sense codons in vivo

(2014) Justin Gardin et al.   eLife

Arrest Peptides:Cis-Acting Modulators of Translation

(2013) Koreaki Ito et al.   Annual Review of Biochemistry

Molecular Chaperone Functions in Protein Folding and Proteostasis

(2013) Yujin E. Kim et al.   Annual Review of Biochemistry

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Rate-Limiting Steps in Yeast Protein Translation

(2013) Premal Shah et al.   CELL

Co-translational mechanisms of protein maturation

(2013) Felix Gloge et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Regulation of pathogenicity by noncoding RNAs in bacteria

(2013) Yanping Han et al.   Future Microbiology

Genetic Code-guided Protein Synthesis and Folding inEscherichia coli

(2013) Shaoliang Hu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Ribosome as a Hub for Protein Quality Control

(2013) Sebastian Pechmann et al.   MOLECULAR CELL

eIF5A Promotes Translation of Polyproline Motifs

(2013) Erik Gutierrez et al.   MOLECULAR CELL

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

Protein synthesis rate is the predominant regulator of protein expression during differentiation

(2013) A. R. Kristensen et al.   Molecular Systems Biology

Erratum: Corrigendum: Global quantification of mammalian gene expression control

(2013) Björn Schwanhäusser et al.   NATURE

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

(2013) Mian Zhou et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Transimulation - Protein Biosynthesis Web Service

(2013) Marlena Siwiak et al.   PLoS One

Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P

(2013) L. Peil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nascent peptides that block protein synthesis in bacteria

(2013) C. J. Woolstenhulme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Escherichia coli Ribosomal Protein S1 Unfolds Structured mRNAs Onto the Ribosome for Active Translation Initiation

(2013) Mélodie Duval et al.   PLOS BIOLOGY

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

(2013) Luca Ciandrini et al.   PLoS Computational Biology

Multiple activities of RNA-binding proteins S1 and Hfq

(2012) Eliane Hajnsdorf et al.   BIOCHIMIE

Kinetic control of translation initiation in bacteria

(2012) Pohl Milón et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme

(2012) Deepa Agashe et al.   MOLECULAR BIOLOGY AND EVOLUTION

The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria

(2012) Gene-Wei Li et al.   NATURE

Real-time assembly landscape of bacterial 30S translation initiation complex

(2012) Pohl Milón et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding

(2012) Sebastian Pechmann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribosomal protein S1 unwinds double-stranded RNA in multiple steps

(2012) X. Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome

(2012) P. Ciryam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EF-P Is Essential for Rapid Synthesis of Proteins Containing Consecutive Proline Residues

(2012) L. K. Doerfel et al.   SCIENCE

Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches

(2012) S. Ude et al.   SCIENCE

Speeding with control: codon usage, tRNAs, and ribosomes

(2012) Eva Maria Novoa et al.   TRENDS IN GENETICS

Prediction of variable translation rate effects on cotranslational protein folding

(2012) Edward P. O'Brien et al.   Nature Communications

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency

(2012) Wenfeng Qian et al.   PLoS Genetics

Coupling between codon usage, translation and protein export in Escherichia coli

(2011) Yaramah M. Zalucki et al.   Biotechnology Journal

Determinants of translation efficiency and accuracy

(2011) H. Gingold et al.   Molecular Systems Biology

The ribosome uses two active mechanisms to unwind messenger RNA during translation

(2011) Xiaohui Qu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Understanding the contribution of synonymous mutations to human disease

(2011) Zuben E. Sauna et al.   NATURE REVIEWS GENETICS

The Ribosome Modulates Nascent Protein Folding

(2011) C. M. Kaiser et al.   SCIENCE

Divergent stalling sequences sense and control cellular physiology

(2010) Koreaki Ito et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation

(2010) Tamir Tuller et al.   CELL

A Role for Codon Order in Translation Dynamics

(2010) Gina Cannarozzi et al.   CELL

Optimization of speed and accuracy of decoding in translation

(2010) Ingo Wohlgemuth et al.   EMBO JOURNAL

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

(2010) Malin Allert et al.   JOURNAL OF MOLECULAR BIOLOGY

Transient Tertiary Structure Formation within the Ribosome Exit Port

(2010) Edward P. O’Brien et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

The mechanism of eukaryotic translation initiation and principles of its regulation

(2010) Richard J. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel

(2010) Shashi Bhushan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy

(2010) C. Eichmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA

(2010) M. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Control of translation efficiency in yeast by codon-anticodon interactions

(2010) D. P. Letzring et al.   RNA

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes

(2010) Wanjun Gu et al.   PLoS Computational Biology

The Native 3D Organization of Bacterial Polysomes

(2009) Florian Brandt et al.   CELL

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Genetic Identification of Nascent Peptides That Induce Ribosome Stalling

(2009) Douglas R. Tanner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Tertiary interactions within the ribosomal exit tunnel

(2009) Andrey Kosolapov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

(2009) Gong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Biased codon usage in signal peptides: a role in protein export

(2009) Yaramah M. Zalucki et al.   TRENDS IN MICROBIOLOGY

Peptidyl-prolyl-tRNA at the ribosomal P-site reacts poorly with puromycin

(2008) Hiroki Muto et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Modulation of the Rate of Peptidyl Transfer on the Ribosome by the Nature of Substrates

(2008) Ingo Wohlgemuth et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cotranslational Folding Promotes β-Helix Formation and Avoids Aggregation In Vivo

(2008) Michael S. Evans et al.   JOURNAL OF MOLECULAR BIOLOGY

Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates

(2008) Jianli Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Ribosome Collisions and Translation Efficiency: Optimization by Codon Usage and mRNA Destabilization

(2008) Namiko Mitarai et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic Checkpoint at a Late Step in Translation Initiation

(2008) Pohl Milon et al.   MOLECULAR CELL

Different aa-tRNAs Are Selected Uniformly on the Ribosome

(2008) Sarah Ledoux et al.   MOLECULAR CELL

Following translation by single ribosomes one codon at a time

(2008) Jin-Der Wen et al.   NATURE

Signal sequence–independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel

(2008) Thomas Bornemann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Slow peptide bond formation by proline and other N-alkylamino acids in translation

(2008) M. Y. Pavlov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pause for thought along the co-translational folding pathway

(2008) Anton A. Komar   TRENDS IN BIOCHEMICAL SCIENCES