Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding

Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

(2020) Ian M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A stochastic model for simulating ribosome kinetics in vivo

(2020) Eric Charles Dykeman   PLoS Computational Biology

Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing

(2020) Kazuki Saito et al.   eLife

Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast

(2020) Leticia Pollo-Oliveira et al.   Biomolecules

Cotranslational Folding of Proteins on the Ribosome

(2020) Marija Liutkute et al.   Biomolecules

Co‐translational insertion and topogenesis of bacterial membrane proteins monitored in real time

(2020) Evan Mercier et al.   EMBO JOURNAL

RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time

(2020) Menglin Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Translation at first sight: the influence of leading codons

(2020) Ilya A Osterman et al.   NUCLEIC ACIDS RESEARCH

The Ccr4-Not complex monitors the translating ribosome for codon optimality

(2020) Robert Buschauer et al.   SCIENCE

Translational regulation of environmental adaptation in bacteria

(2020) Rodney Tollerson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In-cell architecture of an actively transcribing-translating expressome

(2020) Francis J. O’Reilly et al.   SCIENCE

Functionally uncoupled transcription–translation in Bacillus subtilis

(2020) Grace E. Johnson et al.   NATURE

Structural basis of transcription-translation coupling

(2020) Chengyuan Wang et al.   SCIENCE

Structural basis of transcription-translation coupling and collision in bacteria

(2020) Michael William Webster et al.   SCIENCE

Structure of the bacterial ribosome at 2 Å resolution

(2020) Zoe L Watson et al.   eLife

Domains two and three of Escherichia coli ribosomal S1 protein confers 30S subunits a high affinity for downstream A/U-rich mRNAs

(2019) Juan C Cifuentes-Goches et al.   JOURNAL OF BIOCHEMISTRY

Codon-Specific Translation by m1G37 Methylation of tRNA

(2019) Ya-Ming Hou et al.   Frontiers in Genetics

Differences in the path to exit the ribosome across the three domains of life

(2019) Khanh Dao Duc et al.   NUCLEIC ACIDS RESEARCH

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

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

Mechanisms and functions of ribosome-associated protein quality control

(2019) Claudio A. P. Joazeiro   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2019) Fuad Mohammad et al.   eLife

Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control

(2019) Iryna Lytvynenko et al.   CELL

The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin?

(2019) Namit Ranjan et al.   FEBS LETTERS

Re-introducing non-optimal synonymous codons into codon-optimized constructs enhances soluble recovery of recombinant proteins from Escherichia coli

(2019) Jennifer Konczal et al.   PLoS One

Efficiency of protein synthesis inhibition depends on tRNA and codon compositions

(2019) Sophia Rudorf   PLoS Computational Biology

Ribosome pausing, a dangerous necessity for co-translational events

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

From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli

(2019) Mariana H. Moreira et al.   RNA Biology

Mechanism of ribosome stalling during translation of a poly(A) tail

(2019) Viswanathan Chandrasekaran et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Thermodynamic control of −1 programmed ribosomal frameshifting

(2019) Lars V. Bock et al.   Nature Communications

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

(2019) Petr Tesina et al.   EMBO JOURNAL

A short translational ramp determines the efficiency of protein synthesis

(2019) Manasvi Verma et al.   Nature Communications

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli

(2018) Sanchari Bhattacharyya et al.   MOLECULAR CELL

Roadblocks and resolutions in eukaryotic translation

(2018) Anthony P. Schuller et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA

(2018) Irena Andreeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translation in Prokaryotes

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

Riboswitches and Translation Control

(2018) Ronald R. Breaker   Cold Spring Harbor Perspectives in Biology

The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation

(2018) Khanh Dao Duc et al.   PLoS Genetics

Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli

(2018) Guillaume Cambray et al.   NATURE BIOTECHNOLOGY

Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA

(2017) Neva Caliskan et al.   MOLECULAR CELL

Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P

(2017) Paul Huter et al.   MOLECULAR CELL

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evidence of evolutionary selection for cotranslational folding

(2017) William M. Jacobs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Celebrating wobble decoding: Half a century and still much is new

(2017) Paul F. Agris et al.   RNA Biology

Architecture of a transcribing-translating expressome

(2017) R. Kohler et al.   SCIENCE

Widespread position-specific conservation of synonymous rare codons within coding sequences

(2017) Julie L. Chaney et al.   PLoS Computational Biology

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

(2017) Michiel J. M. Niesen et al.   PLoS Computational Biology

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

(2017) David H Burkhardt et al.   eLife

Ribosome rearrangements at the onset of translational bypassing

(2017) Xabier Agirrezabala et al.   Science Advances

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

(2016) Joana Pinto Vieira et al.   BIOPHYSICAL JOURNAL

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

(2016) Caitlin E. Gamble et al.   CELL

Translation regulation via nascent polypeptide-mediated ribosome stalling

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

Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations

(2016) Florian Buhr et al.   MOLECULAR CELL

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

(2016) Grégory Boël et al.   NATURE

An integrated, structure- and energy-based view of the genetic code

(2016) Henri Grosjean et al.   NUCLEIC ACIDS RESEARCH

Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences

(2016) Sharon Penias Navon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing

(2016) Yuhei Chadani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Ribosome-based quality control of mRNA and nascent peptides

(2016) Carrie L. Simms et al.   Wiley Interdisciplinary Reviews-RNA

Roles for Synonymous Codon Usage in Protein Biogenesis

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

A comparative genomics study on the effect of individual amino acids on ribosome stalling

(2015) Renana Sabi et al.   BMC GENOMICS

Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity

(2015) Danny D. Nedialkova et al.   CELL

Initiation of mRNA translation in bacteria: structural and dynamic aspects

(2015) Claudio O. Gualerzi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

Essentiality of threonylcarbamoyladenosine (t6A), a universal tRNA modification, in bacteria

(2015) Patrick C. Thiaville et al.   MOLECULAR MICROBIOLOGY

Inflating bacterial cells by increased protein synthesis

(2015) M. Basan et al.   Molecular Systems 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

Ribosome A and P sites revealed by length analysis of ribosome profiling data

(2015) Andrew T. Martens et al.   NUCLEIC ACIDS RESEARCH

Translational tuning optimizes nascent protein folding in cells

(2015) S. J. Kim et al.   SCIENCE

Slowing Translation between Protein Domains by Increasing Affinity between mRNAs and the Ribosomal Anti-Shine–Dalgarno Sequence Improves Solubility

(2015) Kevin A. Vasquez et al.   ACS Synthetic Biology

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

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

Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function

(2015) Cristian Del Campo et al.   PLoS Genetics

Ribosomes slide on lysine-encoding homopolymeric A stretches

(2015) Kristin S Koutmou et al.   eLife

Understanding the Influence of Codon Translation Rates on Cotranslational Protein Folding

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

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

Timing Is Everything: Unifying Codon Translation Rates and Nascent Proteome Behavior

(2014) Daniel A. Nissley et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic pathways of −1 translational frameshifting

(2014) Jin Chen et al.   NATURE

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

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

Structural basis for the interaction of protein S1 with the Escherichia coli ribosome

(2014) Konstantin Byrgazov 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

Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro

(2014) Sophia Rudorf et al.   PLoS Computational Biology

Arrest Peptides:Cis-Acting Modulators of Translation

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

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

(2013) Mian Zhou et al.   NATURE

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

(2013) Yao Xu et al.   NATURE

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

(2013) Silvi Rouskin et al.   NATURE

Dynamics of translation by single ribosomes through mRNA secondary structures

(2013) Chunlai Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability

(2013) Sibylle E. Wohlgemuth et al.   NUCLEIC ACIDS RESEARCH

Transimulation - Protein Biosynthesis Web Service

(2013) Marlena Siwiak et al.   PLoS One

Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria

(2013) A. R. Subramaniam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding

(2013) V. A. N. Rezgui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Differential Translation Tunes Uneven Production of Operon-Encoded Proteins

(2013) Tessa E.F. Quax et al.   Cell Reports

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

Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling

(2013) Boris Zinshteyn et al.   PLoS Genetics

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

(2012) Matthieu Chartier et al.   BIOINFORMATICS

Kinetic control of translation initiation in bacteria

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

Universal Pattern and Diverse Strengths of Successive Synonymous Codon Bias in Three Domains of Life, Particularly Among Prokaryotic Genomes

(2012) F.-B. Guo et al.   DNA RESEARCH

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

(2012) Gene-Wei Li et al.   NATURE

Bacterial RNA thermometers: molecular zippers and switches

(2012) Jens Kortmann et al.   NATURE REVIEWS MICROBIOLOGY

Synonymous Codon Ordering: A Subtle but Prevalent Strategy of Bacteria to Improve Translational Efficiency

(2012) Zhu-Qing Shao et al.   PLoS One

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

Prediction of variable translation rate effects on cotranslational protein folding

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

Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation

(2012) Bin Zhang et al.   Cell Reports

Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo

(2011) Eugene Oh et al.   CELL

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

(2011) Xiaohui Qu et al.   NATURE

Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli

(2011) Koreaki Ito et al.   PLoS One

Composite effects of gene determinants on the translation speed and density of ribosomes

(2011) Tamir Tuller et al.   GENOME BIOLOGY

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

Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames

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

The role of mRNA structure in translational control in bacteria

(2010) Thomas Geissmann et al.   RNA Biology

Differential Arginylation of Actin Isoforms Is Regulated by Coding Sequence-Dependent Degradation

(2010) F. Zhang et al.   SCIENCE

A NusE:NusG Complex Links Transcription and Translation

(2010) B. M. Burmann et al.   SCIENCE

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

Integrating Protein Homeostasis Strategies in Prokaryotes

(2010) A. Mogk et al.   Cold Spring Harbor Perspectives in Biology

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

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding

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

MDR1 (C3435T) polymorphism: relation to the risk of breast cancer and therapeutic outcome

(2009) M Cizmarikova et al.   PHARMACOGENOMICS JOURNAL

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

Preferred and avoided codon pairs in three domains of life

(2008) Age Tats et al.   BMC GENOMICS

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

(2008) Paul F Agris   EMBO REPORTS

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

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

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

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

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH

Rare Codons Cluster

(2008) Thomas F. Clarke et al.   PLoS One

A pause for thought along the co-translational folding pathway

(2008) Anton A. Komar   TRENDS IN BIOCHEMICAL SCIENCES