Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria

Ribosome Rescue Pathways in Bacteria

(2021) Claudia Müller et al.   Frontiers in Microbiology

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics

(2021) Bertrand Beckert et al.   Nature Communications

Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1

(2020) Jasenko Zivanov et al.   IUCrJ

NONU-1 Encodes a Conserved Endonuclease Required for mRNA Translation Surveillance

(2020) Marissa L. Glover et al.   Cell Reports

The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis

(2020) Heinrich Schäfer et al.   PLoS Genetics

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading

(2020) Anna B. Loveland et al.   NATURE

Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes

(2020) Jennifer N. Wells et al.   PLOS BIOLOGY

Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria

(2020) Erica N Thomas et al.   eLife

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways

(2019) Ken Ikeuchi et al.   EMBO JOURNAL

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

(2019) Fuad Mohammad et al.   eLife

The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay

(2019) Karole N D'Orazio et al.   eLife

Ribosome Collisions Result in +1 Frameshifting in the Absence of No-Go Decay

(2019) Carrie L. Simms et al.   Cell Reports

How do cells cope with RNA damage and its consequences?

(2019) Liewei L. Yan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs

(2019) Angela M. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural dynamics of protein S1 on the 70S ribosome visualized by ensemble cryo-EM

(2018) Anna B. Loveland et al.   METHODS

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1

(2018) Bertrand Beckert et al.   Nature Microbiology

ZNF598 Is a Quality Control Sensor of Collided Ribosomes

(2018) Szymon Juszkiewicz et al.   MOLECULAR CELL

Ribosome Collision Is Critical for Quality Control during No-Go Decay

(2017) Carrie L. Simms et al.   MOLECULAR CELL

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Hydroxyl regioisomerization of anthracycline catalyzed by a four-enzyme cascade

(2017) Zhuan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling

(2017) Ting Su et al.   eLife

Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria

(2017) Michael A Ferrin et al.   eLife

SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana

(2016) Wenjuan Wu et al.   PLANT JOURNAL

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling

(2015) Daniel Sohmen et al.   Nature Communications

An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation

(2014) Arvind R. Subramaniam et al.   CELL

Organization of Ribosomes and Nucleoids inEscherichia coliCells during Growth and in Quiescence

(2014) Qian Chai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The general mode of translation inhibition by macrolide antibiotics

(2014) Krishna Kannan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A-Site mRNA Cleavage Is Not Required for tmRNA-Mediated ssrA-Peptide Tagging

(2013) Brian D. Janssen et al.   PLoS One

PPR-SMRs

(2013) Sheng Liu et al.   RNA Biology

Ribosome engineering to promote new crystal forms

(2012) Maria Selmer et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome

(2012) C. Neubauer et al.   SCIENCE

The crystal structure of unmodified tRNA Phe from Escherichia coli

(2010) Robert T. Byrne et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A ribosome–nascent chain sensor of membrane protein biogenesis in Bacillus subtilis

(2009) Shinobu Chiba et al.   EMBO JOURNAL

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

(2009) G. C. Langridge et al.   GENOME RESEARCH

A Gripping Tale of Ribosomal Frameshifting: Extragenic Suppressors of Frameshift Mutations Spotlight P-Site Realignment

(2009) J. F. Atkins et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH