Prophage excision switches the primary ribosome rescue pathway and rescue‐associated gene regulations in Escherichia coli

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

(2022) Lydia Herzel et al.   NUCLEIC ACIDS RESEARCH

Translational control through ribosome heterogeneity and functional specialization

(2021) David M. Gay et al.   TRENDS IN BIOCHEMICAL SCIENCES

Phenotypic effects of paralogous ribosomal proteins bL31A and bL31B in E. coli

(2020) Silva Lilleorg et al.   Scientific Reports

Conserved Upstream Open Reading Frame Nascent Peptides that Control Translation

(2020) Thomas E. Dever et al.   Annual Review of Genetics

FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

(2020) Chayan Kumar Saha et al.   BIOINFORMATICS

φSa3mw Prophage as a Molecular Regulatory Switch of Staphylococcus aureus β-toxin Production

(2019) Phuong M. Tran et al.   JOURNAL OF BACTERIOLOGY

Symbiosis of a P2‐family phage and deep‐sea Shewanella putrefaciens

(2019) Xiaoxiao Liu et al.   ENVIRONMENTAL MICROBIOLOGY

DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

(2019) Vadim Demichev et al.   NATURE METHODS

Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis

(2019) Naomi Shimokawa-Chiba et al.   Nature Communications

Translation in Prokaryotes

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

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation

(2018) Martina M. Yordanova et al.   NATURE

A New Mechanism for Ribosome Rescue Can Recruit RF1 or RF2 to Nonstop Ribosomes

(2018) Tyler D. P. Goralski et al.   mBio

Structural basis for ArfA–RF2-mediated translation termination on mRNAs lacking stop codons

(2017) Paul Huter et al.   NATURE

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome

(2017) Fuxing Zeng et al.   NATURE

Mechanistic insights into the alternative translation termination by ArfA and RF2

(2017) Chengying Ma et al.   NATURE

Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis

(2016) Zhenshun Zeng et al.   ISME Journal

Translational termination without a stop codon

(2016) Nathan R. James et al.   SCIENCE

The selective tRNA aminoacylation mechanism based on a single G•U pair

(2014) Masahiro Naganuma et al.   NATURE

ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue

(2014) Daisuke Kurita et al.   NUCLEIC ACIDS RESEARCH

The tmRNA website

(2014) Corey M. Hudson et al.   NUCLEIC ACIDS RESEARCH

Ends of the line for tmRNA-SmpB

(2014) Corey M. Hudson et al.   Frontiers in Microbiology

Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence

(2012) Lev Rabinovich et al.   CELL

ArfA Recruits RF2 into Stalled Ribosomes

(2012) Yoshihiro Shimizu   JOURNAL OF MOLECULAR BIOLOGY

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis inEscherichia coli

(2012) Yuhei Chadani et al.   MOLECULAR MICROBIOLOGY

Francisella tularensis tmRNA system mutants are vulnerable to stress, avirulent in mice, and provide effective immune protection

(2012) Anton Svetlanov et al.   MOLECULAR MICROBIOLOGY

Phage-Like Streptococcus pyogenes Chromosomal Islands (SpyCI) and Mutator Phenotypes: Control by Growth State and Rescue by a SpyCI-Encoded Promoter

(2012) Julie Scott et al.   Frontiers in Microbiology

trans-translation-mediated tight regulation of the expression of the alternative ribosome-rescue factor ArfA in Escherichia coli

(2011) Yuhei Chadani et al.   GENES & GENETIC SYSTEMS

tmRNA regulates synthesis of the ArfA ribosome rescue factor

(2011) Fernando Garza-Sánchez et al.   MOLECULAR MICROBIOLOGY

Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways

(2011) Yuhei Chadani et al.   MOLECULAR MICROBIOLOGY

Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli

(2011) Koreaki Ito et al.   PLoS One

Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system

(2010) Yuhei Chadani et al.   MOLECULAR MICROBIOLOGY

Cryptic prophages help bacteria cope with adverse environments

(2010) Xiaoxue Wang et al.   Nature Communications

Control and benefits of CP4-57 prophage excision in Escherichia coli biofilms

(2009) Xiaoxue Wang et al.   ISME Journal

Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli: Analysis of a Bar-Coded Mutant Collection

(2009) E. C. Hobbs et al.   JOURNAL OF BACTERIOLOGY

Escherichia coli RNase R Has Dual Activities, Helicase and RNase

(2009) N. Awano et al.   JOURNAL OF BACTERIOLOGY

Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants

(2009) Takeshi Masuda et al.   MOLECULAR & CELLULAR PROTEOMICS