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Resolution of ribosomal stalling by ABCF ATPases YfmR and YkpA/YbiT

https://doi.org/10.1101/2024.01.25.577322
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bip.22832openalex-snapshot
Review: Translational GTPases
inferredcites →https://doi.org/10.1002/pro.3589openalex-snapshot
Ribosome protection by ABC‐F proteins—Molecular mechanism and potential drug design
inferredcites →https://doi.org/10.1016/j.celrep.2020.03.009openalex-snapshot
Structure and Function of an Elongation Factor P Subfamily in Actinobacteria
inferredcites →https://doi.org/10.1016/j.celrep.2020.108250openalex-snapshot
Proteome-wide Capture of Co-translational Protein Dynamics in Bacillus subtilis Using TnDR, a Transposable Protein-Dynamics Reporter
inferredcites →https://doi.org/10.1016/j.jbc.2022.102774openalex-snapshot
Arginine-rich C9ORF72 ALS proteins stall ribosomes in a manner distinct from a canonical ribosome-associated quality control substrate
inferredcites →https://doi.org/10.1016/j.jmb.2008.08.089openalex-snapshot
Electrostatics in the Ribosomal Tunnel Modulate Chain Elongation Rates
inferredcites →https://doi.org/10.1016/j.jmb.2018.12.013openalex-snapshot
ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance: Structural and Functional Diversification across the Tree of Life
inferredcites →https://doi.org/10.1016/j.molcel.2017.03.003openalex-snapshot
eIF5A Functions Globally in Translation Elongation and Termination
inferredcites →https://doi.org/10.1016/j.molcel.2017.10.014openalex-snapshot
Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P
inferredcites →https://doi.org/10.1016/j.molcel.2017.10.020openalex-snapshot
Intrinsic Ribosome Destabilization Underlies Translation and Provides an Organism with a Strategy of Environmental Sensing
inferredcites →https://doi.org/10.1016/j.tibs.2018.11.003openalex-snapshot
Control of mRNA Translation by Versatile ATP-Driven Machines
inferredcites →https://doi.org/10.1021/jacs.3c07524openalex-snapshot
Elongation Factor P Modulates the Incorporation of Structurally Diverse Noncanonical Amino Acids into Escherichia coli Dihydrofolate Reductase
inferredcites →https://doi.org/10.1021/jacs.8b07247openalex-snapshot
Ribosomal Incorporation of Consecutive β-Amino Acids
inferredcites →https://doi.org/10.1038/nchembio.1001openalex-snapshot
Lys34 of translation elongation factor EF-P is hydroxylated by YfcM
inferredcites →https://doi.org/10.1038/nchembio.1751openalex-snapshot
Arginine-rhamnosylation as new strategy to activate translation elongation factor P
inferredcites →https://doi.org/10.1038/nmeth.2089openalex-snapshot
NIH Image to ImageJ: 25 years of image analysis
inferredcites →https://doi.org/10.1038/nsmb.1889openalex-snapshot
A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P
inferredcites →https://doi.org/10.1038/nsmb.2740openalex-snapshot
The ABC-F protein EttA gates ribosome entry into the translation elongation cycle
inferredcites →https://doi.org/10.1038/nsmb.2741openalex-snapshot
EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics
inferredcites →https://doi.org/10.1038/s41467-019-13408-7openalex-snapshot
Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis
inferredcites →https://doi.org/10.1038/s41467-021-23753-1openalex-snapshot
Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens
inferredcites →https://doi.org/10.1038/s41467-022-28078-1openalex-snapshot
Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1038/s41467-022-29274-9openalex-snapshot
Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics
inferredcites →https://doi.org/10.1038/s41467-024-50627-zopenalex-snapshot
Global regulation via modulation of ribosome pausing by the ABC-F protein EttA
inferredcites →https://doi.org/10.1038/s41564-023-01393-zopenalex-snapshot
Atlas of mRNA translation and decay for bacteria
inferredcites →https://doi.org/10.1038/s41594-019-0331-xopenalex-snapshot
Mechanism of ribosome stalling during translation of a poly(A) tail
inferredcites →https://doi.org/10.1073/pnas.1310642110openalex-snapshot
Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P
inferredcites →https://doi.org/10.1073/pnas.1803313115openalex-snapshot
Ribosome protection by antibiotic resistance ATP-binding cassette protein
inferredcites →https://doi.org/10.1073/pnas.1808535115openalex-snapshot
Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR
inferredcites →https://doi.org/10.1073/pnas.1812025115openalex-snapshot
Elongation factor P is required to maintain proteome homeostasis at high growth rate
inferredcites →https://doi.org/10.1074/jbc.m111.309633openalex-snapshot
Post-translational Modification by β-Lysylation Is Required for Activity of Escherichia coli Elongation Factor P (EF-P)
inferredcites →https://doi.org/10.1074/jbc.m115.712091openalex-snapshot
Translation Control of Swarming Proficiency in Bacillus subtilis by 5-Amino-pentanolylated Elongation Factor P
inferredcites →https://doi.org/10.1074/jbc.m509926200openalex-snapshot
ATP Hydrolysis Is Essential for the Function of the Uup ATP-binding Cassette ATPase in Precise Excision of Transposons
inferredcites →https://doi.org/10.1083/jcb.200904161openalex-snapshot
The Drosophila deoxyhypusine hydroxylase homologue nero and its target eIF5A are required for cell growth and the regulation of autophagy
inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot
UFBoot2: Improving the Ultrafast Bootstrap Approximation
inferredcites →https://doi.org/10.1093/nar/gkaa579openalex-snapshot
Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD
inferredcites →https://doi.org/10.1093/nar/gkac058openalex-snapshot
Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci
inferredcites →https://doi.org/10.1093/nar/gkad193openalex-snapshot
Genome-encoded ABCF factors implicated in intrinsic antibiotic resistance in Gram-positive bacteria: VmlR2, Ard1 and CplR
inferredcites →https://doi.org/10.1093/nar/gkw256openalex-snapshot
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
inferredcites →https://doi.org/10.1093/nar/gky050openalex-snapshot
Antibiotic resistance ABCF proteins reset the peptidyl transferase centre of the ribosome to counter translational arrest
inferredcites →https://doi.org/10.1093/nar/gkz960openalex-snapshot
Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins
inferredcites →https://doi.org/10.1101/2023.06.11.543863openalex-snapshot
Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation
inferredcites →https://doi.org/10.1111/mmi.13760openalex-snapshot
Carbonyl reduction by YmfI in Bacillus subtilis prevents accumulation of an inhibitory EF‐P modification state
inferredcites →https://doi.org/10.1126/science.1228985openalex-snapshot
Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches
inferredcites →https://doi.org/10.1126/science.1229017openalex-snapshot
EF-P Is Essential for Rapid Synthesis of Proteins Containing Consecutive Proline Residues
inferredcites →https://doi.org/10.1128/jb.00370-22openalex-snapshot
Elongation Factor P Is Important for Sporulation Initiation
inferredcites →https://doi.org/10.1128/jb.184.17.4881-4890.2002openalex-snapshot
Genome-Wide Analysis of the Stationary-Phase Sigma Factor (Sigma-H) Regulon ofBacillus subtilis
inferredcites →https://doi.org/10.1128/jb.187.17.5946-5954.2005openalex-snapshot
Transcriptional Termination Control of a Novel ABC Transporter Gene Involved in Antibiotic Resistance in Bacillus subtilis
inferredcites →https://doi.org/10.1128/mbio.00306-18openalex-snapshot
EF-P Posttranslational Modification Has Variable Impact on Polyproline Translation in Bacillus subtilis
inferredcites →https://doi.org/10.1128/mbio.01731-21openalex-snapshot
Beyond Self-Resistance: ABCF ATPase LmrC Is a Signal-Transducing Component of an Antibiotic-Driven Signaling Cascade Accelerating the Onset of Lincomycin Biosynthesis
inferredcites →https://doi.org/10.1128/mbio.01975-15openalex-snapshot
ABC-F Proteins Mediate Antibiotic Resistance through Ribosomal Protection
inferredcites →https://doi.org/10.1128/mcb.11.6.3105openalex-snapshot
Translation initiation factor 5A and its hypusine modification are essential for cell viability in the yeast Saccharomyces cerevisiae.
inferredcites →https://doi.org/10.1146/annurev-micro-090816-093629openalex-snapshot
Elongation Factor P and the Control of Translation Elongation
inferredcites →https://doi.org/10.1186/s12864-015-1289-7openalex-snapshot
The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life
inferredcites →https://doi.org/10.1371/journal.pgen.1008179openalex-snapshot
Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P
inferredcites →https://doi.org/10.1371/journal.pone.0147907openalex-snapshot
Neisseria meningitidis Translation Elongation Factor P and Its Active-Site Arginine Residue Are Essential for Cell Viability
inferredcites →https://doi.org/10.3389/fmicb.2020.00277openalex-snapshot
The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation of ‘Long’ RelA-SpoT Homolog Enzymes by Ribosomal Complexes
inferredcites →https://doi.org/10.3389/fmolb.2021.816398openalex-snapshot
Functions and Regulation of Translation Elongation Factors
inferredcites →https://doi.org/10.7554/elife.05534openalex-snapshot
Ribosomes slide on lysine-encoding homopolymeric A stretches
inferredcites →https://doi.org/10.7554/elife.42591openalex-snapshot
A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-024-54556-9openalex-snapshot
EF-P and its paralog EfpL (YeiP) differentially control translation of proline-containing sequences
inferred← citeshttps://doi.org/10.1093/nar/gkae309openalex-snapshot
The ABCF proteins in Escherichia coli individually cope with ‘hard-to-translate’ nascent peptide sequences
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