EF-P translation stall rescue

A species-neutral bacterial EF-P-family module for elongation factor P-dependent stimulation of peptide-bond formation and rescue of stalled cytosolic ribosomes. Pseudomonas putida KT2440 efp/PP_1858 (UniProtKB:Q88LS0) is the local UPA00345 exemplar, not the defining scope of the module. Lineage-specific EF-P activation chemistry, including pseudomonad EarP-dependent Arg32 rhamnosylation and enterobacterial beta-lysylation, is adjacent context rather than a member of the EF-P step itself.

MODULE:efp_translation_stall_rescueDRAFTBiological Processmodules/efp_translation_stall_rescue.yaml
translational elongationGO:0006414 rescue of stalled cytosolic ribosomeGO:0072344
UniPathway:UPA00345
UniPathway UPA00345
The local UPA00345 membership set contains efp as the elongation factor P member of protein biosynthesis/polypeptide-chain elongation.
GO:0072344
rescue of stalled cytosolic ribosome
GO:0072344 captures EF-P's more specific role in relieving stalled ribosomes during translation.
PANTHER:PTHR30053
PANTHER elongation factor P family
PTHR30053 grounds the annoton as an EF-P-family role and includes broad bacterial representatives such as PSEPK Q88LS0, E. coli K-12 P0A6N4, P. aeruginosa PAO1 Q9HZZ2, Shewanella oneidensis Q8EEP9, Neisseria meningitidis Q9JZQ8, and Thermus thermophilus HB8 Q76G20.
UniProtKB:Q88LS0
PSEPK efp UniProt exemplar
Q88LS0 is the curated P. putida KT2440 EF-P member of UPA00345 and is used here as an exemplar for the local PSEPK pathway bucket.
PMID:25686373
Arginine-rhamnosylation as new strategy to activate translation elongation factor P.
This study supports EF-P as the bacterial factor that rescues stalled ribosomes, with activation by EarP-mediated rhamnosylation in the Arg-type EF-P subfamily.
file:PSEPK/efp/efp-ai-review.yaml
Curated efp review
The efp review accepts translation elongation factor activity, translational elongation, EF-P localization annotations, and stalled-ribosome rescue, while keeping broad peptide biosynthesis and regulation of translation as non-core context.
file:PSEPK/efp/efp-uniprot.txt
UniProtKB reviewed entry for efp
UniProt describes EF-P as involved in peptide-bond synthesis and assigned to protein biosynthesis/polypeptide-chain elongation.
file:modules/efp_translation_stall_rescue-deep-research-openscientist.md
OpenScientist module research for EF-P translation stall rescue
OpenScientist module-level research supports EF-P as a conserved translation factor that rescues polyproline and related elongation stalls, with pseudomonad EarP/rhamnose-dependent activation treated as context rather than as part of the UPA00345 EF-P entry itself.
file:projects/P_PUTIDA/deep-research/PSEPK__efp_translation_stall_rescue__upa00345-deep-research-openscientist.md
OpenScientist PSEPK UPA00345 pathway satisfiability review
The PSEPK-specific OpenScientist report finds the UPA00345 core step satisfied by efp/PP_1858/Q88LS0, with no EfpL/YeiP paralog ambiguity, EpmA/EpmB/EpmC beta-lysylation genes not expected in KT2440, and EarP plus dTDP-L-rhamnose supply correctly treated as adjacent activation context.

First-pass interpretation: the reusable module is a species-neutral bacterial EF-P-family stall-rescue module with two mechanistic roles: engagement of the stalled cytosolic ribosome and EF-P-dependent stimulation of elongation/stall rescue. The PSEPK UPA00345 instantiation is satisfiable with efp/PP_1858/Q88LS0 as the local UniProt exemplar. Treat EarP, Rml dTDP-rhamnose biosynthesis, EpmA/EpmB/EpmC, and other activation dependencies as linked context handled by their own modules. OpenScientist's PSEPK-specific review supports this compact EF-P boundary, notes that KT2440 lacks an EfpL/YeiP paralog and the E. coli-style EpmA/EpmB/EpmC beta-lysylation route, and flags the adjacent EarP/Q88LS1 UniProt "Lys-32" target text as a likely residue-label typo because pseudomonad EF-P is Arg32-rhamnosylated.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
0Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✓ present

  • efp_translation_stall_rescue-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

1 leaf node(s) with no concrete protein grounding:

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (1/2 grounded genes reviewed)

1 complete review(s) · 1 with deep research · 1 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
efp Q88LS0 ✓ ✓ ✓
E. coli K-12 efp exemplar P0A6N4 ✗ — —

Details

Context
bacteriaNCBITaxon:2
cytosolGO:0005829
EF-P translation stall rescueBiological Processefp_translation_stall_rescue
translational elongationGO:0006414 rescue of stalled cytosolic ribosomeGO:0072344
Context
bacteriaNCBITaxon:2
cytosolGO:0005829
Part 1: EF-P engagement of a stalled cytosolic ribosome
EF-P stalled-ribosome engagementBiological Processefp_stalled_ribosome_engagement

EF-P binds a stalled cytosolic ribosome and positions the P-site peptidyl-tRNA/rRNA interface so the nascent chain can continue through difficult motifs such as polyproline stretches.

Annotons

EF-P family: stalled-ribosome binding
efp_ribosome_binding
Participant: Family: elongation factor P family
Family:
elongation factor P familyPANTHER:PTHR30053 Bacterial EF-P-family proteins that bind stalled ribosomes during cytosolic translational elongation.

Function

ribosome bindingGO:0043022

Processes

rescue of stalled cytosolic ribosomeGO:0072344

Locations

cytosolGO:0005829

Binding/positioning role that engages stalled cytosolic ribosomes; tRNA and rRNA binding are supporting mechanistic observations in characterized EF-P exemplars.

Part 2: EF-P-dependent stimulation of stalled translation elongation
EF-P elongation/stall-rescue activityBiological Processefp_translation_stall_rescue_step

EF-P-family translation factors stimulate peptide-bond formation and restore productive elongation at stalled cytosolic ribosomes. The activating post-translational modification is lineage-specific and modeled as adjacent context.

Annotons

EF-P family: translation elongation factor
efp_translation_elongation_factor
Participant: Family: elongation factor P family
Family:
elongation factor P familyPANTHER:PTHR30053 Bacterial EF-P/YeiP-family proteins that stimulate peptide-bond formation and rescue slow elongation. The module core is represented by canonical EF-P; EfpL/YeiP paralogs are related family members and should be handled explicitly when present in a target organism.
Representative Members: PSEPK efp exemplarUniProtKB:Q88LS0 E. coli K-12 efp exemplarUniProtKB:P0A6N4
Select canonical bacterial EF-P-family members with translation elongation factor activity. PSEPK Q88LS0 is an exemplar for the P. putida KT2440 UPA00345 bucket, while the family selector keeps the reusable module from being PSEPK-specific.
file:interpro/panther/PTHR30053/PTHR30053-entries.csv
Local PTHR30053 entries include Q88LS0, P0A6N4, Q9HZZ2, Q8EEP9, Q9JZQ8, and Q76G20 as EF-P-family members.
file:PSEPK/efp/efp-goa.tsv
Q88LS0 GOA cites PANTHER:PTN002409107 for translation elongation factor activity and cellular-component placement.

Function

translation elongation factor activityGO:0003746

Processes

translational elongationGO:0006414 rescue of stalled cytosolic ribosomeGO:0072344

Locations

cytosolGO:0005829

Cytosolic elongation factor that promotes peptide-bond formation and relieves stalled translation elongation.