Bacterial SRP-dependent cotranslational membrane targeting

A reusable bacterial module for cotranslational targeting of hydrophobic nascent membrane proteins to the cytoplasmic membrane. A signal recognition particle made of the Ffh GTPase and a small SRP RNA (4.5S RNA in E. coli and Pseudomonas) binds the signal sequence of a ribosome-nascent-chain complex, the peripheral membrane SRP receptor FtsY captures that complex at the membrane, and reciprocal GTPase activation in the Ffh-FtsY NG-domain heterodimer promotes handoff to the SecYEG insertion machinery and dissociation of Ffh and FtsY. The boundary ends at this handoff; SecYEG-mediated translocation and insertion are downstream modules.

MODULE:bacterial_srp_cotranslational_targetingCOMPLETECONCRETEBiological Processmodules/bacterial_srp_cotranslational_targeting.yaml
SRP-dependent cotranslational protein targeting to membraneGO:0006614
GO:0006614
SRP-dependent cotranslational protein targeting to membrane
GO:0006614 defines the biological-process boundary of the module.
GO:0048501
signal recognition particle, plasma membrane targeting
GO:0048501, the plasma-membrane-targeting child of GO:0048500 signal recognition particle, grounds the bacterial Ffh/SRP-RNA ribonucleoprotein.
RFAM:RF00169
Bacterial small signal recognition particle RNA
RF00169 grounds the conserved bacterial 4.5S SRP RNA family used as a required participant in nascent-chain recognition.
NCBIGene:26969983
Pseudomonas putida KT2440 ffs
NCBI Gene identifies the KT2440 4.5S SRP RNA as ffs, with aliases PP_RS22200 and PP_mr50, on reference chromosome NC_002947.4.
UniProtKB:P0AGD7
Escherichia coli K-12 Ffh
The reviewed E. coli Ffh entry (PTHR11564:SF5) is the experimentally characterized exemplar of bacterial Ffh.
UniProtKB:P10121
Escherichia coli K-12 FtsY
The reviewed E. coli FtsY entry (PTHR43134:SF1) is the experimentally characterized exemplar of the bacterial SRP receptor.
file:ECOLI/ffh/ffh-ai-review.yaml
ECOLI Ffh gene review
P0AGD7 core functions are signal sequence receptor activity, 7S (4.5S) RNA binding and GTPase activity in the plasma-membrane-targeting SRP.
file:ECOLI/ftsY/ftsY-ai-review.yaml
ECOLI FtsY gene review
P10121 core functions are signal recognition particle binding and GTPase activity on the cytoplasmic side of the inner membrane.
file:interpro/panther/PTHR11564/PTHR11564-review.yaml
PTHR11564 SRP54/Ffh family review
GTPase and signal sequence receptor activities are family-wide; SRP RNA binding is family-wide with a member exception for higher-plant chloroplast SRP54, which lost it.
file:interpro/panther/PTHR43134/PTHR43134-review.yaml
PTHR43134 SR alpha/FtsY family review
SRP binding and SRP-dependent targeting are restricted to subfamily SF1; the FlhF subfamily SF3 is a diverged flagellar GTPase.
PMID:8107852
Interaction of E. coli Ffh/4.5S ribonucleoprotein and FtsY mimics that of mammalian signal recognition particle and its receptor.
E. coli Ffh/4.5S RNA binds FtsY in a GTP-dependent manner with stimulation of GTP hydrolysis.
file:PSEPK/ffh/ffh-ai-review.yaml
PSEPK Ffh gene review
Q88MV7 is the SRP RNA-binding GTPase component of the bacterial signal recognition particle.
file:PSEPK/ftsY/ftsY-ai-review.yaml
PSEPK FtsY gene review
Q88CR9 is the membrane-associated SRP receptor and partner GTPase.
file:projects/P_PUTIDA/batches/ppu03060_bacterial_srp_cotranslational_targeting.tsv
Pseudomonas putida KT2440 SRP-targeting batch
The focused batch records the exact KT2440 Ffh and FtsY implementations used as leaf exemplars.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_srp_cotranslational_targeting__ppu03060-deep-research-openscientist.md
PSEPK SRP targeting module-pathway-taxon research
The species-aware retrieval finds the three-part module satisfied by Ffh, the ffs noncoding RNA, and FtsY, while separating downstream SecYEG, YidC, signal-peptidase, and parallel Tat components.

Scope is all Bacteria: Ffh, a small SRP RNA and FtsY are near-universal in bacteria, and the two reviewed exemplar pairs (E. coli K-12, experimentally characterized; Pseudomonas putida KT2440, the originating batch organism) illustrate rather than limit it. The SRP RNA is represented at the conserved-family level by RFAM:RF00169 with E. coli and KT2440 ffs loci as exemplars; Gram-positive bacteria such as Bacillus subtilis use a longer SRP RNA with an Alu domain, which this family-level grounding covers without separate modelling. PANTHER PTHR11564:SF5 (Ffh) is pan-domain and also contains eukaryotic SRP54 and higher-plant chloroplast SRP54; the latter has lost SRP RNA binding, which the family review records as a member exception to a family-wide GO:0008312 scope. PTHR43134 PAINT node PTN000169915 also covers the FlhF subfamily (SF3); the SRP-receptor role applies to SF1. SecYEG is the receiving translocon, not a part of the SRP targeting module itself.

4Nodes
3Parts
0Variant Sets
0Variants
6Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_srp_cotranslational_targeting deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • srp_nascent_chain_recognition → ftsy_receptor_engagement [NOT_CHECKED]
  • ftsy_receptor_engagement → srp_receptor_gtpase_cycle [NOT_CHECKED]

Function consistency and core coverage

10 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (15 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
ffh_signal_sequence_binding ffh (Pseudomonas putida KT2440)
UniProtKB:Q88MV7
Family Representative 		signal sequence receptor activity
GO:0005048 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_signal_sequence_binding ffh (Escherichia coli K-12)
UniProtKB:P0AGD7
Family Representative 		signal sequence receptor activity
GO:0005048 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_srp_rna_binding ffh (Pseudomonas putida KT2440)
UniProtKB:Q88MV7
Family Representative 		7S RNA binding
GO:0008312 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_srp_rna_binding ffh (Escherichia coli K-12)
UniProtKB:P0AGD7
Family Representative 		7S RNA binding
GO:0008312 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ftsy_srp_receptor ftsY (Pseudomonas putida KT2440)
UniProtKB:Q88CR9
Family Representative 		signal recognition particle binding
GO:0005047 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ftsy_srp_receptor ftsY (Escherichia coli K-12)
UniProtKB:P10121
Family Representative 		signal recognition particle binding
GO:0005047 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_gtpase ffh (Pseudomonas putida KT2440)
UniProtKB:Q88MV7
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_gtpase ffh (Escherichia coli K-12)
UniProtKB:P0AGD7
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ftsy_gtpase ftsY (Pseudomonas putida KT2440)
UniProtKB:Q88CR9
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ftsy_gtpase ftsY (Escherichia coli K-12)
UniProtKB:P10121
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ffh_signal_sequence_binding Ffh/SRP54 family
PANTHER:PTHR11564:SF5
Family 		signal sequence receptor activity
GO:0005048 		Family Supported
Family review supports GO:0005048 FAMILY_WIDE. Signal-sequence binding by the M domain is the defining activity of the family, shown directly for the E. coli Ffh/4.5S RNA particle and, as the ER-specific child GO:0030942, for mammalian SRP54.
ffh_srp_rna_binding Ffh/SRP54 family
PANTHER:PTHR11564:SF5
Family 		7S RNA binding
GO:0008312 		Family Supported
Family review supports GO:0008312 FAMILY_WIDE. SRP RNA binding by the M domain holds for eukaryotic SRP54 (four PAINT seeds at PTN000169814) and for bacterial Ffh, which binds 4.5S RNA. The one known loss is in higher-plant chloroplast SRP54, which is classified in the same subfamily (SF5) and is recorded below as a member exception. Parsing PTHR11564-entries.csv for chloroplast-targeted or plant members finds a single chloroplast SRP54 among the reviewed members (Arabidopsis FFC, P37107); the other plant rows (Arabidopsis SRP-54A/B/C, barley and tomato SRP54 1-3) are cytosolic SRP54 paralogs.
ftsy_srp_receptor bacterial FtsY SRP receptor family
PANTHER:PTHR43134:SF1
Family 		signal recognition particle binding
GO:0005047 		Family Supported
Family review supports GO:0005047 for PANTHER:PTHR43134:SF1. Established for the SF1 SRP receptors; FlhF (SF3) is a flagellar biosynthesis GTPase whose SRP binding is unverified, so the term should not descend family-wide.
ffh_gtpase Ffh/SRP54 family
PANTHER:PTHR11564:SF5
Family 		GTPase activity
GO:0003924 		Family Supported
Family review supports GO:0003924 FAMILY_WIDE. Demonstrated for bacterial Ffh (intrinsic and FtsY-stimulated GTP hydrolysis) and for eukaryotic SRP54 (PAINT seed); the G-domain GTP-binding motifs define the family.
ftsy_gtpase bacterial FtsY SRP receptor family
PANTHER:PTHR43134:SF1
Family 		GTPase activity
GO:0003924 		Family Supported
Family review supports GO:0003924 FAMILY_WIDE. The NG-domain GTPase is shared by SR alpha, FtsY and FlhF; experimentally shown for E. coli FtsY.

Gene-review completeness (4/4 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
ffh P0AGD7 ✓ ✓ ✗
ffh Q88MV7 ✓ ✓ ✓
ftsY P10121 ✓ ✓ ✗
ftsY Q88CR9 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Bacterial SRP-dependent cotranslational membrane targetingBiological Processbacterial_srp_cotranslational_targeting
SRP-dependent cotranslational protein targeting to membraneGO:0006614
Context
bacteriaNCBITaxon:2

Connections

Signal recognition by SRP precedes capture of the SRP-RNC complex by membrane-associated FtsY.
Receptor engagement precedes reciprocal GTPase activation, SecYEG handoff, and targeting-factor dissociation.
Part 1: nascent signal-sequence recognition by bacterial SRP
Ffh/4.5S-RNA nascent-chain recognitionBiological Processsrp_nascent_chain_recognition

Ffh associates with bacterial SRP RNA (4.5S RNA in E. coli and Pseudomonas) to form the plasma-membrane-targeting signal recognition particle and recognizes hydrophobic signal or signal-anchor sequences as they emerge from the translating ribosome.

SRP-dependent cotranslational protein targeting to membrane, signal sequence recognitionGO:0006617 signal recognition particle, plasma membrane targetingGO:0048501

Annotons

Ffh nascent signal-sequence binding
ffh_signal_sequence_binding
Participant: Family: Ffh/SRP54 family
Family:
Ffh/SRP54 familyPANTHER:PTHR11564:SF5
Representative Members: ffh (Pseudomonas putida KT2440)UniProtKB:Q88MV7 ffh (Escherichia coli K-12)UniProtKB:P0AGD7

Function

signal sequence receptor activityGO:0005048

Processes

SRP-dependent cotranslational protein targeting to membrane, signal sequence recognitionGO:0006617

Recognizes a hydrophobic signal sequence as it emerges from the translating ribosome.

Bacterial 4.5S SRP RNA
bacterial_srp_rna
Participant: Family: bacterial 4.5S signal recognition particle RNA family
Family:
bacterial 4.5S signal recognition particle RNA familyRFAM:RF00169
Representative Members: ffs (Pseudomonas putida KT2440 4.5S SRP RNA)NCBIGene:26969983 ffs (Escherichia coli K-12 4.5S SRP RNA)NCBIGene:944909

Processes

SRP-dependent cotranslational protein targeting to membrane, signal sequence recognitionGO:0006617

Scaffolds the bacterial SRP ribonucleoprotein and accelerates the Ffh-FtsY targeting cycle.

RFAM:RF00169
Bacterial small signal recognition particle RNA
RF00169 identifies the conserved bacterial small SRP RNA family.
PMID:11735405
Role of SRP RNA in the GTPase cycles of Ffh and FtsY
Kinetic analysis shows that bacterial SRP RNA accelerates Ffh-FtsY complex formation and coordinates their GTPase cycle.
PMID:1701272
An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle.
An antiserum to Ffh co-precipitates E. coli 4.5S RNA, and a dominant 4.5S RNA mutant is lethal, establishing ffs RNA as the RNA component of bacterial SRP.
Ffh binding to bacterial SRP RNA
ffh_srp_rna_binding
Participant: Family: Ffh/SRP54 family
Family:
Ffh/SRP54 familyPANTHER:PTHR11564:SF5
Representative Members: ffh (Pseudomonas putida KT2440)UniProtKB:Q88MV7 ffh (Escherichia coli K-12)UniProtKB:P0AGD7

Function

7S RNA bindingGO:0008312

Processes

SRP-dependent cotranslational protein targeting to membraneGO:0006614

Binds bacterial 4.5S SRP RNA to form the signal recognition particle ribonucleoprotein.

Part 2: membrane receptor engagement
FtsY engagement of the SRP-ribosome complexBiological Processftsy_receptor_engagement

Membrane-associated FtsY, held peripherally on the cytoplasmic face of the cytoplasmic membrane by lipid-binding helices in its A domain, binds the SRP-ribosome-nascent-chain complex and positions it for the GTP-coupled handoff to SecYEG.

Annotons

FtsY SRP receptor
ftsy_srp_receptor
Participant: Family: bacterial FtsY SRP receptor family
Family:
bacterial FtsY SRP receptor familyPANTHER:PTHR43134:SF1
Representative Members: ftsY (Pseudomonas putida KT2440)UniProtKB:Q88CR9 ftsY (Escherichia coli K-12)UniProtKB:P10121

Function

signal recognition particle bindingGO:0005047

Processes

SRP-dependent cotranslational protein targeting to membraneGO:0006614

Locations

cytoplasmic side of plasma membraneGO:0009898

Captures the SRP-ribosome-nascent-chain complex at the membrane.

Part 3: GTP-coupled handoff and targeting-factor recycling
Ffh/FtsY GTPase handoff cycleBiological Processsrp_receptor_gtpase_cycle

Ffh and FtsY form a reciprocal GTPase complex. Its ordered rearrangement and GTP hydrolysis promote transfer of the targeted ribosome-nascent-chain complex toward SecYEG and dissociation of the targeting factors.

Annotons

Ffh GTPase
ffh_gtpase
Participant: Family: Ffh/SRP54 family
Family:
Ffh/SRP54 familyPANTHER:PTHR11564:SF5
Representative Members: ffh (Pseudomonas putida KT2440)UniProtKB:Q88MV7 ffh (Escherichia coli K-12)UniProtKB:P0AGD7

Function

GTPase activityGO:0003924

Processes

SRP-dependent cotranslational protein targeting to membraneGO:0006614

Catalyzes the Ffh half of reciprocal GTP hydrolysis in the composite active site formed with FtsY after receptor engagement; the membrane location belongs to the FtsY partner, so none is asserted for Ffh.

FtsY receptor GTPase
ftsy_gtpase
Participant: Family: bacterial FtsY SRP receptor family
Family:
bacterial FtsY SRP receptor familyPANTHER:PTHR43134:SF1
Representative Members: ftsY (Pseudomonas putida KT2440)UniProtKB:Q88CR9 ftsY (Escherichia coli K-12)UniProtKB:P10121

Function

GTPase activityGO:0003924

Processes

SRP-dependent cotranslational protein targeting to membraneGO:0006614

Locations

cytoplasmic side of plasma membraneGO:0009898

Catalyzes the receptor half of reciprocal GTP hydrolysis during SecYEG handoff and complex dissociation.