Gammaproteobacterial RNase E-centered RNA degradation

Reusable RNA-degradation module in which RNase E initiates decay, an optional recruited DEAD-box helicase assists with structured substrates, and a 3'-to-5' exoribonuclease completes processive degradation. RhlB/RhlE and PNPase/RNase R are represented as lineage-variable implementations.

MODULE:bacterial_rna_degradationDRAFTCONCRETEBiological Processmodules/bacterial_rna_degradation.yaml

mRNA catabolic processGO:0006402

GO:0006402

mRNA catabolic process

Grounds the RNA-decay process implemented by this module.

KEGG:ppu03018

Pseudomonas putida KT2440 RNA degradation

Provides a broad discovery set of PSEPK RNA-metabolism proteins; module membership requires independent functional or interaction evidence.

PMID:16275923

RhlB helicase rather than enolase is the beta-subunit of the Escherichia coli polynucleotide phosphorylase (PNPase)-exoribonucleolytic complex

Establishes direct RhlB-PNPase coupling during degradation of structured RNA and distinguishes that functional complex from enolase association.

PMID:40096066

Critical functions and key interactions mediated by the RNase E scaffolding domain in Pseudomonas aeruginosa

Maps Pseudomonas RNase E scaffold interactions with RhlB and PNPase.

PMID:15705581

Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W.

Establishes a same-genus RNase E-RhlE-RNase R degradation-complex variant.

file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_rna_degradation__ppu03018-deep-research-openscientist.md

OpenScientist PSEPK RNase E-centered RNA degradation review

Species-aware synthesis of the pathway boundary, partner alternatives, and evidence for the selected PSEPK proteins.

file:PSEPK/rne/rne-ai-review.yaml

PSEPK rne annotation review

Curated review of the initiating RNase E activity.

file:PSEPK/rhlB/rhlB-ai-review.yaml

PSEPK rhlB annotation review

Curated review of the RhlB helicase implementation.

file:PSEPK/rhlE/rhlE-ai-review.yaml

PSEPK rhlE annotation review

Curated review of the alternative RhlE helicase implementation.

file:PSEPK/pnp/pnp-ai-review.yaml

PSEPK pnp annotation review

Curated review of the PNPase exonuclease implementation.

file:PSEPK/rnr/rnr-ai-review.yaml

PSEPK rnr annotation review

Curated review of the alternative RNase R implementation.

The boundary is RNase E-mediated cleavage plus conditional helicase-assisted and exonuclease-mediated RNA decay. It does not reproduce the broad KEGG bucket: RppH priming, PAP I, Hfq regulation, polyphosphate metabolism, chaperones, RecQ, Rho, and ribosome-biogenesis machinery are adjacent but outside this module. Enolase is excluded because its physical association has not been established for the PSEPK realization. The helicase part is optional because not every RNA substrate requires unwinding and exact partner composition varies among Gammaproteobacteria. Connections describe functional flow rather than an obligatory sequence for every substrate. Molecular functions are asserted only on leaf annotons.

8Nodes

3Parts

2Variant Sets

4Variants

5Annotons

3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_rna_degradation 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.

Gene-review completeness (5/10 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 5 missing review · 3 reviewed but lacking deep research

Gene	Review	Complete	Deep research
Escherichia coli K-12 PNPase exemplar P05055	✗	—	—
Escherichia coli K-12 RhlB exemplar P0A8J8	✗	—	—
Escherichia coli K-12 RNase R exemplar P21499	✗	—	—
Escherichia coli K-12 RNase E exemplar P21513	✗	—	—
Escherichia coli K-12 RhlE exemplar P25888	✗	—	—
pnp Q88DW0	✓	✓	✓
rhlB Q88NB7	✓	✓	✗
rhlE Q88D48	✓	10/11	✗
rne Q88LM4	✓	✓	✓
rnr Q88DE6	✓	✓	✗

Tree

Gammaproteobacterial RNase E-centered RNA degradationBiological Processbacterial_rna_degradation

Parts
1. 1. endonucleolytic initiation and complex organization
2. RNase E cleavage of RNAReactionrne_endonucleolytic_cleavage
  
  Annotons
  - RNase E catalytic and scaffolding activity Family: bacterial RNase E family
3. 2. ATP-dependent unwinding of structured RNA optional
4. DEAD-box-helicase-assisted RNA unwindingReactiondegradosome_helicase_assistance
  
  Variants
  1. Recruited DEAD-box helicase variants by helicase partner identity (One Or More)
    
    RhlB-assisted unwindingReactionrhlb_helicase_variant
    
    Annotons
    
    RhlB RNA helicase activity Family: DEAD-box RNA helicase RhlB family
    
    RhlE-assisted unwindingReactionrhle_helicase_variant
    
    Annotons
    
    RhlE RNA helicase activity Family: DEAD-box RNA helicase RhlE family
5. 3. processive 3'-to-5' exonucleolysis
6. Processive 3'-to-5' RNA degradationReactionrna_exonucleolysis
  
  Variants
  1. Recruited 3'-to-5' exonuclease variants by exonuclease partner identity (One Or More)
    
    PNPase phosphorolysisReactionpnpase_exonuclease_variant
    
    Annotons
    
    PNPase activity Family: bacterial polynucleotide phosphorylase family
    
    RNase R hydrolytic exonucleolysisReactionrnase_r_exonuclease_variant
    
    Annotons
    
    RNase R activity Family: bacterial RNase R family

Details

Context

GammaproteobacteriaNCBITaxon:1236

Gammaproteobacterial RNase E-centered RNA degradationBiological Processbacterial_rna_degradation

mRNA catabolic processGO:0006402

Context

GammaproteobacteriaNCBITaxon:1236

Connections

rne_endonucleolytic_cleavage -> degradosome_helicase_assistance Provides Input For

RNase E cleavage products can be unwound before exonucleolysis.

rne_endonucleolytic_cleavage -> rna_exonucleolysis Provides Input For

RNase E cleavage generates substrates for processive 3'-to-5' degradation.

degradosome_helicase_assistance -> rna_exonucleolysis Provides Input For

Helicase-assisted unwinding makes structured substrates accessible to exonucleases.

Part 1: endonucleolytic initiation and complex organization

RNase E cleavage of RNAReactionrne_endonucleolytic_cleavage

Annotons

RNase E catalytic and scaffolding activity

rne_activity

Participant: Family: bacterial RNase E family

Family:

bacterial RNase E familyInterPro:IPR028878

Representative Members: PSEPK RNase E exemplarUniProtKB:Q88LM4 Escherichia coli K-12 RNase E exemplarUniProtKB:P21513

Function

ribonuclease E activityGO:0008995

Initiates decay by endonucleolytic cleavage and recruits downstream RNA-processing partners through its scaffold region.

Part 2: ATP-dependent unwinding of structured RNA (optional)

DEAD-box-helicase-assisted RNA unwindingReactiondegradosome_helicase_assistance

Variant set: Recruited DEAD-box helicase variants by helicase partner identity (One Or More)

RhlB-assisted unwindingReactionrhlb_helicase_variant

PMID:40096066

Pseudomonas RNase E directly recruits RhlB.

Annotons

RhlB RNA helicase activity

rhlb_activity

Participant: Family: DEAD-box RNA helicase RhlB family

Family:

DEAD-box RNA helicase RhlB familyInterPro:IPR023554

Representative Members: PSEPK RhlB exemplarUniProtKB:Q88NB7 Escherichia coli K-12 RhlB exemplarUniProtKB:P0A8J8

Function

RNA helicase activityGO:0003724

Unwinds structured RNA in an RhlB-containing implementation.

RhlE-assisted unwindingReactionrhle_helicase_variant

PMID:15705581

A Pseudomonas syringae RNase E complex recruits RhlE with RNase R.

Annotons

RhlE RNA helicase activity

rhle_activity

Participant: Family: DEAD-box RNA helicase RhlE family

Family:

DEAD-box RNA helicase RhlE familyPANTHER:PTHR47959:SF13

Representative Members: PSEPK RhlE exemplarUniProtKB:Q88D48 Escherichia coli K-12 RhlE exemplarUniProtKB:P25888

Function

RNA helicase activityGO:0003724

Unwinds structured RNA in an RhlE-containing implementation.

Part 3: processive 3'-to-5' exonucleolysis

Processive 3'-to-5' RNA degradationReactionrna_exonucleolysis

Variant set: Recruited 3'-to-5' exonuclease variants by exonuclease partner identity (One Or More)

PNPase phosphorolysisReactionpnpase_exonuclease_variant

PMID:40096066

Pseudomonas RNase E directly recruits PNPase.

Annotons

PNPase activity

pnpase_activity

Participant: Family: bacterial polynucleotide phosphorylase family

Family:

bacterial polynucleotide phosphorylase familyInterPro:IPR012162

Representative Members: PSEPK PNPase exemplarUniProtKB:Q88DW0 Escherichia coli K-12 PNPase exemplarUniProtKB:P05055

Function

polyribonucleotide nucleotidyltransferase activityGO:0004654

Degrades RNA processively by phosphorolysis.

RNase R hydrolytic exonucleolysisReactionrnase_r_exonuclease_variant

PMID:15705581

A Pseudomonas syringae complex contains RNase R rather than PNPase.

Annotons

RNase R activity

rnase_r_activity

Participant: Family: bacterial RNase R family

Family:

bacterial RNase R familyInterPro:IPR011805

Representative Members: PSEPK RNase R exemplarUniProtKB:Q88DE6 Escherichia coli K-12 RNase R exemplarUniProtKB:P21499

Function

exoribonuclease II activityGO:0008859

Degrades structured RNA hydrolytically in an RNase R-containing implementation.