bacterial degradosome

GO:1990061 · Ribonucleoprotein · Multiprotein complex · Proposed

The degradosome is a protein complex playing a key role in mRNA degradation and RNA processing. It includes a RNA helicase, a 3'-5' phosphate-dependent PNPase and a RNase E bound-enolase. [GO:1990061]

Synonyms: RNA degradosome; Escherichia coli RNA degradosome

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
RNase E scaffold endoribonuclease	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	rne	UNKNOWN	Large endoribonuclease scaffold whose C-terminal half carries binding sites for the other principal E. coli RNA degradosome components. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 mapped binding sites for RhlB, enolase and polynucleotide phosphorylase to the carboxy-terminal half of E. coli RNase E. `DOI:10.1146/annurev.micro.61.080706.093440` Carpousis 2007 reviewed RNase E as the multidomain scaffold of the E. coli RNA degradosome.
polynucleotide phosphorylase	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	pnp	UNKNOWN	3-to-5 phosphorolytic exoribonuclease that associates with RNase E in the degradosome. `DOI:10.1016/0092-8674(94)90363-8` Carpousis et al. 1994 copurified E. coli RNase E with PNPase, providing evidence for a specific association between the enzymes. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 identified a PNPase interaction site in the RNase E scaffold region.
RhlB DEAD-box RNA helicase	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	rhlB	UNKNOWN	DEAD-box RNA helicase recruited to the RNase E scaffold and coupled to degradosome-mediated RNA decay. `DOI:10.1038/381169a0` Py et al. 1996 identified a DEAD-box RNA helicase in the E. coli RNA degradosome. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 localized the RhlB binding site to the RNase E scaffold region.
enolase degradosome component	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	eno	UNKNOWN	Glycolytic enzyme recruited as a principal E. coli RNA degradosome constituent. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 identified an enolase interaction site in the RNase E scaffold region. `DOI:10.1016/j.jmb.2006.02.012` Chandran and Luisi 2006 analyzed recognition of enolase in the E. coli RNA degradosome.

Taxonomic distribution

NCBITaxon:1224 Pseudomonadota — VARIABLE: RNase E-based degradosome-like complexes are described across Proteobacteria, with composition varying among lineages. [DOI:10.1146/annurev.micro.61.080706.093440]

Canonical examples

NCBITaxon:562 Escherichia coli — Model bacterium in which the RNase E scaffold interactions with PNPase, RhlB and enolase were mapped. [DOI:10.1101/gad.12.17.2770]

Functions

mRNA catabolic process GO:0006402 — The E. coli RNase E-based degradosome participates in bacterial mRNA degradation.
- GO:0006402 GO:0006402 is the Gene Ontology biological-process term for mRNA catabolism.
- DOI:10.1146/annurev.micro.61.080706.093440 Carpousis 2007 reviewed the E. coli RNA degradosome as an mRNA-degrading machine assembled on RNase E.

Mechanism graphs

RNase E scaffolds the E. coli RNA degradosome (ASSEMBLY)

In Escherichia coli, RNase E provides a scaffold that recruits PNPase, the RhlB DEAD-box helicase and enolase into a degradosome machine for bacterial mRNA decay.

Subject	Predicate	Object	Evidence
RNase E scaffold endoribonuclease	recruits	polynucleotide phosphorylase	`DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 identified the C-terminal half of RNase E as the region carrying PNPase, RhlB and enolase binding sites.
RNase E scaffold endoribonuclease	recruits	RhlB DEAD-box RNA helicase	`DOI:10.1038/381169a0` Py et al. 1996 identified RhlB as a DEAD-box RNA helicase within the E. coli RNA degradosome. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 mapped the RhlB binding site to the RNase E scaffold.
RNase E scaffold endoribonuclease	recruits	enolase degradosome component	`DOI:10.1016/j.jmb.2006.02.012` Chandran and Luisi 2006 analyzed recognition of enolase in the E. coli RNA degradosome. `DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 mapped the enolase binding site to the RNase E scaffold.
RNase E scaffold endoribonuclease	scaffolds	bacterial degradosome	`DOI:10.1101/gad.12.17.2770` Vanzo et al. 1998 established RNase E as the interaction scaffold for the E. coli RNA degradosome.
bacterial degradosome	supports	mRNA catabolic process	`DOI:10.1146/annurev.micro.61.080706.093440` Carpousis 2007 reviewed the E. coli RNA degradosome as an RNase E-assembled complex involved in mRNA degradation.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral InterPro or Pfam groundings and component boundaries for the E. coli RNase E, PNPase, RhlB and enolase degradosome components. This first bacterial degradosome record models the four principal E. coli components as reviewed, label-only constituents. Exact family accessions, paralog boundaries and degradosome-like substitutions in other proteobacterial lineages need a focused grounding pass.

Evidence

GO:1990061 Gene Ontology cellular-component term for the bacterial degradosome.
GO:0006402 Gene Ontology biological-process term for mRNA catabolic process.
DOI:10.1016/0092-8674(94)90363-8 Carpousis et al. 1994, Copurification of E. coli RNAase E and PNPase: Evidence for a specific association between two enzymes important in RNA processing and degradation, Cell.
DOI:10.1038/381169a0 Py et al. 1996, A DEAD-box RNA helicase in the Escherichia coli RNA degradosome, Nature.
DOI:10.1101/gad.12.17.2770 Vanzo et al. 1998, Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome, Genes and Development.
DOI:10.1016/j.jmb.2006.02.012 Chandran and Luisi 2006, Recognition of Enolase in the Escherichia coli RNA Degradosome, Journal of Molecular Biology.
DOI:10.1146/annurev.micro.61.080706.093440 Carpousis 2007, The RNA Degradosome of Escherichia coli: An mRNA-Degrading Machine Assembled on RNase E, Annual Review of Microbiology.

Curation history

2026-09-12T00:48:27Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-12T00:49:18Z codex · EXPANDED_RECORD — Added RNA degradosome synonymy, label-only RNase E, PNPase, RhlB and enolase constituents, Pseudomonadota distribution, an Escherichia coli canonical example, an mRNA catabolic function, GO/DOI evidence, an RNase E-centered assembly graph and a component-grounding TODO.
2026-09-12T00:49:47Z codex · TIGHTENED_SYNONYM — Changed the unqualified RNA degradosome synonym from exact to related because GO:1990061 denotes the bacterial degradosome specifically.
2026-09-12T00:58:34Z codex · RESOLVED_REVIEW — Resolved #560 by removing the unsupported ams alias; resolved #558 by narrowing the Escherichia coli canonical example to Vanzo-supported RNase E scaffold mapping; resolved #559 by simplifying the mRNA catabolic process description.

Source: data/structures/ribonucleoprotein/bacterial_degradosome.yaml