bacterial aggresome

cellstructuremech:bacterial_aggresome · Inclusion · Inclusion body · Proposed

A stress-associated, membraneless cytoplasmic inclusion in bacteria that concentrates endogenous proteins and can sequester mRNA; Escherichia coli aggresomes exhibit liquid-like dynamics and preserve selected transcripts during stress. [DOI:10.1038/s41564-025-02086-5]

Synonyms: bacterial stress granule

Part of: GO:0005737 — cytoplasm (no local record)

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
Heat shock protein HslU	Protein	part of	`InterPro:IPR004491`	hslU	UNKNOWN	Endogenous protein constituent used as an aggresome marker in E. coli; its enrichment does not establish that it is an essential assembly scaffold. `DOI:10.1126/sciadv.abh2929` Chromosomal fluorescent fusions accumulate in aggresomes and co-localize with Kbl and AcnB. HslU responds earliest among these three tested markers. `InterPro:IPR004491` Verified whole-protein HslU family. This is the ATPase subunit, not HslV or the complete HslUV protease complex.
2-amino-3-ketobutyrate coenzyme A ligase	Protein	part of	`InterPro:IPR011282`	kbl	UNKNOWN	Metabolic-enzyme constituent detected in E. coli aggresomes; incorporation kinetics differ from those of HslU and AcnB. `DOI:10.1126/sciadv.abh2929` Chromosomal Kbl fluorescent fusions form foci co-localizing with the other aggresome markers; photobleaching experiments examine its internal mobility. `InterPro:IPR011282` Verified Kbl whole-protein family, not a generic pyridoxal-phosphate-dependent enzyme superfamily.
Aconitase B	Protein	part of	`InterPro:IPR004406`	acnB	UNKNOWN	Metabolic-enzyme constituent recruited into E. coli aggresomes with slower observed clustering than HslU or Kbl. `DOI:10.1126/sciadv.abh2929` Chromosomal AcnB fluorescent fusions co-localize with the aggresome markers; the study does not establish an assembly requirement for AcnB. `InterPro:IPR004406` Verified Aconitase B family, distinct from generic aconitase groupings.
mRNA	Rna	part of	`SO:0000234`		UNKNOWN	Selectively enriched RNA cargo. Longer transcripts partition preferentially under the tested stresses; this is not a claim that every mRNA enters the bodies or that mRNA is the only RNA class present. `DOI:10.1038/s41564-025-02086-5` Fractionation/RNA-seq, RNA-FISH and tagged-transcript imaging support enrichment. nuoJ, nlpE, glpK and mukF are experimentally followed examples; other tested transcripts remain cytosolic.

Canonical examples

NCBITaxon:511145 Escherichia coli str. K-12 substr. MG1655 — Methods identify MG1655 carrying a chromosomal HslU-GFP fusion for aggresome isolation after arsenite exposure, starvation or HokB induction. These are experimentally induced states, not strain-wide prevalence estimates. [DOI:10.1038/s41564-025-02086-5]

Functions

mRNA stabilization GO:0048255 — Preserves selected mRNAs during the assayed E. coli stress conditions. Preserved transcripts can return to the cytosol and support translation after stress removal.
- DOI:10.1038/s41564-025-02086-5 Isolated-fraction RNA integrity assays, RNase charge mutants and transcription/translation-inhibitor controls support RNA protection and subsequent reuse.

Mechanism graphs

Selective RNase exclusion preserves mRNA for reuse after stress (FUNCTION)

E. coli aggresomes sequester selected transcripts while limiting access by tested mRNA-degrading RNases; stress relief releases RNA that can support renewed translation.

Subject	Predicate	Object	Evidence
bacterial aggresome	sequesters	mRNA	`DOI:10.1038/s41564-025-02086-5` RNA enrichment measurements and fluorescent localization independently identify transcript recruitment.
bacterial aggresome	restricts RNase access through	Charge-dependent exclusion of tested mRNA-degrading RNases	`DOI:10.1038/s41564-025-02086-5` Wild-type RNases are depleted from the bodies; charge-altering mutants enter them. Other RNA-processing proteins are enriched, precluding a blanket exclusion claim.
Charge-dependent exclusion of tested mRNA-degrading RNases	protects RNA through	mRNA stabilization	`DOI:10.1038/s41564-025-02086-5` The active, charge-altered RNB-MO variant enters bodies and depletes their RNA; the inactive RNB-ME variant enters without the same depletion.
Removal of arsenite stress	triggers	Release of stored mRNA to the cytosol	`DOI:10.1038/s41564-025-02086-5` Time-resolved imaging follows glpK and three other tagged mRNAs after stress removal.
mRNA stabilization	retains templates for	Translation from preserved mRNA	`DOI:10.1038/s41564-025-02086-5` GlpK-GFP fluorescence recovery after bleaching and stress removal exceeds the maturation-only control when new transcription is inhibited.
Release of stored mRNA to the cytosol	supplies mRNA for	Translation from preserved mRNA	`DOI:10.1038/s41564-025-02086-5` Rifampicin-only versus rifampicin-plus-tetracycline conditions separate protein synthesis from maturation of pre-existing fluorescent protein.

Discussions

CURATION_TODO (RESOLVED): Keep bacterial aggresomes distinct from the dynein-dependent GO aggresome and RNase E-containing BR-bodies. The GO aggresome definition specifies microtubules and dynein, whereas the bacterial entity is a stress-associated protein/RNA condensate. Shared use of stress-granule terminology does not establish identity with every bacterial or eukaryotic RNA granule.
CURATION_TODO (RESOLVED): Separate observed constituents from upstream stress triggers and normally excluded enzymes. Co-localization establishes constituent membership but not assembly essentiality. HokB induces ATP depletion upstream, while wild-type RNB, RBN and ORN are normally excluded from the condensate under the tested stresses.
CURATION_TODO (RESOLVED): Avoid inferring lineage prevalence or a universal survival effect from induced cellular experiments. Presence after stress in MG1655 is an experimental example, not a measure of how consistently a lineage carries the structure. Growth recovery, dormancy and antibiotic survival are distinct outcomes affected by the perturbations used.

Evidence

DOI:10.1126/sciadv.abh2929 Jin et al. 2021, Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Results and methods read through NCBI PMC BioC (PMC8528417). Protein tracking, fusion and photobleaching support liquid-like dynamics in the assayed states.
DOI:10.1038/s41564-025-02086-5 Pei et al. 2025, Aggresomes protect mRNA under stress in Escherichia coli. Results, methods and Figures 5-6 read in the openly available accepted manuscript at https://eprints.whiterose.ac.uk/id/eprint/229675/ .

Curation history

2026-10-03T12:38:30Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-03T12:40:13Z codex · EXPANDED_RECORD — Added four grounded constituents, a strain-scoped canonical example, mRNA-stabilization function, six-edge mechanistic graph, verified inclusion-body parentage and explicit identity, composition and fitness boundaries.

Source: data/structures/inclusion/bacterial_aggresome.yaml