H-body

cellstructuremech:h_body · Ribonucleoprotein · Other · Proposed

A stress-responsive, polar, membraneless ribonucleoprotein condensate organized by Hfq in Escherichia coli, with polyphosphate-modulated assembly and enrichment of polyadenylated transcripts and RNA-processing proteins. [DOI:10.1371/journal.pbio.3003775]

Synonyms: Hfq condensate

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
RNA-binding protein Hfq	Protein	part of	`InterPro:IPR005001`	hfq	ESSENTIAL	Defining RNA-binding scaffold of the H-body; many Hfq molecules assemble into a mesoscale condensate, rather than one Hfq hexamer constituting the entire structure. `DOI:10.1371/journal.pbio.3003775` Endogenous fluorescent reporters locate Hfq in polar bodies. Purified Hfq phase separates above a concentration threshold, reduced by polyphosphate within a concentration window (Figures 1 and 4).
polyphosphate	Small molecule	part of	`CHEBI:16838`		DISPENSABLE	Inorganic polyanion that co-partitions with Hfq and modulates condensation, client enrichment and body persistence. Its absence does not eliminate all nitrogen-starvation-induced Hfq bodies. `DOI:10.1371/journal.pbio.3003775` Figure 3 reports modest but significant Hfq/polyP colocalization, with strong enrichment in only a subset of foci. Figures 1 and 4 show residual foci in nitrogen-starved ppk mutants and Hfq-only droplets at high protein concentrations; excess polyP redissolves reconstituted droplets. The grounding denotes the polymer class, not a fixed chain length.
mRNA	Rna	part of	`SO:0000234`		UNKNOWN	Polyadenylated transcript cargo; the RNA-class grounding does not assert that all mRNAs localize to the body or that RNA is universally required for its assembly. `DOI:10.1371/journal.pbio.3003775` Figure 5E FISH shows poly(A)-transcript colocalization with Hfq in a subset of nitrogen-starved WT cells, with limited signal-to-noise. Figure 4 uses an rA30 oligonucleotide, not a full mRNA, for ternary Hfq/polyP/RNA reconstitution. RNase A does not dissolve the lysate HMW Hfq assemblies in the tested assay.
Ribonuclease E	Protein	part of	`InterPro:IPR028878`	rne	UNKNOWN	RNA-processing client enriched with Hfq in nitrogen-starvation bodies; neither catalytic inactivity within the body nor a requirement for H-body assembly is asserted. `DOI:10.1371/journal.pbio.3003775` Figure 4G-I shows RNase E in polyP-dependent HMW Hfq assemblies and endogenous fluorescent RNase E enrichment at Hfq foci. Hfq is the organizing scaffold here; the Caulobacter BR-body RNase E-scaffold essentiality is not transferred.
ATP-dependent RNA helicase RhlB type	Protein	part of	`InterPro:IPR023554`	rhlB	UNKNOWN	RNA-helicase client whose endogenous fluorescent foci colocalize with Hfq under nitrogen starvation in the presence of polyP. `DOI:10.1371/journal.pbio.3003775` Figure 5C directly images RhlB/Hfq colocalization in WT and its loss in the ppk deletion background. The verified E. coli RhlB product maps to the IPR023554 family, not the Xanthomonadaceae-focused IPR022077 family or the RhlB helicase domain.
TmaR	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	tmaR	CONDITIONAL	Co-condensing polar regulator required for Hfq-body assembly during the tested nitrogen-starvation condition. It also forms distinct foci without Hfq, and is not universally required under stronger osmotic stress. `DOI:10.1371/journal.pbio.3003775` Figure 1L compares endogenous Hfq/TmaR localization and deletion backgrounds; Hfq foci are lost without TmaR during nitrogen starvation. Figure 1M retains some Hfq foci without TmaR at 1.17 M NaCl. The Results discuss prior direct co-condensation evidence.

Canonical examples

NCBITaxon:511145 Escherichia coli str. K-12 substr. MG1655 — The study uses MG1655-derived strains with endogenous fluorescent fusions, nitrogen starvation in defined Gutnick medium, and strong osmotic stress at 1.17 M NaCl. This is an experimentally demonstrated strain example, not a prevalence assertion across E. coli or bacteria. [DOI:10.1371/journal.pbio.3003775]

Functions

RNA and protein sequestration — Concentrates polyadenylated transcripts and selected RNA-processing proteins during nitrogen starvation. PolyP-dependent body organization is associated with selective transcript stabilization; the genetic comparisons do not isolate condensation from all other Hfq and polyP activities.
- DOI:10.1371/journal.pbio.3003775 Figures 4H-I and 5C,E directly localize RNase E, RhlB and poly(A) RNA. Transcript half-life and poly(A)-tail measurements in WT versus ppk deletion strains support selective preservation, but the Discussion calls for separation-of-function mutants before attributing survival specifically to condensation.

Mechanism graphs

Polyphosphate modulates stress-induced H-body assembly (ASSEMBLY)

Nitrogen starvation increases polyphosphate, which promotes Hfq condensation within a concentration window; the assembled bodies enrich selected RNA and protein cargo.

Subject	Predicate	Object	Evidence
Nitrogen starvation	induces accumulation of	polyphosphate	`DOI:10.1371/journal.pbio.3003775` Figure 1A measures polyP accumulation after entry into nitrogen starvation; the ppk deletion strain lacks detectable polyP.
polyphosphate	promotes	Hfq condensation	`DOI:10.1371/journal.pbio.3003775` Figure 4A-D shows concentration-dependent reconstitution and ternary complexes. Figure 1 compares cellular ppk deletion and Ppk10k-driven polyP accumulation. Excess polyP dissolves droplets, so the effect is not monotonic.
RNA-binding protein Hfq	undergoes	Hfq condensation	`DOI:10.1371/journal.pbio.3003775` Purified Hfq forms droplets at high protein concentration without polyP, while native gels show polyP-dependent HMW Hfq assemblies in starved WT lysates (Figure 4).
TmaR	enables under nitrogen starvation	Hfq condensation	`DOI:10.1371/journal.pbio.3003775` Figure 1L and S1H show loss of nitrogen-starvation Hfq foci in tmaR mutants, not rescued by Ppk10k. Figure 1M shows residual Hfq foci in tmaR mutants under strong osmotic stress.
Hfq condensation	forms	H-body	`DOI:10.1371/journal.pbio.3003775` Endogenous Hfq imaging, focus dynamics, hexanediol sensitivity and FRAP support the cellular condensate interpretation (Figures 1-3); purified droplets are a reconstitution, not an assertion that every cellular constituent is reconstituted.
H-body	concentrates	Ribonuclease E	`DOI:10.1371/journal.pbio.3003775` Figure 4G-I combines HMW-complex association with live-cell RNase E/Hfq colocalization. These experiments do not establish whether the sequestered enzyme is catalytically inactive.
H-body	sequesters	mRNA	`DOI:10.1371/journal.pbio.3003775` Figure 5E shows poly(A)-RNA/Hfq colocalization in a subset of WT cells. Low FISH signal-to-noise limits quantification; no universal transcript occupancy or assembly requirement is inferred.

Discussions

CURATION_TODO (RESOLVED): Distinguish H-body from BR-body, one Hfq hexamer and unrelated polyphosphate stores. Shared RNA or RNase E membership does not establish identical condensate identity. GO:0140365 has a broad minimal-component definition but an exact BR-body synonym and Caulobacter RNase E-scaffold provenance; it does not specifically denote Hfq-organized H-bodies.
CURATION_TODO (RESOLVED): Keep direct localization evidence separate from candidate proteomic associations. The native-gel screen can include polyP-binding proteins that do not interact with Hfq. The final paper reports mostly diffuse enolase fluorescence, unlike a stronger interpretation of the preprint.
CURATION_TODO (RESOLVED): Do not equate polyphosphate promotion with universal necessity or transcript preservation with proven RNase inhibition. Residual Hfq foci persist without polyP during nitrogen starvation, whereas effects are stronger under 1.17 M NaCl. Knockouts affect multiple processes and cannot uniquely assign survival or transcript-stability changes to condensation.
CURATION_TODO (OPEN): Establish an exact source-neutral family grounding for the TmaR pole-localizer class. Verified sequence-family membership alone does not show that the wider DUF496 or UPF0265 families are coextensive with the named TmaR functional class.

Evidence

DOI:10.1371/journal.pbio.3003775 Guan et al. 2026, peer-reviewed PLOS Biology article. Full Results, relevant Methods and Discussion read through the publisher and NCBI PMC BioC (PMC13193609); Figures 1, 4 and 5 visually inspected. Uses the final H-body terminology and revised results, not unqualified claims from the earlier HP-body preprint.

Curation history

2026-10-03T13:17:51Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-03T13:19:26Z codex · EXPANDED_RECORD — Added six source-bounded components, MG1655 example, RNA/protein sequestration function, seven-edge assembly graph, identity and evidence boundaries, and an explicit TmaR family-grounding follow-up.

Source: data/structures/ribonucleoprotein/h_body.yaml