Chen T et al. (2023), The Holothuria leucospilota genome elucidates s...

ECB-ART-51490

Proc Natl Acad Sci U S A 2023 Apr 18;12016:e2213512120. doi: 10.1073/pnas.2213512120.

Show Gene links Show Anatomy links

The Holothuria leucospilota genome elucidates sacrificial organ expulsion and bioadhesive trap enriched with amyloid-patterned proteins.

Chen T , Ren C , Wong NK , Yan A , Sun C , Fan D , Luo P , Jiang X , Zhang L , Ruan Y , Li J , Wu X , Huo D , Huang J , Li X , Wu F , E Z , Cheng C , Zhang X , Wang Y , Hu C .

???displayArticle.abstract???
Some tropical sea cucumbers of the family Holothuriidae can efficiently repel or even fatally ensnare predators by sacrificially ejecting a bioadhesive matrix termed the Cuvierian organ (CO), so named by the French zoologist Georges Cuvier who first described it in 1831. Still, the precise mechanisms for how adhesiveness genetically arose in CO and how sea cucumbers perceive and transduce danger signals for CO expulsion during defense have remained unclear. Here, we report the first high-quality, chromosome-level genome assembly of Holothuria leucospilota, an ecologically significant sea cucumber with prototypical CO. The H. leucospilota genome reveals characteristic long-repeat signatures in CO-specific outer-layer proteins, analogous to fibrous proteins of disparate species origins, including spider spidroin and silkworm fibroin. Intriguingly, several CO-specific proteins occur with amyloid-like patterns featuring extensive intramolecular cross-β structures readily stainable by amyloid indicator dyes. Distinct proteins within the CO connective tissue and outer surface cooperate to give the expelled matrix its apparent tenacity and adhesiveness, respectively. Genomic evidence offers further hints that H. leucospilota directly transduces predator-induced mechanical pressure onto the CO surface through mediation by transient receptor potential channels, which culminates in acetylcholine-triggered CO expulsion in part or in entirety. Evolutionarily, innovative events in two distinct regions of the H. leucospilota genome have apparently spurred CO's differentiation from the respiratory tree to a lethal defensive organ against predators.

???displayArticle.pubmedLink??? 37036994
???displayArticle.pmcLink??? PMC10120082
???displayArticle.link??? Proc Natl Acad Sci U S A
???displayArticle.grants??? [+]

???attribute.lit??? ???displayArticles.show???

	Fig. 1. Geographical niches, genome landscape, and defense behavior of the tropical sea cucumber H. leucospilota. (A) Global distribution of H. leucospilota within or near coral reefs. (B) Schematic diagram showing the Cuvierian organ within the anatomy of H. leucospilota. The Cuvierian organ is located in the posterior coelomic cavity and is expelled toward a potential predator (crab). Details on Cuvierian tubules being ejected from the anus, with a crab being subsequently ensnared by Cuvierian tubules. (C) From outer to inner circles: CI, marker distribution across 23 chromosomes on megabase scales; CIIgene density; CIIIabundance of repetitive sequences; CIVSNP density and CVsequencing depth across the genome; CII–CV are drawn in non-overlapping 500-kb sliding windows. (D) Phylogeny of Deuterostomia, highlighting the position of H. leucospilota. Divergence times were estimated, as shown.
	Fig. 2. (A) Microstructures as revealed by H&E staining. AI: Single Cuvierian tubules; AII: Adhesive Cuvierian tubules; middle layer with mutable collagenous tissues in single (AIII) and adhesive (AIV) Cuvierian tubules; outer-layer granular cells in single (AV) and adhesive (AVI) Cuvierian tubules. (B) Ultrastructures by TEM. BI: Overall appearance of a coronal section; BII–BIII: Middle-layer collagen-like fibrils; BIV–BV: Outer-layer granular cells. (C) Ultrastructures as revealed by SEM. Surface (CI) and inner (CII) of a Cuvierian tubule; BII–BIII: Middle-layer collagen-like fibrils; BIV–BV: Outer-layer amyloid fibrils. (D) Congo red-stained amyloid fibrils. Mt, mesothelium; CLT, connective tissue layer; IE, inner epithelium; Gc, granular cells; Pc, peritoneocytes; Vc, vacuole; MCT, mutable collagenous tissues; AM, adhesive materials; CF, collagen-like fibrils; AF: Amyloid-like fibrils. (E) Heatmap illustrating the most abundantly expressed genes with tandem repeats among different tissues. Full details on genes with tandem repeats in H. leucospilota and their expression patterns in different tissues are provided in Datasets S1 Q and S1 R. CO, Cuvierian organ; TS, testis; In, intestine; RM, rete mirabile; TV, transverse vessel; Cc, coelomocytes; Ms, muscle; BW, body wall; polian vesicle, PV; Ov, ovary; OT, oral tentacles; RT, respiratory tree. (F) Localization of putative CO-specific adhesive and reinforced proteins by immunofluorescence, including Hl-25083, Hl-25084, Hl-25088, Hl-30757, Hl-19376, Hl-19378, and Hl-25085. (G) Schematic diagram illustrating components of the Cuvierian tubules subserving tenacity and adhesion.
	Fig. 3. Amyloid-patterned Cuvierian organ outer-layer proteins (COOLPs) with long tandem repeats signatures. (A) Repeat units in H. leucospilota COOLPs Hl-25083, Hl-25084, Hl-25088, and Hl-30757. (B) Secondary structures, repeat lengths, and repeat numbers of COOLPs Hl-25083, Hl-25084, Hl-25088, and Hl-30757, as analyzed in a comparative perspective with silkworm fiborin (BM_001113262.1) and spider spidroins (EF595246.1 and MG021196.1). (C) AlphaFold-generated three-dimensional structures of the amyloid-patterned proteins COOLPs Hl-25083, Hl-25084, Hl-25088, and Hl-30757 in H. leucospilota. (D) Three-dimensional structures of other pathogenic and functional amyloids including human amyloid-beta (classical cross-β architecture), S. aureus PSMa3 (cross-α architecture), and adhesive or cement proteins from polychaete S. alveolate and P. californica, and barnacles B. improvises, F. albicostatus, and M. rosa.
	Fig. 4. Pressure sensing governs H. leucospilota Cuvierian organ expulsion. (A) of Cuvierian organ expulsion upon three different modes of stimulation at five different parts of the organism. The stimulation methods were pressure by squeezing, piercing, and tactile stimulation. The stimulated parts included the oral tentacles, anterior, middle-, and posterior-bodies, and anus. (B) Phylogenetic tree of the transient receptor potential channel genes in H. leucospilota and other deuterostome animals. A detailed version of the tree is provided in Dataset S1. (C) Heatmap illustrating the tissue distribution of TRP genes in H. leucospilota. (D) Fluorescence in situ hybridization (FISH) of TRPCs Hl-21915 and Hl-16258 mNRA in the Cuvierian tubules. (E) Involvement of TRPCs on Cuvierian organ expulsion induced by pressure. EI: Effects of RNAi targeting the TRPCs Hl-21915 and Hl-16258 and PIZ2 Hl-13522 on CO expulsion; EII: Effects of TRPC signaling blockage by SKF-96365 on CO expulsion. Behavioral data presented are expressed as mean ± SE (n = 3 individual groups, each of which containing 10 biological replicates). P <0.05 and *P <0.01.
	Fig. 5. Roles of acetylcholine signal transduction in H. leucospilota Cuvierian organ expulsion. (A) Phylogenetic tree of ligand-gated ion channel superfamily genes in H. leucospilota and other deuterostome animals. A detailed version of the tree is provided in Dataset S2. (B) Heatmap illustrating the tissue distribution of nAchR-like genes in H. leucospilota. (C) Functional coupling of acetylcholine and putative Cuvierian tubule specifically expressed LGICs (Hl-07241, Hl-07242, Hl-07243, Hl-09749, Hl-33848) in Ca2+ mobilization. (D) Pharmacological effects of acetylcholine and nicotine on the behaviors of body contraction, Cuvierian organ expulsion, and non-CO organ expulsion in H. leucospilota. Behavioral data presented are expressed as mean ± SE (n = 30 individuals). (E) Phylogenetic analysis on H. leucospilota CO-specifically expressed nAchR-like LGIC genes, as viewed within Holothuroidea. (F) A model for chromosomal organization and expansion of CO-specific expressed nAchR-like LGIC genes, as viewed within the H. leucospilota chromosome 3.

References [+] :

Babb, The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression. 2017, Pubmed