Pendola M et al. (2019), Skeletal development in the sea urchin relies u...

ECB-ART-47468

PLoS One 2019 Jan 01;1410:e0222068. doi: 10.1371/journal.pone.0222068.

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Skeletal development in the sea urchin relies upon protein families that contain intrinsic disorder, aggregation-prone, and conserved globular interactive domains.

Pendola M , Jain G , Evans JS .

Abstract
The formation of the sea urchin spicule skeleton requires the participation of hydrogel-forming protein families that regulate mineral nucleation and nanoparticle assembly processes that give rise to the spicule. However, the structure and molecular behavior of these proteins is not well established, and thus our ability to understand this process is hampered. We embarked on a study of sea urchin spicule proteins using a combination of biophysical and bioinformatics techniques. Our biophysical findings indicate that recombinant variants of the two most studied spicule matrix proteins, SpSM50 and SpSM30B/C (S. purpuratus) have a conformational landscape that include a C-terminal random coil/intrinsically disordered MAPQG sequence coupled to a conserved, folded N-terminal C-type lectin-like (CTLL) domain, with SpSM50 > SpSM30B/C with regard to intrinsic disorder. Both proteins possess solvent-accessible unfolded MAQPG sequence regions where Asn, Gln, and Arg residues may be accessible for protein hydrogel interactions with water molecules. Our bioinformatics study included seven other spicule matrix proteins where we note similarities between these proteins and rare, unusual proteins that possess folded and unfolded traits. Moreover, spicule matrix proteins possess three types of sequences: intrinsically disordered, amyloid-like, and folded protein-protein interactive. Collectively these reactive domains would be capable of driving protein assembly and hydrogel formation. Interestingly, three types of global conformations are predicted for the nine member protein set, wherein we note variations in the arrangement of intrinsically disordered and interactive globular domains. These variations may reflect species-specific requirements for spiculogenesis. We conclude that the molecular landscape of spicule matrix protein families enables them to function as hydrogelators, nucleators, and assemblers of mineral nanoparticles.

PubMed ID: 31574084
PMC ID: PMC6771980
Article link: PLoS One

Genes referenced: LOC100887844 LOC583082

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	Fig 1. Far-UV circular dichroism spectra of rSpSM30B/C-G (7.5 μM) and rSpSM50 (3 μM) proteins in 100 μM HEPES, pH 8.0.Dashed line extrapolates the ellipticity minima for each protein.
	Fig 2. Homonuclear 800 MHz 1H TOCSY spectra (exchangeable sidechain amide chemical shift region) of 22μM rSpSM30B/C-G and rSpSM50 hydrogel particle samples, 100 μM HEPES, pH 7.5.Diagonal and off-diagonal regions for sidechain and backbone NH Arg, Asn, and Gln resonances are shown, along with corresponding 1-D spectra.
	Fig 3. Primary sequences of SpSM30B/C-G and SpSM50.Arg, Gln, and Asn residues are presented in red. MAQPG domains are highlighted in yellow. Note high concentration of Arg, Asn, Gln within disordered MAQPG regions.
	Fig 4. Predicted regions of intrinsic disorder (GLOBPLOT 2.3, DISOPRED, IUP) and aggregation-prone amyloid-like (AGGRESCAN, FOLD_AMYLOID, ZIPPER_DB).Shaded areas (red = intrinsic disorder; blue = amyloid-like cross-beta strand) denote sequence regions predicted as positive by each cohort of algorithms. Grey area denotes regions that do not score as positive for either intrinsic disorder or amyloid-like sequences. Purple color denotes sequence region overlap between aggregation-prone and intrinsic disorder.

	Fig 6. Categories of spicule matrix protein backbone conformations predicted by DISOclust/Intfold 4.0 (ribbon representation, lowest energy conformer) for nine sea urchin spicule matrix proteins (Table 1).Under each Type is a cartoon representation of global conformation (circle = folded conformation; squiggle line = disordered conformation). Best template model for the globular domain, confidence levels, P scores, and global model quality scores can be found in Table 2. N- and C-terminal ends are denoted.