Genomic perspectives of spider silk genes through target capture sequencing: Conservation of stabilization mechanisms and homology-based structural models of spidroin terminal regions

Abstract

A powerful system for studying protein aggregation, particularly rapid self-assembly, is spider silk. Spider silks are proteinaceous and silk proteins are synthesized and stored within silk glands as liquid dope. As needed, liquid dope is near-instantaneously transformed into solid fibers or viscous adhesives. The dominant constituents of silks are spidroins (spider fibroins) and their terminal domains are vital for the tight control of silk self-assembly. To better understand spidroin termini, we used target capture and deep sequencing to identify spidroin gene sequences from six species representing the araneoid families of Araneidae, Nephilidae, and Theridiidae. We obtained 145 terminal regions, of which 103 are newly annotated here, as well as novel variants within nine diverse spidroin types. Our comparative analyses demonstrated the conservation of acidic, basic, and cysteine amino acid residues across spidroin types that had been proposed to be important for monomer stability, dimer formation, and self-assembly from a limited sampling of spidroins. Computational, protein homology modeling revealed areas of spidroin terminal regions that are highly conserved in three-dimensions despite sequence divergence across spidroin types. Analyses of our dense sampling of terminal regions suggest that most spidroins share stabilization mechanisms, dimer formation, and tertiary structure, despite producing functionally distinct materials.

Aquatic caddisworm silk is solidified by environmental metal ions during the natural fiber‐spinning process

“…Polyalanine (A) [4][5][6][7][8][9][10][11][12] central core motifs can form b-sheet networks, analogous to the b-sheet forming poly(GA) motifs in silkworm H-fibroin, that impart the famous toughness of spider dragline silks (18,19). The sequence of the spidroin central core varies among species and silk types, but the termini have conserved similarities that are believed to play a critical role during fiber spinning (20)(21)(22). As with silkworm H-fibroin, fluid spider silk precursors, as stored in the major ampullate gland, lack b-sheet secondary structure, and instead are ;30% a-helices, ;40% random coil, and ;30% b-turns (23).…”

Advances in Plant-Derived Scaffold Proteins

“…The short non-repetitive C-termini of MaSp1 and MaSp2 share 75% identity (Beckwitt and Arcidiacono, 1994). Three conserved sites were identified between N. clavipes MaSp and minor ampullate spidroin (MiSp) CTDs (Collin et al, 2018). The CTD folds into five parallel helices and forms a homodimer stabilized through a disulfide bond between conserved cysteine residues and two salt bridges (Hagn et al, 2010).…”

“…The non-repetitive, hydrophilic NTD is conserved among species, within different types of spider silk proteins (dragline, flagelliform, and cylindriform silk), and among waxmoth and silkworm fibroins (Bini et al, 2004;Motriuk-Smith et al, 2005;Rising et al, 2006;Collin et al, 2018). In spun dragline silk, the NTD can be detected in both inner and outer core regions (Andersson et al, 2013), indicating it is not being cleaved in the process of fiber assembly.…”

Semi‐aquatic spider silks: transcripts, proteins, and silk fibres of the fishing spider, Dolomedes triton (Pisauridae)

“…Thus, we refer to our ampullate-like transcripts with the more general abbreviation, 'AmSp', then 'N' or 'C' for whether the transcript contains an amino or carboxylterminal region, followed by a letter for each variant (v) type. Our nomenclature follows Collin et al (2018), e.g., D. tri_ AmSp_C_vA, D. tri_AmSp_C_vB; Fig. 2).…”