1000 spider silkomes: Linking sequences to silk physical properties

Abstract

Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

Fig. 1.. Overview of the taxonomic distribution of spidroins and physical properties of dragline silks.

Left: The phylogenetic tree of spider families constructed from the transcriptome data obtained from 1000 spiders in this work. The Araneoidea superfamily and the RTA clade are highlighted in red and blue, respectively. Family names in red represent those without previous report of spidroins in the NCBI Protein Database. Family names marked with orange circle represent those without previous transcriptome data. Total number of species sequenced in this work for each family, as well as species-level decomposition of unreported spidroin and transcriptome, are shown to the right of the family names. As this table shows, the vast majority of species reported in this work is previously unreported for their spidroin sequences or transcriptome. Middle: Heatmap of the conservation level of spidroin types within the spider families. For example, MaSp3 of family Araneidae has a value of around 0.5, as can be seen from the color code shown in the bottom left corner, which indicates that around 50% of the 191 species studied in this work contains MaSp3. The orb-weaving spiders in the superfamily Araneoidea (highlighted in pink) have greater diversity of spidroin types, and the RTA clade (highlighted in light blue) lost the capture web silks Flag and AgSp. MaSp sequence subtypes are not well differentiated in the RTA clade, where MiSp, ampullate spidroin (AmSp), and MaSp are more conserved than MaSp1 and MaSp2. Right: Distribution of physical properties among the spider families. Mirrored with the diversity of spidroins, orb-weaving Araneoidea spiders tend to have higher performance than other clades.

Fig. 2.. Some insights from analysis of large spidroin dataset.

(A) Spidroin N-terminal domains obtained from basal Mesothelae bear close resemblance to CrSp sequences. H.k., Heptathela kimurai (Liphistiidae); H.y., Heptathela yanbaruensis (Liphistiidae); R.n., Ryuthela nishihirai (Liphistiidae); S.sp., Stegodyphus sp. (Eresidae); O.s., Octonoba sybotides (Uloboridae). (B and C) Analysis of residue composition in spidroin repetitive regions, with residue types colored according to the legend. (B) Conservation of amino acid abundance in CrSp repetitive sequences across spider taxa. H.t., H. troglodytes; D.sp., Deinopis sp.; M.o., Miagrammopes orientalis; N.a., Nurscia albofasciata; C.h., Callobius hokkaido. (C) Conservation of amino acid abundance in Flag repetitive sequence among araneoid species. E.a., E. affinis; N.r., Nesticodes rufipes; C.b., Coleosoma blandum; D.p., Doenitzius peniculus; L.m., Lepthyphantes minutus; U.o., Ummelatia osakaensis; W.c., Weintrauboa contortripes; Z.h., Zygiella hiramatsui; N.l., Nephilingis livida; C.d., Caerostris darwini; C.y., Cyrtarachne yunoharuensis; G.k., Gasteracantha kuhli; T.e., Tetragnatha extensa; L.s., Leucauge subgemmea; M.sp., Mesida sp.

Fig. 3.. Overview of the physical properties of 446 spider silk samples.

(A) Pearson correlation heatmap of the physical properties of dragline silk fibers measured in this work. Toughness is not only correlated with tensile strength and strain at break but also correlated with Young’s modulus. Supercontraction is correlated with strain at break. (B) Scatter plot of toughness versus strain at break (with spot size proportional to tensile strength). The collected samples represent an almost continuous spectrum of toughness from <0.01 to >0.40 GJ/m³. Spots are colored according to broad phylogenetic grouping: Araneoidea (red) includes the orb-weaving spiders and tends to show a relatively high toughness distribution relative to wandering species (such as the RTA clade, indicated in light blue). (C) Screenshots of the Spider Silkome Database (https://spider-silkome.org), a fully searchable, public repository of all spidroin sequences and material property data generated from the 1000 spider silkome project (the main page and individual profile data for Trichonephila clavata are shown).

Fig. 4.. Linking sequences to the physical properties of dragline silk.

The different ampullate-like spidroin sequences found across the different spider taxa were classified according to conserved patterns within repetitive domains; this led to the categorization into 20 sequence groups, which comprised seven MiSp subtypes, seven MaSp1 subtypes, four MaSp2 subtypes, and two MaSp3 subtypes (figs. S3 to S5). MaSp groups most strongly contributing to the physical properties were selected through statistical screening (see Materials and Methods). (A) Toughness distribution among different spider families, as correlated with the presence or absence of selected MaSp subtypes: MaSp3 (group 19), MaSp2 (group 17), and MaSp1 (group 17). (B) Supercontraction distribution among different spider families, compared with the presence (+) or absence (−) of specific MaSp subtypes. Four MaSp2 groups (groups 14, 13, 11, and 17) showed higher average supercontraction than Araneidae. (C) Scatterplot of physical properties (toughness or supercontraction) as a function of the average abundance per repeat (%) of certain amino acid motifs. See data file S4 for comprehensive screening of amino acid sequence motifs contributing to the physical properties. Abundance of motifs was normalized by the number of repetitive sequences within a spidroin fragment, and this normalized abundance was correlated with the physical properties to screen for highly contributing motifs. Spot color denotes the spider family, and Pearson correlation values are shown in the top right corners. Here, AGQG motif in MaSp1 is positively correlated with supercontraction, and AAAAAAAA motif of MaSp2 is negatively correlated. Likewise, YGQGG motif in MaSp1 is positively correlated with toughness.