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Integrative and Comparative Biology Integrative and Comparative Biology, pp. 1–9 doi:10.1093/icb/icab048 Society for Integrative and Comparative Biology

SYMPOSIUM

Repeat Variation Resolves a Complete Aggregate Silk Sequence of

Bolas phrynosoma Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021 Sarah D. Stellwagen 1,* and Mercedes Burns†

*Department of Biological Sciences, UNC Charlotte, 9201 University City Blvd, NC 28223, USA; †Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, MD 21250, USA From the symposium “The biology of sticky: Adhesive silk, fiber, and glue biomaterials across Eukaryota” presented at the virtual annual meeting of the Society for Integrative and Comparative Biology, January 3–7, 2020.

1E-mail: [email protected]

Synopsis Many species of spider use a modified silk adhesive, called aggregate glue, to aid in prey capture. Aggregate spidroins (spider fibroins) are modified members of the family; however, they are not spun into fibers as are their solid silk relatives. The genes that encode for aggregate spidroins are the largest of the known spidroin genes and are similarly highly repetitive. In this study, we used long read sequencing to discover the aggregate spidroin genes of the toad-like , Mastophora phrynosoma, which employs the glue in a unique way, using only a single, large droplet to capture . While Aggregate Spidroin 1 (AgSp1) remains incomplete, AgSp2 is more than an extraordi- nary 62 kb of coding sequence, 20 kb longer than the longest spidroin on record. The structure of repeats from both aggregate silk proteins follows a similar pattern seen in other species, with the same strict conservation of amino acid residue number for much of the repeats’ lengths. Interestingly, AgSp2 lacks the elevated number and groupings of glutamine residues seen in the other reported AgSp2 of a classic orb weaving species. The role of gene length in glue functionality remains a mystery, and thus discovering length differences across species will allow understanding and harnessing of this attribute for the next generation of bio-inspired adhesives.

Introduction use aggregate glue for prey capture, how- Spiders use a remarkable set of silks throughout their ever the glue is employed in a variety of web mor- lives for a variety of tasks. Each fiber type contributes phologies. In orb webs, the glue is extruded onto the unique material properties tuned for specific functions, spiral silk of the web’s central region (Apstein 1889). such as forming lifelines or wrapping egg sacs. In ad- Cobweb weavers deposit the glue at the base of dition to the familiar solid silk fibers, some spiders “gumfoot” lines loosely attached to the substrate also use a specialized silk glue to retain prey that that easily release when intercepted by prey, sus- have intercepted a web. Most silk proteins belong to pending the targets in mid-air until the spider can the spidroin (spider fibroin) family and most spidroins reel them in (Wiehle 1931; Benjamin and Zschokke are transformed from a liquid dope that is produced 2002; Argintean et al. 2006). Bolas spiders in the and stored within a spider’s glands, into a solid fiber Mastophora and some species from related as the material moves through glandular ducts and genera use a particularly fascinating hunting tech- exits via spigots on the spinnerets. In contrast, aggre- nique where females produce a single droplet of gate spider glues, which are largely composed of mod- glue suspended at the end of a silk strand (Fig. 1) ified silk proteins (Collin et al. 2016), are extruded as and release pheromone mimics that draw in male a liquid similarly to how they are stored. Furthermore, moths prior to capture (Hutchinson 1903; unlike other silks, aggregate glue proteins are exten- Eberhard 1977). While not uncommon and relatively sively glycosylated, which contributes to glue stickiness large with abdominal widths 1.5 cm or more (Levi (Sahni et al. 2010; Singla et al. 2018). 1955), these spiders are extremely difficult to collect

ß The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: [email protected]. 2 S. D. Stellwagen and M. Burns due to their cryptic daytime resting behavior, which introns) across repeats if they are shorter than the resembles bird droppings on the upper surface of a repetitive regions, nor be confidently placed within leaf, and lack of an obvious web that aids locating the repetitive region itself. Long-read sequencing other spider species. technology has vastly improved gene and genome The biomechanics of spider glues have been stud- assemblies, aiding in the resolution of repetitive ied extensively in orb and cobweb weavers, and regions via scaffolding or direct assembly with ap- many species’ aggregate silks exhibit unique material propriate depth of coverage. However, these third- properties, including different stretching, adhesion,

generation sequencing technologies, which can con- Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021 and energy absorption capabilities, as well as differ- sistently produce reads upward of 40 kb or more, ing responses to ambient conditions like humidity may similarly struggle to produce adequate depth (Opell et al. 2011, 2013; Sahni et al. 2011a, 2011b). of coverage to scaffold very long single or limited Recently, research on the glue of -specialist spe- exon genes. cies akirai, which is related to bolas spi- In this study, we used long reads to sequence the ders, showed that, combined with large droplet size, complete, yet unpolished Aggregate Spidroin 2 low viscosity allows effective glue spreading around (AgSp2) from the moth specialist bolas spider, and beneath the fragile scales of moth prey, which Mastophora phrynosoma, yielding a glue gene se- otherwise allows these moths to escape typical orb quence spanning over 100 kb and more than 60 kb weaving spider webs (Diaz et al. 2018). Further re- of coding sequence, the longest spidroin discovered search showed that the glue actually cements the to date. While we were successful in discovering the scales together, effectively using them as a weapon complete genomic sequence for one of the two main against the moths themselves (Diaz et al. 2020). aggregate genes, AgSp1 remains unresolved due to Although bolas spiders use their glues in a unique the challenges of obtaining a sufficient number of mode, their phylogenetic position within the orb reads with a larger genome size. Here, however, we weaving family Araneidae, and sister to Araneus, demonstrate a strategy for the assembly of long re- one of several genera within the Araneidae that petitive reads using unique patterns formed from make classic orb webs (Blackledge et al. 2009), sug- single base variations across repeats. We end by dis- gests that the glues of the two groups should be cussing future-minded evolutionary questions eli- similarly encoded. Furthermore, while biomechanical cited by the study of these massively repetitive genes. research on glues is an important aspect of under- standing glue function, the contribution of genetics Materials and methods to performance is far less understood. Only two full- length glue genes from a single species have thus far Adult female M. phrynosoma were collected from the been published despite thousands of glue-producing Living Farm Heritage Museum grounds in West spider species and a variety of unique web structures, Friendship, Maryland and the Howard County habitats, and prey targets (Stellwagen and Renberg Conservancy in Woodstock, Maryland during late 2019). As traditional short-read sequencing alone is September 2019. Genomic DNA was extracted from not capable of uncovering complete repetitive spider prosomal and leg tissue using the MasterPure silk sequences, it is only recently that long-read se- Complete DNA and RNA Purification Kit following quencing has allowed a more detailed look at the the DNA Purification section protocol (cat. no. variation of repeat number and gene length, which MC89010). Four samples each with a total of 10 mg will promote understanding of the contributions of of the gDNA extraction were loaded onto a Sage these traits to glue functionality. Science BluePippin High Pass Plus cassette (cat. no. Similar to the solid fiber members from this ex- BPLUS10) and run with a 15 kb high pass threshold tensive gene family, aggregate spidroins are encoded overnight. The resultant elutions were cleaned with by large, highly repetitive genes that are difficult to 1 AMPure XP beads (cat. no. A63880) and eluted fully sequence. The challenge of sequencing repetitive overnight in water. The cleaned DNA was then used genes lies in the current technologies commonly ap- directly in Oxford Nanopore’s 1D Genomic DNA by plied to DNA sequencing. Techniques that validate Ligation protocol (SQK-LSK109). A total of two polymorphisms and scaffold the full length of non- runs were completed using SpotON Flow Cells repetitive genes using short reads (i.e., less than 250 (R9.4; cat. no. FLO-MIN106) and resultant fast5 files base pairs per read) are not successful in sequencing were basecalled using Oxford Nanopore’s program aggregate glues due to repeat size and extreme uni- Guppy (v3.6.1 þ 249406c). A total of 26.7 Gbp and formity. Short reads cannot connect anchoring se- 10.8 million reads across two Nanopore flow cells quence (such as unique portions of the termini or were produced. Complete aggregate silk sequence of M. phrynosoma 3

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Fig. 1 Female M. phrynosoma and smaller red male resting on the surface of a leaf during the day (A) and female hunting with a bolas (arrow points to glue droplet) at night (B). Images courtesy of Bonnie Ott (A) and MJ Hatfield (B).

A custom M. phrynosoma BLAST database was Results created from the sequence data using Geneious We sequenced and assembled the complete AgSp2 v11.1.5 (Kearse et al. 2012), and termini and and partial AgSp1 from the toad-like bolas spider repeat-encoding sequences from Argiope trifasciata species M. phrynosoma. AgSp1 and AgSp2 are mem- aggregate spidroins were used as query sequences bers of the spider silk (spidroin) family (Collin et al. to initially identify aggregate reads from the M. phry- 2016) and conform to the same N-terminus/ nosoma data set. After AgSp reads were discovered, Repeat(n)/C-terminus structure. AgSp2 was manu- repeat motifs were used as queries against the data ally assembled from six long reads (Supplementary set to extract all repeat-containing reads. In addition File S1) and is encoded by nearly 63 kb, dwarfing the to searching manually for short matching sequences previous spidroin record holder from A. trifasciata’s using command line, and adjusting BLAST parame- AgSp1, which is just over 42 kb. Interestingly, the ters within Geneious to ensure discovery of all AgSp AgSp2 ortholog in A. trifasciata is approximately reads, using the default parameters for Megablast 20.5 kb, only a third of the size of that of the bolas recovered all applicable reads gathered via other spider. Similar to AgSp2 of A. trifasciata, the N-ter- methods. Once the longest reads available were se- minal encoding region of AgSp2 of M. phrynosoma is lected, the repeats of each read were identified and separated from the rest of the gene by a massive annotated. Repeats from a single read were then intron. The intron in M. phrynosoma is approxi- extracted and aligned, and the resultant alignment mately 37.5 kb, similar to that of A. trifasciata’s visually inspected to identify single base variations 31.5 kb intron. Unlike A. trifasciata, the bolas spider across repeats, which could be separated from errors AgSp2 does not have the same glutamine-rich due to their consistency from repeat to repeat regions between sections of repeats. (Fig. 2A). Repeat annotations from each read were Mastophora phrynosoma’s AgSp2 is comprised of then color coded to reflect the base variation at the approximately 47 repeats, however, repeats near the chosen position (Fig. 2B). Using the pattern formed termini, particularly toward the N-terminus, tend to by variations across repeats, reads were manually be less strictly conserved as the central repeats, which combined to approximate the complete genetic se- can result in difficulties assigning consistent begin- quence length (Fig. 2C), as short read data are cur- nings and ends. Central repeats are formed from rently unavailable for long read correction. 1,326 bp encoding 442 amino acids, which can be fur- Additionally, a limited number of repeats are either ther divided into four sub-repeat units, each highly significantly shorter or longer than the standard re- similar to the main repeat found in AgSp2 of A. peat size, which provided further evidence for align- trifasciata (Fig. 3). As the full length of AgSp1 from ment precision. Sequence alignments and analysis M. phrynosoma has not been resolved, it is not pos- was conducted using Geneious with the Geneious sible to determine the number of repeat units within alignment tools. the gene, however there are more than 70 repeats 4 S. D. Stellwagen and M. Burns

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B

C

Fig. 2 Long-read alignment strategy used to resolve the complete AgSp2 spidroin from the bolas spider M. phrynosoma. Alignment of the relevant portion from all 21 repeats of an AgSp2 read that contains a single-nucleotide variant (schematic of this read is between arrows in B and C). Random highlighted bases generally represent sequencing errors (blue highlight), however the base at position 29 is variable and can be either C or T, or occasionally, another base or sequencing error (yellow highlight) (A). After annotating each repeat as containing a T (purple), C (grey), or alternate/unknown (white) at the variable base location, the pattern between these bases across repeats can be used to align long repetitive reads (B). The resultant gene after alignment of all relevant reads, including non-coding sequence (black line) and coding sequence (N-terminal encoding region in green and C-terminal encoding region in red), is just over 100 kb (C). The coding sequence of AgSp2 is approximately 62.7 kb, however as the gene contains sequencing errors, exact length and polished sequence is still unclear. within the acquired overlapping reads, totaling more and, based on unique repeat structure of the terminal- than 42 kb. The gene is at least somewhat larger than adjacent repeats, there are additional reads needed to this, as there are repeats not included in the count bridge these terminal reads to the remainder of the total within the N- and C-terminal encoding reads, central repeats. Complete aggregate silk sequence of M. phrynosoma 5

Fig. 3 Translated AgSp1 and AgSp2 repeat motifs from the bolas spider Mastophora phryosoma (Mph) and orb weaving spider A. trifasciata (Atr). Mastophora phrynosoma repeat motifs are longer and consist of sub-repeats that are each similar to entire repeats of A. trifasciata. Variations from sub-repeat to sub-repeat result in a longer overall repeating unit, however M. phrynosoma sub-repeats are Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021 still highly similar to full repeats of A. trifasciata. Each sub-repeat or repeat is separated into four subgroups and a tail region as in Stellwagen and Renberg (2019). The number of amino acid residues within the subgroups is highly conserved across species, and this pattern in maintained in M. phrynosoma. The tail region is highly variable, and there are several different tail organizations across sub- repeats of M. phrynosoma aggregate spidroins. Yellow highlight indicates conserved residues across both species and genes.

Both AgSp1 and AgSp2 had variable bases that Repeat variant structure of bolas spider aggregate allowed proper alignment of the long repetitive spidroins regions. They varied, however, in the frequency of Due to the extreme repetition of the aggregate spi- synonymous changes to the translated amino acids. droin genes in the bolas spider, we relied on the While AgSp2 repeat variants were differentiated by a presence of variable DNA bases in repeating se- single base change (Fig. 3B) that led to a synony- quence units of the gene for alignment. The transla- mous substitution in a tyrosine residue, AgSp1 re- tional impact of these base variations is minimal for peat variants differed at a total of six bases. These AgSp2, which had only one variant that led to a included three synonymous substitutions at histidine synonymous substitution. This result speaks to the and valine residues, and three non-synonymous sub- overwhelmingly conserved structure of the M. phry- stitutions convert serine, glutamine, and leucine to nosoma AgSp2, even in comparison with the AgSp2 arginine, arginine, and phenylalanine residues, respectively. gene of A. trifasciata, which lacks the second order, Consistent with previous reports for AgSp1 and sub-repetition found in M. phrynosoma. AgSp2 of both orb weavers and cobweb weavers We found six variable bases that were well- (Stellwagen and Renberg 2019), the number of characterized by reads of repeat variants in the M. amino acids for much of M. phrynosoma repeats is phrynosoma AgSp1. Half of these resulted in synony- highly conserved, and variable within the tail region mous substitutions. The other half produced nonsy- (Fig. 3). Mastophora phrynosoma repeats, however, nonymous substitutions that involved transitions of are formed from larger, variable sub-repeats that amino acids with either polar (Ser, Gln) or hydropho- are each similar to the full repeat units of other bic (Leu) side chains to those with positively-charged species. Sequence deviations across sub-repeat units, (Arg) or hydrophobic side chains (Phe). That the particularly in the tail region, increase the size of the charge and polarity of these residues is not maintained overall repetitive pattern of amino acids. in repeat variants suggests that these nonsynonymous substitutions may have functional significance for Discussion AgSp1 protein. This is particularly true for residues The toad-like bolas spider M. phrynosoma produces a that vary in post-translational modification, particularly large droplet of aggregate glue that it uses to capture O-glycosylation of serine, which confers stickiness moth prey. In other closely related orb-weaving spe- (Dreesbach et al. 1983; Tillinghast et al. 1993). The cies, the main glue proteins are encoded by two ex- functional distinguishment of the two aggregate spi- tremely large, repetitive genes AgSp1 and AgSp2 droin products remains unclear, but it seems apparent (Choresh et al. 2009; Collin et al. 2016; Stellwagen that mechanisms of purifying selection and/or gene and Renberg 2019). We sequenced part of AgSp1 conversion (Garb et al. 2007) for repeat conservancy and discovered the complete, though unpolished, arenotequallyappliedtotheseparategenecopies. AgSp2 from M. phrynosoma. AgSp2 has a generally similar structure to that of A. trifasciata, except it is Sequence comparison of aggregate spidroins three times larger with more than 60 kb of coding Interestingly, we found that the AgSp2 of M. phryno- sequence, and lacks the glutamine rich regions. The soma lacked the distinctive glutamine-rich regions repeats of both glue proteins are similar to those found in AgSp2 of A. trifasciata. It has been hypothe- reported in other species. sized that glutamine promotes self-aggregation of silk 6 S. D. Stellwagen and M. Burns proteins into fibers (Geurts et al. 2010). However, un- to long reads for error correction can lead to mis- like the aggregate glues of orb weavers that adhere and mapping. Any repeats with a few non-typical bases then stretch to help dissipate energy and retain fast- (which are common near spidroin termini and can moving prey, M. phrynosoma glue must spread rapidly be difficult to discern from sequencing errors) be- under moth scales before solidifying (Diaz et al. 2018, come overwhelmed by the large number of reads 2020),makingproteinaggregationapotentialhin- from the central repeats that otherwise map success- drance to the accelerated glue flow. Additionally, pro- fully, resulting in an incorrect consensus (Fig. 4). tein aggregation is highly concentration dependent Base-to-base confidence in extreme-length sequences Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021 (Poulson et al. 2020), whether by the action of catalysts like aggregate spidroins can currently only be derived (Sandberg et al. 2009; Braun et al. 2013)orviaself- from adequate long-read sequencing coverage of 30– assembly under particular temperatures (Bansil and 40. Moreover, the reads at this depth of coverage Turner 2006). The aqueous solution that surrounds must be long enough to be placed confidently, as we the bulk of the central protein core of a droplet of were able to do only for AgSp2 in this study. This spider aggregate glue contains low molecular weight methodology is therefore currently out of the realm compounds and salts, which are known for their role of standard sequencing projects for organisms with in ambient water absorption and glue protein lubrica- larger genomes like those of spiders [usually larger tion (Vollrath et al. 1990; Sahni et al. 2014). than 1–2 GBp; (Gregory and Shorthouse 2003)]. Furthermore, salt concentration has been shown to Even though sufficient depth of coverage is possible be an important factor for both solubility and aggre- for most regions of the genome, achieving this depth gation for other spidroins (Knight and Vollrath 2001; with sufficiently long reads necessary to assemble Eisoldtetal.2010), however their contribution to ag- extreme-length repetitive spidroins is currently a great gregation of spidroin glues has not been investigated. challenge. Furthermore, while the technology is avail- While M. phrynosoma aggregate spidroins are extremely able for tedious, by-hand reconstruction and correction large, it is not known how the density of the glue’s of these genes with a combination of long and short proteins or concentration of other compounds in the reads, building a substantial catalog of high quality, aqueous material compares between species, or the role full-length glue genes will come only after obtaining this variation might play in functional differences. consistently long reads either of higher quality or Longer protein length may provide the protein linkage higher depth becomes more feasible. necessary for adhesion, while limiting concentrations that would result in detrimental viscous aggregations, Conclusion inhibiting flow on prey. In order to evaluate this hy- pothesis, glycoprotein concentrations of M. phrynosoma Aggregate spidroins are the largest members of the couldbeestimatedandcomparedwiththosefrom spider silk gene family, and the bolas spider has now more traditional orb weaving glue droplets. After size extended the known length of these genes to an in- correction, we would expect M. phrynosoma glues to be credible >60 kb of coding sequence. Using long read less concentrated than droplets of orb weaver spiders. sequencing and single-nucleotide variations across There is likely a delicate balance between protein size repeats, the massive AgSp2 gene size was discovered and concentration, as well as the concentration of other and the repeat units of both AgSp1 and AgSp2 were small molecules within glue droplets that help regulate resolved. While sequencing technology still struggles protein behavior. Future focus on the role of aggrega- to allow for consistent resolution of extreme-length tion in regulating solubility and viscosity would be im- repetitive sequences from many species, we are able portant for evaluating the suitability of spidroins for to begin investigating repeat number and size, and, medical application (Abdelrahman et al. 2020)oras subsequently, their potential contributions to glue models of fibril behavior (Kenney et al. 2002). functionality. However, until either long-read error Repeats across M. phrynosoma aggregate spidroin rates improve or greater depth of coverage is more genes contain variable bases at specific positions cost effective, broad-scale data sets of these large, (Fig. 2). The unique pattern of these variations repetitive spidroins from many species will remain from repeat to repeat allows alignment of long reads out of reach, hampering efforts to uncover the fun- that is not otherwise possible. However, likely due to damental adhesive gene structures for bio-inspired the error rate within long reads and the length of material applications. Moreover, a broader question these repetitive sequences, the alignment algorithms remains: why are aggregate spidroin repeats so con- we applied were unable to identify and utilize nucle- served, and yet so repetitive? The order of evolution- otide variations across repeats for alignment. ary events leading to the genomic duplication and Furthermore, using short sequence reads mapped functional specialization remains in question. Complete aggregate silk sequence of M. phrynosoma 7 Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021

Fig. 4 Nanopore long reads and corresponding alignment consensus (Nanopore Consensus), Illumina short reads mapped to the Nanopore Consensus, and the consensus formed from Illumina read mapping (Illumina Consensus). An initial consensus sequence (Nanopore Consensus, gray box) for a section of a terminal-adjacent repeat (which typically contain a few base variations compared with the bulk of central repeats) from a spidroin of a species that was not part of this study is obtained by aligning Nanopore reads 1– 5. Depth of coverage using Nanopore long reads is not sufficient to resolve all errors with confidence and is therefore often corrected using Illumina data. After mapping RNA-seq Illumina short reads (GenBank accession: SRR5131057) to the Nanopore Consensus to correct sequencing errors (e.g., Fig. 2(A), blue highlighted bases), Illumina reads 1–3 (above dotted line) map correctly. However, Illumina reads 4–20 (below dotted line) incorrectly map due to general repeat similarity, overwhelming the few accurate reads, and producing a new incorrect consensus (Illumina Consensus, gray box). Red highlights over read bases indicate consistency with the Nanopore Consensus, while yellow highlights indicate consistency with the mis-mapped Illumina reads 4–20.

Furthermore, the means by which repetitive units are Additionally they thank the Living Farm Heritage serially modified invites more substantial research Museum and the Howard County Conservancy into the mechanisms of gene conversion or unequal in Maryland for generous permission to collect crossing-over (Garb et al. 2007) that could be capa- specimens on their premises. They also wish ble of exerting such extreme homogenization. to acknowledge SICB for supporting our sympo- sium and three anonymous reviewers who Author contributions provided helpful comments to improve this S.D.S. conceived and conducted the experiment(s). manuscript. S.D.S. and M.B. analyzed the results, and wrote and reviewed the manuscript. Funding This research was funded in part by the Herb Levi Acknowledgments Memorial Fund for Arachnological Research The authors sincerely thank Bonnie Ott for administered by the American Arachnological her help locating M. phrynosoma specimens. Society. 8 S. D. Stellwagen and M. Burns

Data availability statement Garb JE, DiMauro T, Lewis RV, Hayashi CY. 2007. Expansion and intragenic homogenization of spider silk genes since All data are incorporated into the article and its on- the Triassic: evidence from Mygalomorphae (tarantulas and line supplementary material. their kin) spidroins. Mol Biol Evol 24:2454–64. Geurts P, Zhao L, Hsia Y, Gnesa E, Tang S, Jeffery F, Mattina Supplementary data CL, Franz A, Larkin L, Vierra C. 2010. Synthetic spider silk Supplementary data are available at ICB online. fibers spun from pyriform spidroin 2, a glue silk protein discovered in orb-weaving spider attachment discs. Biomacromolecules 11:3495–503. Downloaded from https://academic.oup.com/icb/advance-article/doi/10.1093/icb/icab048/6263861 by guest on 25 September 2021 Competing interests Gregory TR, Shorthouse DP. 2003. Genome sizes of spiders. J The authors declare no competing interests. Hered 94:285–90. Hutchinson CE. 1903. A bolas-throwing spider. Sci Am 89:172. 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