Molecular Architecture and Evolution of a Modular Spider Silk Protein Gene

Abstract

Spider flagelliform silk is one of the most elastic natural materials known. Extensive sequencing of spider silk genes has shown that the exons and introns of the flagelliform gene underwent intragenic concerted evolution. The intron sequences are more homogenized within a species than are the exons. This pattern can be explained by extreme mutation and recombination pressures on the internally repetitive exons. The iterated sequences within exons encode protein structures that are critical to the function of silks. Therefore, attributes that make silks exceptional biomaterials may also hinder the fixation of optimally adapted protein sequences.

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

“…This gene's sequence similarity and phylogenetic affinity to canonical flagelliform FLAG-a 18 ( Supplementary Figs. 2 and 3) suggest that it arose as a second genomic copy from a duplication event, yet FLAG-b transcripts are highly abundant in venom glands.…”

“…In total, >32 million features are annotated on the N. clavipes draft genome (Supplementary Table 8), which was achieved using (i) our transcriptome from all isolates, (ii) results from two gene prediction algorithms, (iii) libraries of transposable elements and repeated motifs, and (iv) coding sequences from related species 18,19 (Supplementary Table 8). Using gene modeling, we conservatively predict 14,025 genes present in the N. clavipes genome; 2,023 gene models transcribe >1 alternative spliceoform, resulting in 3,937 additional transcripts for a total of 17,962 mRNAs in the final gene set (Supplementary Table 9).…”

“…One motif group consisted of GXGGX-containing motif variants, including the well-known motif variant GPGGY 18,29 (Fig. 2a).…”

“…The silk classes of a typical 'gluey silk' orb-weaver (Araneoidea) female include (i) major ampullate silk, which exhibits great tensile strength and is employed in draglines, bridgelines, and web radii 11,12 ; (ii) minor ampullate silk, used for inelastic temporary spirals during web building 11,12 ; (iii) cement-like piriform silk that bonds fibers together and to other substrates 13,14 ; (iv) strong, yet flexible aciniform silk used for prey wrapping and egg case insulation 15 ; (v) tubuliform and cylindriform silk that constitutes the tough outer layer of egg cases 16,17 ; (vi) flagelliform silk that exhibits unparalleled extensibility and is used in the capture spiral 18,19 ; and (vii) the viscous and sticky aggregate silk that aids in prey capture [20][21][22][23][24] . Many spider species produce just a subset of these silk classes, and some produce yet other silk types, including cribellate silk 25 .…”

Silk-based biomaterials

“…This strategy has provided new opportunities in fundamental studies of spider silk genetics, silk protein structure and function, and materials processing [2,[4][5][6]. In general, interest in spider silk has increased in recent years due to the differences in mechanical properties when compared to silkworm silk and the presence of the multi-gene family encoding this group of silks as a basis for the study of protein structurefunction relationships [4,[6][7][8][9][10][11].…”