Molecular atlas of spider silk production can help bring unique material to market

Chromosomal-scale genome assembly and full spidroin gene set of T. clavata. one Photo of T. clavata shows an adult female and an adult male on the golden orb tissue (above) and female and male karyotypes (below). SCS, sex chromosome system. b Circular diagram showing the genomic landscape of the 13 pseudochromosomes (Chr113 on Mb scale). c Twenty eight T. clavata spidroin genes anchored on chromosomes. d Spidroin gene clusters from another orb web spider, T. antipodiana. The published genomic data of T. antipodiana were analyzed to identify the location information of spidroin genes. e Spidroin gene catalog of six orb-web spider species. f Expression grouping of silk glands (major and minor ampullate (Ma and Mi), flagelliform (Fl), tubuliform (Tu), aggregate (Ag), and aciniform and pyriform (Ac & Py) glands) and venom glands. The pink line shows the closest relationship between the Ma and Mi glands. g Morphology of T. clavata silk glands. Similar results were obtained in three independent experiments and summarized in source data. h Expression patterns of 28 spidro genes in different types of silk glands. Source data is provided as a source data file. Credit: Nature communication (2023). DOI: 10.1038/s41467-023-36545-6

Researchers from Southwest University in China have constructed the entire chromosome-scale genome assembly and complete spidroin gene set of the golden orb-weaving spider, Trichonephila clavata, known for its particularly strong, golden webs.

They attest that their work “Provides multidimensional data that significantly expands knowledge of spider dragline silk generation…” and the researchers plan to use this new “molecular atlas” to better understand how spiders produce their silk.

Published in the journal Nature communicationThe paper describes the steps the researchers took, from wild spider capture to multiomic analysis, to reveal the interplay of genes in the spider’s large ampoule gland, the gland responsible for producing dragline silk.

Spider dragline silk is a real marvel of material with many potential medical and industrial applications. It is lighter and stronger than steel while maintaining an elastic tensile strength that rivals rubber. Unlike many synthetic materials, spider silk is non-toxic, biodegradable and biocompatible, making it an ideal material for surgical implants, biosensors and tissue reconstruction.

The only limitation to adopting spider silk as a replacement for a long list of materials we currently use is how difficult it is to manufacture. There was an earlier attempt to produce the proteins in goat’s milk by a company called Nexia, and it worked, but not on a scale required for mass production.

And despite the obvious benefits of spider silk, no one has stepped up to start spider farming on the scale required. Researchers expect that by better understanding silk production at a molecular level in spiders, they will gain practical insights to help bring this unique material to market.

Creating a molecular atlas with multiomics

To obtain the genome, the research team used the Oxford Nanopore platform, which can produce the most extended contiguous reads of any gene sequencer, as well as Illumina sequencing machines for more accurate but shorter read capture lengths and Hi-C for chromosome mapping. By combining these three different sets of genomic data, the researchers were able to bioinformatically reconstruct a detailed model of the spider’s chromosome-scale genome assembly and complete spidroin gene set.

Having this genomic data makes it possible to make connections between gene expression and ultimately the proteins found in spider silk, which is exactly what the researchers did next. The team performed transcriptome (messenger RNA), protein and metabolite (signaling molecule) analysis of the three segments of the large ampullate gland; the tail, sac and canal.

Liquid chromatography-mass spectrometry analysis identified 28 proteins: 10 were spidroins, the proteins that make up spider silk, 15 were spider silk-constituent elements, and one was related to venom. With the core components identified, the researchers were able to rank them in order of intensity-based absolute quantification.

Further analysis allowed them to characterize the specific biological functions of the tail, sac and duct related to silk production based on the function of genes and gene products. Tail-omics were mostly about organic acid synthesis, those in Sac focused primarily on lipid production, and Duct-omics were related to ion exchange and chitin synthesis.

Previous research has found some elements discovered in the current study, but none has put the whole picture together in such a complete and comprehensive way.

More information:
Wenbo Hu et al., A molecular atlas reveals the tripartite spinning mechanism of spider dragline silk, Nature communication (2023). DOI: 10.1038/s41467-023-36545-6

Journal information:
Nature communication

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