Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit

Abstract

BackgroundSpiders (Order Araneae) are essential predators in every terrestrial ecosystem largely because they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel protein functions. However, genomic level resources remain limited for spiders.ResultsWe de novo assembled a transcriptome for the Western black widow (Latrodectus hesperus) from deeply sequenced cDNAs of three tissue types. Our multi-tissue assembly contained ~100,000 unique transcripts, of which > 27,000 were annotated by homology. Comparing transcript abundance among the different tissues, we identified 647 silk gland-specific transcripts, including the few known silk fiber components (e.g. six spider fibroins, spidroins). Silk gland specific transcripts are enriched compared to the entire transcriptome in several functions, including protein degradation, inhibition of protein degradation, and oxidation-reduction. Phylogenetic analyses of 37 gene families containing silk gland specific transcripts demonstrated novel gene expansions within silk glands, and multiple co-options of silk specific expression from paralogs expressed in other tissues.ConclusionsWe propose a transcriptional program for the silk glands that involves regulating gland specific synthesis of silk fiber and glue components followed by protecting and processing these components into functional fibers and glues. Our black widow silk gland gene repertoire provides extensive expansion of resources for biomimetic applications of silk in industry and medicine. Furthermore, our multi-tissue transcriptome facilitates evolutionary analysis of arachnid genomes and adaptive protein systems.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-365) contains supplementary material, which is available to authorized users.

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

“…Previous experimental findings have suggested that spidroin expression is not exclusively gland specific [50][51][52][53][54] . Our RNA sequencing studies also suggested broader patterns of spidroin transcript expression across silk glands ( Supplementary Fig.…”

“…To identify non-spidroin candidate genes potentially involved in silk production, we cataloged transcripts that were (i) highly expressed and/or (ii) uniquely expressed in N. clavipes silk glands, resulting in a list of 649 candidates from our RNA sequencing data ( Supplementary Fig. 12 and Supplementary Table 15); 183 of these genes exhibited homology to documented silk gland-specific transcripts [50][51][52][53][54] . The candidates included catalytic enzymes such as kinases, proteases, dehydrogenases, acetyltransferases, and synthases, many of which are active in eukaryotic secretory systems 57 .…”

“…The candidates included catalytic enzymes such as kinases, proteases, dehydrogenases, acetyltransferases, and synthases, many of which are active in eukaryotic secretory systems 57 . We expect this catalog to include genes encoding proteins involved in the conversion of liquid silk dope to solid silk thread 52,53 , such as enzymes that maintain the pH gradient along the gland body to spigots on the spinnerets 50,54 . Candidates that might generate ions for the pH gradient include three carbonic anhydrase orthologs (Ca10, Ca13, and Ca14), four thyroid peroxidase (Tpo) paralogs, and five chorion peroxidase (Pxt) paralogs (Supplementary Table 15).…”

“…The normalized expression data set of 14,025 'gold' genes was filtered to identify putative SST loci that could be categorized as (i) 'HighInSilk' , with >1,000 absolute normalized mapped RNA reads in ≥1 silk gland and <200 reads in non-silk tissues; (ii) 'ExclusiveToSilk' , with >100 absolute normalized mapped RNA reads in ≥1 silk gland and zero reads in non-silk tissues; (iii) 'GlandEnriched' , with >400 absolute normalized mapped reads in only a single silk gland and <350 in all non-silk tissues; and (iv) 'Literature' , corresponding to the BLASTP 84 homologs (e value: ≤ 1 × 10 −6 ) of 282 unique SSTs from studies of spider silk gland transcriptomes and proteomes [50][51][52][53][54] plus peroxidase or anhydrase gene family members hypothesized to be involved in silk production 50,54 ( Supplementary Fig. 12 and Supplementary Table 15).…”

With great structure comes great functionality: Understanding and emulating spider silk

“…57 Additionally, the analysis of RNA transcripts within silk glands has indicated a host of potential proteins that may be involved in silk biogenesis. 63,64 In particular, Clarke et al elegantly determined 647 silkgland specific transcripts for Latrodectus hesperus (western black widow) by removing transcripts also found in other spider tissues (venom and cephalothorax). Transcripts can be broadly categorized according to function and ranked according to the number of transcripts associated with that category.…”