Co-Expression Network and Time-Course Expression Analyses to Identify Silk Protein Regulatory Factors in Bombyx mori

Comprehensive Transcriptomic Analyses of Silk-Associated Genes and Functional Characterization of Key Silk Fibroins in Plutella xylostella

The diamondback moth (DBM), Plutella xylostella (Lepidoptera: Plutellidae), is a serious agricultural pest that utilizes silk as a defensive mechanism, with silk fibroins playing a pivotal role in this process. Through comprehensive transcriptomic analyses, we identified 3452 differentially expressed genes (DEGs) co-expressed in the silk gland of P. xylostella and associated with silk production. The Gene Ontology (GO) analysis revealed enrichment in categories related to protein synthesis, secretion, and extracellular matrix organization, while Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis linked these genes to amino acid metabolism and protein processing pathways. Additionally, we identified three key silk fibroin genes: silk fibroin heavy chain (FibH), silk fibroin light chain (FibL), and fibrohexamerin (P25). We characterized the structure of these genes and analyzed the phylogenetic relationships, amino acid composition, hydrophilicity, and other physicochemical properties of the encoded silk fibroin proteins. The expression profiles revealed peak expression levels of these genes in the silk glands of fourth instar larvae. This integrative study enhances our understanding of the molecular mechanisms underlying silk production in P. xylostella and provides a foundation for future research into the biological roles, evolutionary trajectories, and potential applications of these silk fibroin genes in agricultural pest management and biotechnology.

Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain)

Time-course transcriptome expression data were constructed for four parts of the silk gland (anterior, middle, and posterior parts of the middle silk gland, along with the posterior silk gland) in the domestic silkworm, Bombyx mori, from days 0 to 7 of the last-instar larvae. For sample preparation, silk glands were extracted from one female and one male larva every 24 hours accurately after the fourth ecdysis. The reliability of these transcriptome data was confirmed by comparing the transcripts per million (TPM) values of the silk gene and quantitative reverse transcription PCR results. Hierarchical cluster analysis results supported the reliability of transcriptome data. These data are likely to contribute to the progress in molecular biology and genetic research using B. mori, such as elucidating the mechanism underlying the massive production of silk proteins, conducting entomological research using a meta-analysis as a model for lepidopteran insect species, and exploring medical research using B. mori as a model for disease species by utilising transcriptome data.

Evaluating bio-physicochemical properties of raw powder prepared from whole larvae containing liquid silk of the domestic silkworm

The domestic silkworm, Bombyx mori, has been widely used in silk production for centuries. It is also used as a bioreactor by the textile and pharmaceutical industries to mass produce recombinant bioactive proteins containing silk-based materials. Furthermore, silkworms are well-known as a source of food and have also been orally administered to prevent and treat several human disorders. In this study, we aimed to investigate the inherent bio-physicochemical properties of edible silkworms to accurately evaluate their clinical and nutritional potential. We prepared raw powder from whole larvae of silkworm. The yield rate of the powder derived from dried larvae was almost 100% (98.1-99.1% in replicates). As "percentage yield" translates to "Budomari" in Japanese, this raw powder was named "B100rw." We further prepared B100dn that was denatured through autoclaving. Thereafter, we examined whether B100rw sustained the original bio-physicochemical properties by comparing it with B100dn. There was no significant difference in nutritional content between B100rw and B100dn. B100rw contained proteins derived from silkworm larvae and mulberry leaves, whereas the proteins of B100dn were mostly degraded. On measuring the enzymatic activity of both powders using trehalase as an indicator enzyme, B100rw was found to maintain trehalase activity. B100rw also maintained a random coil conformation, similar to that of liquid silk. This suggested that B100rw sustained the unique bio-physicochemical properties of living larvae. These findings may facilitate the development of novel food products or orally administered vaccines.

Silkworm and Silk: Traditional and Innovative Applications

The various subjects covered in the present Special Issue "Silkworm and Silk: Traditional and Innovative Applications" demonstrate how sericulture, a practice deeply rooted in human history, can act as a bridge to bring together an exceptionally wide range of scientific and technical expertise in both conventional topics and cutting-edge technologies [...].

Meta-Analysis of the Public RNA-Seq Data of the Western Honeybee Apis mellifera to Construct Reference Transcriptome Data

The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. Approximately 50-60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune-response-related RNA-Seq and reference transcriptome data. Three to twenty candidate transcripts including autophagy-related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.