Comparative Proteomic Analysis of Posterior Silk Glands of Wild and Domesticated Silkworms Reveals Functional Evolution during Domestication

Genomic Analysis Reveals Novel Genes and Adaptive Mechanisms for Artificial Diet Utilization in the Silkworm Strain Guican No.5

The transition from traditional mulberry leaf feeding to artificial diet cultivation represents a major advancement in modern sericulture, yet the genetic mechanisms driving this adaptation remain largely unexplored. This study investigates the genomic basis of artificial diet adaptation in the silkworm strain Guican No.5 through whole-genome resequencing and transcriptome analysis. We identified 8,935,179 single-nucleotide polymorphisms (SNPs) across all chromosomes, accounting for 2.01% of the genome, with particularly high densities observed in chromosomes 23, 26, and 28. Our analysis also revealed 879 novel transcripts, many of which are involved in digestion, detoxification, and stress response pathways. Key novel genes, including three carboxylesterases, two cytochrome P450s, one heat shock protein, and one copper/zinc superoxide dismutase, exhibited varying degrees of sequence similarity to known proteins, suggesting modifications to existing genetic frameworks. Notably, one novel P450 gene displayed only 74.07% sequence identity with its closest homolog, indicating the emergence of a new protein sequence. Additionally, several key genes showed high similarity to wild silkworm (Bombyx mandarina) proteins, underscoring their evolutionary origins. These findings provide valuable insights into the molecular mechanisms underpinning artificial diet adaptation in silkworms and offer genomic resources to enhance artificial diet formulations and breeding programs in sericulture.

Fatty Acid Desaturase Bmdesat5, Suppressed in the Salivary Glands by Domestication, is Involved in Regulation of Food Intake in Silkworms

Understanding the evolutionary genetics of food intake regulation in domesticated animals has relevance to evolutionary biology, animal improvement, and obesity treatment. Here, we observed that the fatty acid desaturase gene (Bmdesat5), which regulates food intake, is suppressed in domesticated silkworms, but expressed in the salivary glands of the wild silkworm Bombyx mandarina. The content of its catalytic product, cis-vaccenic acid, was related to the expression levels of Bmdesat5 in the salivary glands of domesticated and wild silkworm strains. These two strains also showed significant differences in food intake. Using orally administering cis-vaccenic acid and transgenic-mediated overexpression, we verified that cis-vaccenic acid functions as a satiation signal, regulating food intake and growth in silkworms. Selection analysis showed that Bmdesat5 experienced selection, especially in the potential promoter, 5'-untranslated, and intron regions. This study highlights the importance of the decrement of satiety in silkworm domestication and provides new insights into the potential involvement of salivary glands in the regulation of satiety in animals, by acting as a supplement to gut-brain nutrient signaling.

Cytotoxin-mediated silk gland organ dysfunction diverts resources to enhance silkworm fecundity by potentiating nutrient-sensing IIS/TOR pathways

Energy reserves, primarily stored in the insect's fat body, are essential for physiological processes such as reproduction and cocoon formation. However, whether these processes are mutually constraining is unknown. Here, we showed that cocoon-free silkworms accumulate amino acid constituents of silk proteins in the hemolymph and maintain lipid and sugar reserves in the pupal fat body by repressing the expression of sericin and fibroin genes in the middle and posterior silk glands, respectively, via butterfly pierisin-1A catalytic domain expression. This, in turn, upregulates insulin/insulin-like signaling and target of rapamycin (IIS/TOR) signaling, which enhances vitellogenesis and accelerates ovarian development, thus contributing to increased fecundity. The impacts of semi-starvation on fecundity and egg hatchability were also less pronounced in cocoon-free silkworms compared with wildtype silkworms. These data uncover the resource allocation trade-off between cocoon formation and fecundity and demonstrate that nutritional signaling plays a role in regulating silkworm reproduction.

Identification of genes associated with the silk gland size using multi-omics in silkworm (Bombyx mori)

Silk gland size in silkworms (Bombyx mori) affects silk output. However, the molecular mechanisms by which genes regulate silk gland size remain unclear. In this study, silk glands from three pure silkworm strains (A798, A306 and XH) with different silk gland weight phenotypes were compared using transcriptomics and proteomics to identify differentially expressed genes (DEGs) and proteins (DEPs). When comparing A798 to A306 and A798 to XH, 830 and 469 DEGs were up-regulated, respectively. These genes were related to the gene ontology terms, metabolic process, transport activity and biosynthesis process. In addition, 372 and 302 up-regulated differentially expressed proteins were detected in A798 to A306 and A798 to XH, respectively, related to the gene ontology terms, ribosome and protein export, ribosome and polypeptide biosynthesis processes. Moreover, combined transcriptomics, proteomics and weighted correlation network analyses showed that five genes (BGIBMGA002524, BGIBMGA002629, BGIBMGA005659, BGIBMGA005711 and BGIBMGA010889) were significantly associated with the silk gland weight. Reverse Transcription-quantitative real-time Polymerase Chain Reaction (RT-qPCR) and Enzyme linked immunosorbent assay (ELISA) were used to verify the mRNA and protein expression of five genes in the silk glands and tissues of 18 silkworm strains. The results showed that four genes have higher expression levels in heavier silk glands. These genes are associated with glycogen metabolism, fatty acid synthesis and branched chain amino acid metabolism, thus potentially promoting growth and silk protein synthesis. These findings provide valuable insights into the molecular mechanisms underlying the relationship between silk gland weight and silk yield in silkworms.

Non-classical digestive lipase BmTGL selected by gene amplification reduces the effects of mulberry inhibitor during silkworm domestication

Efficient utilization of dietary lipids is crucial for Bombyx mori, also known as domesticated silkworms. However, the effects of domestication on the genes encoding lipases remain unknown. In this study, we investigated the expression difference of one triacylglycerol lipase (BmTGL) between B.mori and wild (ancestor) silkworm strains (Bombyx mandarina). An immunofluorescence localization analysis showed that BmTGL was present in all parts of the gut and was released into the intestinal lumen. BmTGL expression was significantly enhanced in different domesticated silkworm strains compared to that in the B. mandarina strains. The BmTGL copy numbers in the genomes of the domesticated silkworm strains were 2-to-3 folds that of the B. mandarina strains and accounted for the enhanced expression of BmTGL in the domesticated silkworm strains. The Ser144Asn substitution in the Ser-Asp-His catalytic triads of BmTGL resulted in relatively lower lipase activity and reduced sensitivity to the lipase inhibitor morachalcone A. Moreover, BmTGL overexpression significantly increased the weights of the B. mori silkworms compared to those of the non-transgenic controls. Thus, the selection of BmTGL by gene amplification may be a trade-off between maintaining high enzymatic activity and reducing the effects of mulberry inhibitors during silkworm domestication.

Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield

We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.

Progress in recycling and valorization of waste silk

Due to the improvements in living standards and the "throw away" culture of mankind, large amount of waste textiles is constantly generated. In particular, silk is an abundant high-grade textile material with characteristics of wear comfort, high profit, and low supply with high demand, but it transforms into waste when discarded. This paper reviews the current progress of recycling and reuse of waste silk from the aspects of energy, yarn and fabric, reinforcement of composites, silk fibroin, biological tissue engineering, filtration of air and water, and electrode. The modification, optimization and application of regenerated silk fibroin extracted from waste silk are promising to industrialization and sustainable development. Making waste silk functional and intelligently wearable are two ways of recycling waste silk with low cost and high return value in the near future. The recovery and utilization of waste silk provide a paradigm for valorization of other fiber-based waste such as wool, cotton, bast and synthetic fibers.

Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori

Naked pupa sericin and Naked pupa are two mutant strains of Bombyx mori with extremely low or no fibroin production compared to the Qiufeng and Baiyu strains, both of which exhibit very high silk fibroin production. However, the molecular mechanisms by which long non-coding RNAs regulate fibroin synthesis need further study. In this study, we performed high-throughput RNA-seq to investigate lncRNA and mRNA expression profiles in the posterior silk gland of Qiufeng, Baiyu, Nd-s^D, and Nd silkworms at the third day of the 5th instar. Our efforts yielded 26,767 novel lncRNAs and 6,009 novel mRNAs, the expression levels of silk protein genes and silk gland transcription factors were decreased in Qiufeng vs. Nd-s^D and Qiufeng vs. Nd, while those of many genes related to autophagy, apoptosis, RNA degradation, ubiquitin-mediated proteolysis and heat shock proteins were increased. Moreover, the expression of a large number of genes responsible for protein synthesis and secretion was significantly decreased in Nd. GO and KEGG analysis results showed that nucleotide excision repair, mRNA surveillance pathways, amino acid degradation, protein digestion and absorption, ER-associated degradation and proteasome pathways were significantly enriched for the Qiufeng vs. Nd-s^D and Qiufeng vs. Nd comparisons. In conclusion, our findings contribute to the lncRNA and mRNA database of Bombyx mori, and the identified differentially expressed mRNAs and lncRNAs help to reveal the molecular mechanisms of low silk production in Nd-s^D and Nd, providing new insights for improvement of silk yield and elucidation of silk mechanical properties.

Characterization and potential application of an α-amylase (BmAmy1) selected during silkworm domestication

Efficient resource utilization plays a central role in the high productivity of domesticated plants and animals. Whether artificial selection acts on digestive enzymes in the domesticated silkworm (Bombyx mori), which is larger than its wild ancestor, Bombyx mandarina (B. mandarina), remains unknown. In this study, we present the characteristics of a novel alpha-amylase, BmAmy1, in B. mori. The activity of recombinant BmAmy1 was maximal at 35 °C and pH 9.0, and could be suppressed by amylase inhibitors from mulberry, the exclusive food source of silkworms. Three different transposable element fragments, which were independently inserted in the 5'-upstream regulatory region, might be responsible for the enhanced expression of BmAmy1 in different domesticated silkworm strains as revealed by dual-luciferase reporter assay. The BmAmy1 overexpression increased the weight of female and male B. mori by 11.9% and 6.8%, respectively, compared with non-transgenic controls. Our results emphasize that, by exploring the genetic mechanisms of human-selected traits, the domestication process could be further accelerated through genetic engineering and targeted breeding.

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

Long-term domestication and selective breeding have increased the silk yield of the domestic silkworm (Bombyx mori) by several times the amount of the silk yield of its wild ancestor (Bombyx mandarina). However, little is known about the molecular mechanisms behind the increase in silk yield during domestication. Based on dynamic patterns of functional divergence in the silk gland between domestic and wild silkworms, we found that at early and intermediate stages of silk gland development, the up-regulated genes of the domestic silkworm were mainly involved in DNA integration, nucleic acid binding, and transporter activity, which are related to the division and growth of cells. This has led to the posterior silk gland (PSG) of the domestic silkworm having significantly more cells (“factories” of fibroin protein synthesis) than that of the wild silkworm. At the late stage of silk gland development, the up-regulated genes in the domestic silkworm was enriched in protein processing and ribosome pathways, suggesting protein synthesis efficiency is greatly improved during silkworm domestication. While there was an increase in fibroin protein synthesis, the production of sericin protein was simultaneously reduced in the silk gland of the domestic silkworm. This reflects that domestic and wild silkworms have been under different selection pressures. Importantly, we found that the network co-expressed with the silk-coding genes of the domestic silkworm was larger than that of the wild silkworm. Furthermore, many more genes co-expressed with silk-coding genes in the domestic silkworm were subjected to artificial selection than those in the wild silkworm. Our results revealed that the increase of silk yield during silkworm domestication is involved in improvement of a biological system which includes not only expansion of “factories” (cells of PSG) of protein synthesis, but also a high expression of silk-coding genes and silk production-related genes such as biological energy, transport, and ribosome pathway genes.

Degradation Behavior and Immunological Detection of Silk Fibroin Exposure to Enzymes

The degradation behavior of silk fibroin (SF) is a significant and intriguing subject in the area of archaeological ancient silk research. In the present study, the immunological detection techniques combined with traditional characterization methods, jointly studied the degradation process of SF from Bombyx mori (B. mori) and Antheraea pernyi (A. pernyi) through exposure to alkaline proteinase, α-chymotrypsin, pepsin, and trypsin. Spectroscopic analysis revealed that different enzymes showed similar hydrolysis effects on the secondary structure, but the changes of B. mori SF and A. pernyi SF were mainly reflected in the decrease of β-sheet and the reduction of α-helical structure, respectively. In further research of immunology, two diagnostic antibodies were prepared corresponding to SF of B. mori and A. pernyi, respectively. The enzyme-linked immunosorbent assay (ELISA) and western blot indicated the enzyme-treated SF proteins still exhibited higher immunoreactivity because the epitopes on the surface of SF molecules are retained. Although α-chymotrypsin possesses the most cleavage sites among these enzymes, the α-chymotrypsin-treated SF did not exhibit significant changes in secondary structures and high antibody binding capacity. The results deepen our understanding of the SF degradation process during enzymatic hydrolysis, and show far-reaching guiding significance in trace detection of SF.

Comparative analysis of proteins from Bombyx mori and Antheraea pernyi cocoons for the purpose of silk identification

Achieving efficient identification of silk protein requires highly sensitive analytical techniques and favorable extraction methods, which is of great significance to the research of ancient silk, especially for the controversial issue of the silk origin. In this paper, proteomics and western blot were proposed to analyze the silk proteins of Bombyx mori (B. mori) and Antheraea pernyi (A. pernyi) dissolved by different methods. First, the differences in secondary structure were detected via spectroscopy. LC-MS/MS was then employed to characterize the peptides of silk proteins precisely. LiBr solution exhibited outstanding dissolution effect on B. mori cocoon, with 87 proteins detected; while copper-ethylenediamine solution (CED) was more appropriate for A. pernyi cocoon, and 16 proteins were identified in A. pernyi-CED. In addition to fibroin and sericin, abundant seroins, enzymes, protease inhibitors, other functional proteins and uncharacterized proteins were detected. Based on the LC-MS/MS data, diagnostic antibodies for the two species were prepared, and fibroin was successfully identified by western blot assay because both dissolution methods were gentle and did not destroy the antigenic epitopes in the protein molecule. Owing to their good specificity and high sensitivity, these diagnostic antibodies have good application prospects in immunoassays of different silk species. SIGNIFICANCE: This study presents the comprehensive analysis on silk identification of proteins from B. mori and A. pernyi extracted by different methods via the proteomic and immunology as well as the conventional approaches. Great coverage of two cocoon proteomes was accomplished, which demonstrated the outstanding difference in components and abundance. Based on the proteomics analysis, the diagnostic antibodies against two species were prepared and identified the corresponding fibroin successfully in the completed protein mixtures. To our knowledge, the proteomic and immunology procedures with high efficiency, sensitivity and specificity are novel analysis on the silk identification and has great potential in the field of ancient silk detection.

Improving Silkworm Genome Annotation Using a Proteogenomics Approach

The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.

Species identification of Bombyx mori and Antheraea pernyi silk via immunology and proteomics

In recent years, increasing attention has been paid to the origin, transmission and communication of silk. However, this is still an unsolved mystery in archaeology. The identification of silk-producing species, especially silk produced by Bombyx mori (B. mori) and Antheraea pernyi (A. pernyi), is of key significance to address this challenge. In this study, two innovative methods, i.e. immunology and proteomics, were proposed and successfully established for the species identification of silks. ELISAs result demonstrated that the two prepared antibodies exhibited high sensitivity and specificity in distinguishing B. mori and A. pernyi silk. No cross-reactivity with each other was observed. Moreover, biomarkers were obtained for Bombyx and Antheraea through proteomic analysis. It was also confirmed that the biomarkers were suitable for identifying the species that produced a given silk sample. Compared with conventional methods for distinguishing silk species, immunological and proteomics techniques used in tandem can provide intact information and have the potential to provide accurate and reliable information for species identification.