Identification of novel members reveals the structural and functional divergence of lepidopteran-specific Lipoprotein_11 family

The circadian clock affects starvation resistance through the pentose phosphate pathway in silkworm, Bombyx mori

Disruption of the circadian clock can affect starvation resistance, but the molecular mechanism is still unclear. Here, we found that starvation resistance was significantly reduced in the core gene BmPer deficient mutant silkworms (Per-/-), but the mutant's starvation resistance increased with larval age. Under natural physiological conditions, the weight of mutant 5th instar larvae was significantly increased compared to wild type, and the accumulation ability of triglycerides and glycogen in the fat bodies was upregulated. However, under starvation conditions, the weight consumption of mutant larvae was increased and cholesterol utilization was intensified. Transcriptome analysis showed that beta-oxidation was significantly upregulated under starvation conditions, fatty acid synthesis was inhibited, and the expression levels of genes related to mitochondrial function were significantly changed. Further investigations revealed that the redox balance, which is closely related to mitochondrial metabolism, was altered in the fat bodies, the antioxidant level was increased, and the pentose phosphate pathway, the source of reducing power in cells, was activated. Our findings suggest that one of the reasons for the increased energy burden observed in mutants is the need to maintain a more robust redox balance in metabolic tissues. This necessitates the diversion of more glucose into the pentose phosphate pathway to ensure an adequate supply of reducing power.

Proteomic Analysis of the Midgut Contents of Silkworm in the Pupal Stage

The silkworm Bombyx mori, a lepidopteran insect, possesses an 8-10-day pupal stage, during which significant changes occur in the midgut, where it first condenses into the yellow body, and then undergoes decomposition. To gain insights into this transformation process, proteomics was performed on Bombyx mori midgut contents on day 2 and day 7 after pupation. The results revealed the identification of 771 proteins with more than one unique peptide. An analysis using AgriGO demonstrated that these proteins were predominantly associated with catalytic activity. Among the identified proteins, a considerable number were found to be involved in carbohydrate metabolism, amino acid metabolism, lipid metabolism, nucleic acid degradation, and energy support. Additionally, variations in the levels of certain proteases were observed between the midgut contents on day 2 and day 7 after pupation. An in-depth analysis of the two-dimensional electrophoresis of the midgut contents on day 7 after pupation led to the identification of twelve protein spots with potential gelatinolytic activity. Among these, six proteases were identified through mass spectrometry, including the p37k protease, vitellin-degrading protease, chymotrypsin-2, etc. These proteases may be responsible for the digestion of the yellow body during the later stages of pupal development.

Vitellogenin receptor transports the 30K protein LP1 without cell-penetrating peptide, into the oocytes of the silkworm, Bombyx mori

Vitellogenin receptors (VgRs) transport vitellogenin (Vg) into oocytes, thereby promoting egg growth and embryonic development. VgRs recognize and transport multiple ligands in oviparous animals, but their role in insects is rarely reported. In this study, we investigated whether Bombyx mori VgR (BmVgR) binds and transports lipoprotein-1 (BmLP1) and lipoprotein-7 (BmLP7) of the 30 kDa lipoproteins (30 K proteins), which are essential for egg formation and embryonic development in B. mori. Protein sequence analysis showed BmLP7, similar to reported lipoprotein-3 (BmLP3), contains the cell-penetrating peptides and Cysteine position, while BmLP1 has not. Assays using Spodoptera frugiperda ovary cells (sf9) indicated the direct entry of BmLP7 into the cells, whereas BmLP1 failed to enter. However, co-immunoprecipitation (Co-IP) assays indicated that BmVgR could bind BmLP1. Western blotting and immunofluorescence assays further revealed that over-expressed BmVgR could transport BmLP1 into sf9 cells. Co-IP assays showed that SE11C (comprising LBD1+EGF1+OTC domains of BmVgR) or SE22C (comprising LBD2+EGF2+OTC domains of BmVgR) could bind BmLP1. Over-expressed SE11C or SE22C could also transport BmLP1 into sf9 cells. Western blotting revealed that the ability of SE11C to transport BmLP1 might be stronger than that of SE22C. In the vit mutant with BmVgR gene mutation (vit/vit), SDS-PAGE and western blotting showed the content of BmLP1 in the ovary, like BmVg, was lower than that in the normal silkworm. When transgenic with hsp70 promoter over-expressed BmVgR in the vit mutant, we found that the phenotype of the vit mutant was partly rescued after heat treatment. And contents of BmLP1 and BmVg in vit mutant over-expressed BmVgR were higher than in the vit mutant. We conclude that BmVgR and its two repeat domains could bind and transport BmLP1 into the oocytes of the silkworm, besides BmVg. These results will provide a reference for studying the molecular mechanism of VgR transporting ligands in insects.

Hemocyte Clusters Defined by scRNA-Seq in Bombyx mori: In Silico Analysis of Predicted Marker Genes and Implications for Potential Functional Roles

Within the hemolymph, insect hemocytes constitute a heterogeneous population of macrophage-like cells that play important roles in innate immunity, homeostasis and development. Classification of hemocytes in different subtypes by size, morphology and biochemical or immunological markers has been difficult and only in Drosophila extensive genetic analysis allowed the construction of a coherent picture of hemocyte differentiation from pro-hemocytes to granulocytes, crystal cells and plasmatocytes. However, the advent of high-throughput single cell technologies, such as single cell RNA sequencing (scRNA-seq), is bound to have a high impact on the study of hemocytes subtypes and their phenotypes in other insects for which a sophisticated genetic toolbox is not available. Instead of averaging gene expression across all cells as occurs in bulk-RNA-seq, scRNA-seq allows high-throughput and specific visualization of the differentiation status of individual cells. With scRNA-seq, interesting cell types can be identified in heterogeneous populations and direct analysis of rare cell types is possible. Next to its ability to profile the transcriptomes of individual cells in tissue samples, scRNA-seq can be used to propose marker genes that are characteristic of different hemocyte subtypes and predict their functions. In this perspective, the identities of the different marker genes that were identified by scRNA-seq analysis to define 13 distinct cell clusters of hemocytes in larvae of the silkworm, Bombyx mori, are discussed in detail. The analysis confirms the broad division of hemocytes in granulocytes, plasmatocytes, oenocytoids and perhaps spherulocytes but also reveals considerable complexity at the molecular level and highly specialized functions. In addition, predicted hemocyte marker genes in Bombyx generally show only limited convergence with the genes that are considered characteristic for hemocyte subtypes in Drosophila.

Allergenic characterization of Bomb m 4, a 30 kDa lipoprotein Bombyx mori lipoprotein 6 from silkworm pupa

BACKGROUND

Silkworm pupa (SWP) food anaphylaxis has been described frequently in Asian countries. However, false-positive reactions by skin pricks and serum IgE (sIgE) tests to the extract complicate diagnosis, requiring identification of clinically relevant major allergens.

OBJECTIVES

In this study, we characterized a novel SWP allergen, Bomb m 4, a 30 kDa lipoprotein, and evaluated its diagnostic sensitivity.

METHODS

Bomb m 4 was identified by a proteomic analysis. This recombinant (r)Bomb m 4 was overexpressed in Escherichia coli, and the IgE reactivity by ELISA was compared with other reported allergenic proteins: Bomb m 1 (arginine kinase), 27 kDa glycoprotein, Bomb m 3 (tropomyosin) using the serum samples from 17 SWP allergy patients and 11 asymptomatic sensitized subjects.

RESULTS

rBomb m 4 specific IgE was recognized by all 17 SWP allergy patients. The 27 kDa glycoprotein and Bomb m 1 sIgE were found in 35.3% and 0%, respectively in the SWP allergic patients. ELISA sIgE reactivity increased significantly, when 4 M urea was added in serum samples. However, only 16% inhibition of sIgE reactivity to the whole SWP extract was exhibited by rBomb m 4, whereas more than 93% of self-inhibition of rBomb m 4 sIgE was obtained, possibly due to the low abundance of Bomb m 4 in the extract. Three linear epitopes (81-95, 191-205, and 224-238 residues) of rBomb m 4 were identified. These epitopes are shown to be released by pepsin digestion. ROC analysis showed the highest diagnostic value of Bomb m 4 followed by Bomb m 1, 27 kDa glycoprotein, and Bomb m 3.

CONCLUSION

Bomb m 4 is the major allergen of SWP allergy patients. It has cryptic epitopes which are exposed to IgE antibodies with digestive enzymes. This recombinant Bomb m 4 allergen permits exact diagnosis of SWP allergy.

Five Silkworm 30K Proteins Are Involved in the Cellular Immunity against Fungi

Simple Summary

The molecular mechanism of 30K proteins in anti-fungal immunity remains unclear. Here, we examined the mRNA levels of 30K proteins, including BmLP1, BmLP2, BmLP3, BmLP4, and BmLP7, and found that all of these proteins were significantly upregulated after injection of pathogen-associated molecular patterns to the fifth instar larvae, implying their involvement in immune response. The binding assay results showed that only BmLP1 and BmLP4 can bind to both fungal cells and silkworm hemocytes. In vitro, the encapsulation of hemocytes on day 5 of the fifth instar larval stage was promoted by the coating of agarose beads with recombinant BmLP1 and BmLP4. Therefore, these results demonstrate that 30K proteins are involved in the cellular immunity of silkworms by acting as pattern recognition molecules to directly recruit hemocytes to the fungal surface. We believe that our study makes a significant contribution to the literature because it provides insights into the 30K-mediated cellular immunity in silkworms.

Abstract

Background: 30K proteins are a major group of nutrient storage proteins in the silkworm hemolymph. Previous studies have shown that 30K proteins are involved in the anti-fungal immunity; however, the molecular mechanism involved in this immunity remains unclear. Methods: We investigated the transcriptional expression of five 30K proteins, including BmLP1, BmLP2, BmLP3, BmLP4, and BmLP7. The five recombinant 30K proteins were expressed in an Escherichia coli expression system, and used for binding assays with fungal cells and hemocytes. Results: The transcriptional expression showed that the five 30K proteins were significantly upregulated after injection of pathogen-associated molecular patterns to the fifth instar larvae, indicating the possibility of their involvement in immune response. The binding assay showed that only BmLP1 and BmLP4 can bind to both fungal cells and silkworm hemocytes. Furthermore, we found that BmLP1-coated and BmLP4-coated agarose beads promote encapsulation of hemocytes in vitro. The hemocyte encapsulation was blocked when the BmLP1-coated beads were preincubated with BmLP1 specific polyclonal antibodies. Conclusions: These results demonstrate that 30K proteins are involved in the cellular immunity of silkworms by acting as pattern recognition molecules to directly recruit hemocytes to the fungal surface.

Insect Hemolymph Immune Complexes

Insects possess powerful immune systems that have evolved to defend against wounding and environmental pathogens such as bacteria, fungi, protozoans, and parasitoids. This surprising sophistication is accomplished through the activation of multiple immune pathways comprised of a large array of components, many of which have been identified and studied in detail using both genetic manipulations and traditional biochemical techniques. Recent advances indicate that certain pathways activate arrays of proteins that interact to form large functional complexes. Here we discuss three examples from multiple insects that exemplify such processes, including pathogen recognition, melanization, and coagulation. The functionality of each depends on integrating recognition with the recruitment of immune effectors capable of healing wounds and destroying pathogens. In both melanization and coagulation, protein interactions also appear to be essential for enzymatic activities tied to the formation of melanin and for the recruitment of hemocytes. The importance of these immune complexes is highlighted by the evolution of mechanisms in pathogens to disrupt their formation, an example of which is provided. While technically difficult to study, and not always readily amenable to dissection through genetics, modern mass spectrometry has become an indispensable tool in the study of these higher-order protein interactions. The formation of immune complexes should be viewed as an essential and emerging frontier in the study of insect immunity.

Comparative analysis of integument transcriptomes identifies genes that participate in marking pattern formation in three allelic mutants of silkworm, Bombyx mori

The diversity markings and pigment patterns in insects are outcomes of adaptive evolution. The elucidation of the molecular mechanism underlying variations in pigment patterns may improve our understanding of the origin and evolution of these spectacular diverse phenotypes. Melanin, ommochrome, and pteridine are the three main types of insect pigments, and the genes that directly participate in pigment biosynthesis have been extensively studied. However, available information on gene interactions and the whole pigment regulatory network is limited. In this study, we performed integument transcriptome sequencing to analyze three larval marking allelic mutants, namely, multi lunar (L), L^C, and L^Ca, which have similar twin-spot markings on the dorsal side of multiple segments. Further analysis identified 336 differentially expressed genes (DEGs) between L and Dazao (wild type which exhibits normal markings), 68 DEGs between L^C/+ and +^LC/+^LC, and 188 DEGs between L^Ca/+ and +^LCa/+^LCa. Gene Ontology (GO) analysis indicated a significant DEG enrichment of the functional terms catalytic activity, binding, metabolic process, and cellular process. Furthermore, three mutants share six common enriched KEGG pathways. We finally identified eight common DEGs among three pairwise comparisons, including Krueppel-like factor, TATA-binding protein, protein patched, UDP-glycosyltransferase, an unknown secreted protein, and three cuticular proteins. Microarray-based gene expression analysis revealed that the eight genes are upregulated during molting, which coincides with marking formation, and are significantly differentially expressed between marking and non-marking regions. The results suggest that the eight common genes are involved in the construction of the multiple twin-spot marking patterns in the three mutants.

Proteomic Identification of Immune-Related Silkworm Proteins Involved in the Response to Bacterial Infection

Bombyx mori (Lepidoptera: Bombycidae) is an important economic insect and a classic Lepidopteran model system. Although immune-related genes have been identified at a genome-wide scale in the silkworm, proteins involved in immune defense of the silkworm have not been comprehensively characterized. In this study, two types of bacteria were injected into the silkworm larvae, Gram-negative Escherichia coli (Enterobacteriales: Enterobacteriaceae), or Gram-positive Staphylococcus aureus (Bacillales: Staphylococcaceae). After injection, proteomic analyses of hemolymph were performed by liquid chromatography-tandem mass spectrometry. In total, 514 proteins were identified in the uninduced control group, 540 were identified in the E. coli-induced group, and 537 were identified in the S. aureus-induced group. Based on Uniprot annotations, 32 immunological recognition proteins, 28 immunological signaling proteins, and 21 immunological effector proteins were identified. We found that 127 proteins showed significant upregulation, including 10 immunological recognition proteins, 4 immunological signaling proteins, 11 immunological effector proteins, and 102 other proteins. Using real-time quantitative polymerase chain reaction in the fat body, we verified that immunological recognition proteins, signaling proteins, and effector proteins also showed significant increases at the transcriptional level after infection with E. coli and S. aureus. Five newly identified proteins showed upregulation at both protein and transcription levels after infection, including 30K protein, yellow-d protein, chemosensory protein, and two uncharacterized proteins. This study identified many new immune-related proteins, deepening our understanding of the immune defense system in B. mori. The data have been deposited to the iProX with identifier IPX0001337000.

The physiological differentiation along the midgut of Bombyx mori - inspirations from proteomics and gene expression patterns of the secreted proteins in the ectoperitrophic space

The ectoperitrophic space (EcPS) between the insect midgut epithelial cells and the peritrophic matrix is an unexplored, clean resource for concentrated proteins secreted by the midgut epithelial cells, which offers an ideal opportunity to uncover the midgut functions. In this study, we used Bombyx mori as a model organism and performed comparative proteomic analyses of the secreted proteins in the EcPS at the feeding and wandering stages. A total of 372 proteins were identified from both stages and 70 proteins were predicted to be secreted. Amongst these proteins, 17 secreted digestive proteins were identified and their temporal and spatial transcriptional expression patterns demonstrated that all these proteins were up-regulated at the feeding stage and differentially expressed in different parts of the midgut. Proteins with nutrient reservoir activity and defence activity were found to be up-regulated at the wandering stage. This work is the first to show the presence of digestive enzymes in the EcPS of the insect midgut using a proteomic approach, which provides evidence that suggests a physiological functional differentiation of the insect midgut. It is very clear that the EcPS undergoes dynamic changes in its composition of proteins in response to the changing needs of the insect at different developmental stages.

Segmental duplications: evolution and impact among the current Lepidoptera genomes

Background

Structural variation among genomes is now viewed to be as important as single nucleoid polymorphisms in influencing the phenotype and evolution of a species. Segmental duplication (SD) is defined as segments of DNA with homologous sequence.

Results

Here, we performed a systematic analysis of segmental duplications (SDs) among five lepidopteran reference genomes (Plutella xylostella, Danaus plexippus, Bombyx mori, Manduca sexta and Heliconius melpomene) to understand their potential impact on the evolution of these species. We find that the SDs content differed substantially among species, ranging from 1.2% of the genome in B. mori to 15.2% in H. melpomene. Most SDs formed very high identity (similarity higher than 90%) blocks but had very few large blocks. Comparative analysis showed that most of the SDs arose after the divergence of each linage and we found that P. xylostella and H. melpomene showed more duplications than other species, suggesting they might be able to tolerate extensive levels of variation in their genomes. Conserved ancestral and species specific SD events were assessed, revealing multiple examples of the gain, loss or maintenance of SDs over time. SDs content analysis showed that most of the genes embedded in SDs regions belonged to species-specific SDs (“Unique” SDs). Functional analysis of these genes suggested their potential roles in the lineage-specific evolution. SDs and flanking regions often contained transposable elements (TEs) and this association suggested some involvement in SDs formation. Further studies on comparison of gene expression level between SDs and non-SDs showed that the expression level of genes embedded in SDs was significantly lower, suggesting that structure changes in the genomes are involved in gene expression differences in species.

Conclusions

The results showed that most of the SDs were “unique SDs”, which originated after species formation. Functional analysis suggested that SDs might play different roles in different species. Our results provide a valuable resource beyond the genetic mutation to explore the genome structure for future Lepidoptera research.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1007-y) contains supplementary material, which is available to authorized users.

Bombyx mori and Aedes aegypti form multi-functional immune complexes that integrate pattern recognition, melanization, coagulants, and hemocyte recruitment

The innate immune system of insects responds to wounding and pathogens by mobilizing multiple pathways that provide both systemic and localized protection. Key localized responses in hemolymph include melanization, coagulation, and hemocyte encapsulation, which synergistically seal wounds and envelop and destroy pathogens. To be effective, these pathways require a targeted deposition of their components to provide protection without compromising the host. Extensive research has identified a large number of the effectors that comprise these responses, but questions remain regarding their post-translational processing, function, and targeting. Here, we used mass spectrometry to demonstrate the integration of pathogen recognition proteins, coagulants, and melanization components into stable, high-mass, multi-functional Immune Complexes (ICs) in Bombyx mori and Aedes aegypti. Essential proteins common to both include phenoloxidases, apolipophorins, serine protease homologs, and a serine protease that promotes hemocyte recruitment through cytokine activation. Pattern recognition proteins included C-type Lectins in B. mori, while A. aegypti contained a protein homologous to Plasmodium-resistant LRIM1 from Anopheles gambiae. We also found that the B. mori IC is stabilized by extensive transglutaminase-catalyzed cross-linking of multiple components. The melanization inhibitor Egf1.0, from the parasitoid wasp Microplitis demolitor, blocked inclusion of specific components into the IC and also inhibited transglutaminase activity. Our results show how coagulants, melanization components, and hemocytes can be recruited to a wound surface or pathogen, provide insight into the mechanism by which a parasitoid evades this immune response, and suggest that insects as diverse as Lepidoptera and Diptera utilize similar defensive mechanisms.

Protein content of the Hylesia metabus egg nest setae (Cramer [1775]) (Lepidoptera: Saturniidae) and its association with the parental investment for the reproductive success and lepidopterism

Hylesia metabus is a neotropical moth possessing toxic setae, which once in contact with the skin cause a severe dermatitis to humans known as lepidopterism. The only known function of the setae in the life cycle is to provide protection during the mating and egg-hatching stages. Approximately 65% of the protein content of the setae is a cluster of five proteases (28-45kDa) showing sequence homology to other S1A serine proteases. The N-glycans of a 40kDa protease are a mixture of neutral and sulfated G0F structures. The sulfated N-glycans have an important role in triggering the inflammatory response typical of lepidopterism while the proteolytic activity may promote the erosion of blood vessels and tissues causing focal hemorrhages. The presence of Chitinase and a 30kDa lipoprotein is probably related to the antifungal defense. In addition, chitin digestion of the setae may potentiate the inflammatory reaction caused by the toxins due to the formation of chitin adjuvants fragments. The combined effect of proteases and a chitinase may dissuade predating arthropods, by damaging their exoskeletons. Vitellogenin, a bacteriostatic protein, is able to recognize pathogen-associated patterns, which suggests its possible role in protecting the embryonated eggs from pathogenic microorganisms.

SIGNIFICANCE

The present study is the first report describing the different protein species present in the urticating egg nest setae of the neotropical moth Hylesia metabus - the most harmful of the Hylesia moths - causing a severe urticating dermatitis in humans known as lepidopterism. A distinctive feature of the venom is the presence of five different S1A serine proteases probably used to guarantee a more efficient degradation of a wider number of protein substrates. This work confirms that the presence of sulfated N-glycans is not an isolated finding since its presence has been demonstrated in two different proteases affirming that this PTM is of importance for the activation of the inflammatory response typical of lepidopterism. Additionally, this study gives useful information on the defense mechanisms used for protection of its progeny vs. vertebrate predators, fungus, bacteria or other arthropods such as ants. The proteins detected in the egg nest should be seen as an extended parental effort made by the females in order to achieve an optimal reproductive success, thus compensating for the considerable loss of progeny during the larval stages that seriously limits the number of sexually mature adults reaching the reproductive phase.

Serine protease P-IIc is responsible for the digestion of yolk proteins at the late stage of silkworm embryogenesis

In silkworms, yolk proteins comprise vitellin, egg-specific protein and 30K proteins, which are sequentially degraded by endogenous proteases strictly regulated during embryogenesis. Although the process has been extensively investigated, there is still a gap in the knowledge about the degradation of silkworm yolk proteins on the last two days of embryonic development. In the present study, we isolated and purified a gut serine protease P-IIc, which demonstrated optimal activity at 25 °C and pH 11. Semi-quantitative RT-PCR combined with western blotting showed that P-IIc was actively expressed and significantly accumulated in the gut on the last two days of embryogenesis. When natural yolk proteins were incubated with P-IIc in vitro, vitellin and ESP were selectively degraded. P-IIc also demonstrated activity towards 30K proteins as evidenced by rapid and complete digestion of BmLP1 and partial digestion of BmLP2 and BmLP3. Furthermore, RNAi knockdown of P-IIc in silkworm embryos significantly reduced the degradation rate of residual yolk proteins on embryonic day 10. Taken together, our results indicate that P-IIc represents an embryonic gut protease with a relatively broad substrate specificity, which plays an important role in the degradation of yolk proteins at the late stage of silkworm embryogenesis.

Identification and Characterization of a Novel Microvitellogenin from the Chinese Oak Silkworm Antheraea pernyi

Microvitellogenin (mVg) is a relatively small vitellogenic protein only characterized in the eggs of the lepidopteran insects Manduca sexta and Bombyx mori. In the present study, we report a novel mVg (ApmVg) isolated from the Chinese oak silkworm Antheraea pernyi. The obtained ApmVg cDNA sequence contains an open reading frame of 783 bp encoding a protein of 260 amino acids with a predicted molecular weight of 29.96 kDa. This gene does not contain introns. Structural analysis revealed that this protein shares putative conserved domains with the lepidopteran low-molecular weight lipoprotein, which belongs to the lipoprotein_11 superfamily. The protein sequence of ApmVg exhibits 48% sequence identity with mVg from M. sexta and 40-47% sequence identity with the 30K lipoproteins from B. mori. Phylogenetic analysis suggests that ApmVg is a novel member of the lepidopteran low-molecular weight lipoproteins. Transcriptional analysis indicated that ApmVg mRNA is mainly expressed in the fat body (both female and male) during post-diapause development of the pupal stage, and it was also detected in ovaries and spermaries in smaller amounts. RT-PCR and Western blot analyses revealed that ApmVg is synthesized by the fat body and secreted into hemolymph and ultimately accumulates in eggs. The ApmVg transcript can be detected in the fat bodies of female pupae four days after treatment with 20-hydroxyecdysone and shows an expression pattern distinct from that of vitellogenin (Vg), which is detectable throughout diapausing and in post-diapause development. ApmVg decreased dramatically during embryonic development. These results represent the first study of mVg outside M. sexta and B. mori and provide insight into the physiological role and evolution of mVgs.

Identification and Characterization of 30 K Protein Genes Found in Bombyx mori (Lepidoptera: Bombycidae) Transcriptome

The 30 K proteins, the major group of hemolymph proteins in the silkworm, Bombyx mori (Lepidoptera: Bombycidae), are structurally related with molecular masses of ∼30 kDa and are involved in various physiological processes, e.g., energy storage, embryonic development, and immune responses. For this report, known 30 K protein gene sequences were used as Blastn queries against sequences in the B. mori transcriptome (SilkTransDB). Twenty-nine cDNAs (Bm30K-1-29) were retrieved, including four being previously unidentified in the Lipoprotein_11 family. The genomic structures of the 29 genes were analyzed and they were mapped to their corresponding chromosomes. Furthermore, phylogenetic analysis revealed that the 29 genes encode three types of 30 K proteins. The members increased in each type is mainly a result of gene duplication with the appearance of each type preceding the differentiation of each species included in the tree. Real-Time Quantitative Polymerase Chain Reaction (Q-PCR) confirmed that the genes could be expressed, and that the three types have different temporal expression patterns. Proteins from the hemolymph was separated by SDS-PAGE, and those with molecular mass of ∼30 kDa were isolated and identified by mass spectrometry sequencing in combination with searches of various databases containing B. mori 30K protein sequences. Of the 34 proteins identified, 13 are members of the 30 K protein family, with one that had not been found in the SilkTransDB, although it had been found in the B. mori genome. Taken together, our results indicate that the 30 K protein family contains many members with various functions. Other methods will be required to find more members of the family.

Genome-wide patterns of genetic variation among silkworms

Although the draft genome sequence of silkworm is available for a decade, its genetic variations, especially structural variations, are far from well explored. In this study, we identified 1,298,659 SNPs and 9,731 indels, of which 32 % of SNPs and 92.2 % of indels were novel compared to previous silkworm re-sequencing analysis. In addition, we applied a read depth-based approach to investigate copy number variations among 21 silkworm strains at genome-wide level. This effort resulted in 562 duplicated and 41 deleted CNV regions, and among them 442 CNV were newly identified. Functional annotation of genes affected by these genetic variations reveal that these genes include a wide spectrum of molecular functions, such as immunity and drug detoxification, which are important for the adaptive evolution of silkworms. We further validated the predicted CNV regions using q-PCR. 94.7 % (36/38) of the selected regions show divergent copy numbers compared to a single-copy gene OR2. In addition, potential presence/absence variations are also observed in our study: 11 genes are present in the reference genome, but absent in other strains. Overall, we draw an integrative map of silkworm genetic variation at genome-wide level. The identification of genetic variations in this study improves our understanding that these variants play important roles in shaping phenotypic variations between wild and domesticated silkworms.

Proteomic analysis of silkworm midgut cellular proteins interacting with the 5' end of infectious flacherie virus genomic RNA

The flacherie disease in the silkworm is caused by the infectious flacherie virus (IFV). IFV relies on its 5' region of genomic RNA to recruit host-related factors to implement viral translation and replication. To identify host proteins bound to the 5'-region of IFV RNA and identify proteins important for its function, mass spectrometry was used to identify proteins from silkworm midgut extracts that were obtained using RNA aptamer-labeled 5' region of IFV RNA. We found 325 protein groups (unique peptide≥2) bound to the 5' region of IFV RNA including translation-related factors (16 ribosomal subunits, 3 eukaryotic initiation factor subunits, 1 elongation factor subunit and 6 potential internal ribosome entry site trans-acting factors), cytoskeleton-related proteins, membrane-related proteins, metabolism enzymes, and other proteins. These results can be used to study the translation and replication related factors of IFV interacting with host silkworm and to control flacherie disease in silkworm.

Crystal structure of Bombyx mori lipoprotein 6: comparative structural analysis of the 30-kDa lipoprotein family

The 30-kDa lipoprotein (LP) family of mulberry silkworm comprises major hemolymph proteins specific to the fifth instar larvae. The family consists of 46 members, 24 of which are referred to as typical 30-kDa LPs. To date, two crystal structures of 30-kDa LPs from Bombyx mori have been described (Bmlp3 and Bmlp7). Here, we present the crystal structure of Bmlp6, another 30-kDa LP member. Bmlp6 is comprised of two domains characteristic of this family, the VHS-type N-terminal domain and β-trefoil C-terminal domain. The structures of the three 30-kDa LPs have been compared and a number of differences are noted, including loop conformation, the surface electrostatic potential, and the potential binding cavities. We discuss the observed structural differences in the light of the potential different roles of the particular 30-kDa LP members in silkworm physiology.

Establishment of transgenic silkworms expressing GAL4 specifically in the haemocyte oenocytoid cells

Insect haemocytes play significant roles in innate immunity. The silkworm, a lepidopteran species, is often selected as the model for studies into the functions of haemocytes in immunity; however, our understanding of the role of haemocytes remains limited because the lack of haemocyte promoters for transgene expression makes genetic manipulations difficult. In the present study, we aimed to establish transgenic silkworm strains expressing GAL4 in their haemocytes. First, we identified three genes with strong expression in haemocytes, namely, lp44, Haemocyte Protease 1 (HP1) and hemocytin. Transgenic silkworms expressing GAL4 under the control of the putative promoters of these genes were then established and expression was examined. Although GAL4 expression was not detected in haemocytes of HP1-GAL4 or hemocytin-GAL4 strains, lp44-GAL4 exhibited a high level of GAL4 expression, particularly in oenocytoids. GAL4 expression was also detected in the midgut but in no other tissues, indicating that GAL4 expression in this strain is mostly oenocytoid-specific. Thus, we have identified a promoter that enables oenocytoid expression of genes of interest. Additionally, the lp44-GAL4 strain could also be used for other types of research, such as the functional analysis of genes in oenocytoids, which would facilitate advances in our understanding of insect immunity.

Segmental duplications in the silkworm genome

Background

Segmental duplications (SDs) or low-copy repeats play important roles in both gene and genome evolution. SDs have been extensively investigated in many organisms, however, there is no information about SDs in the silkworm, Bombyx mori.

Result

In this study, we identified and annotated the SDs in the silkworm genome. Our results suggested that SDs constitute ~1.4% of the silkworm genome sequence (≥1 kb in length and ≥90% in the identity of sequence); the number is similar to that in Drosophila melanogaster but smaller than mammalian organisms. Almost half (42%) of the SD sequences are not assigned to chromosomes, indicating that the SDs are challenges for the assembling of genome sequences. We also provided experimental validation of large duplications using qPCR. The analysis of SD content indicated that the genes related to immunity, detoxification, reproduction, and environmental signal recognition are significantly enriched in the silkworm SDs.

Conclusion

Our results suggested that segmental duplications have been problematic for sequencing and assembling of the silkworm genome. SDs may have important biological significances in immunity, detoxification, reproduction, and environmental signal recognition in the silkworm. This study provides insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.

Functional analysis of 30K proteins during silk gland degeneration by a caspase-dependent pathway in Bombyx

The 30K proteins are involved with important functions in the growth and development of Bombyx mori. In this study, the synthesis and regulation of 30K proteins were examined during the degeneration of Bombyx silk glands. On day 3 of the fifth instar, the protein level of 30Kc19 was low, whereas the silk proteins were rapidly synthesized. However, synthesis and accumulation of the 30Kc19 protein significantly increased at the prepupal stage and on day 1 of the pupal stage. At this stage, the silk gland cells were filled with 30Kc19 and genomic DNA. Moreover, the transcript levels of the 30K-encoding genes, including 30Kc6, 30Kc12, 30Kc19 and 30Kc23 were up-regulated during the degeneration of the Bombyx silk glands. During the time that the levels of the 30Kc19 protein were significantly up-regulated, it is notable that the transcript levels of the BmAtg8, BmAtg6 and BmDronc genes dramatically increased to regulate the programmed cell death of this gland. On day 1 of the pupal stage, intense fragmentation of genomic DNA occurred in the silk gland cells, and the putative active form of caspase was detected in the cytoplasm, showing the complete degradation of the silk glands in one day. In conclusion, the 30K proteins are synthesized in high concentrations, while proteolysis mediates silk gland degeneration in Bombyx by a caspase-dependent pathway. We propose that the 30K proteins may be nutrients and energy vectors to be absorbed by the developing tissues of pupae or moths.

Two crystal structures of Bombyx mori lipoprotein 3 - structural characterization of a new 30-kDa lipoprotein family member

The 30-kDa family of lipoproteins from insect hemolymph has been the focus of a number of studies over the last few years. Recently, four crystal structures of Bombyx mori lipoprotein 7 have been determined. Here we report two crystal structures of another member of the 30-kDa lipoprotein family, Bombyx mori lipoprotein 3 (Bmlp3). The protein was isolated from its natural source, mulberry silkworm hemolymph. It crystallized in two different crystal forms, Bmlp3-p21 (space group P21) and Bmlp3-c2 (space group C2). The crystal structures were solved by molecular replacement using the coordinates of Bmlp7 as a starting model. The crystals of Bmlp3-p21 diffracted X-rays to 2.4 Å resolution and of Bmlp3-c2 to 2.1 Å resolution. Bmlp3 has an overall fold characteristic of 30-kDa lipoproteins, with a VHS-type N-terminal domain and β-trefoil C-terminal domain. Structural comparison of Bmlp3 and Bmlp7 shows that the loops present in the C-terminal domain are flexible and participate in dimer formation. Additionally, new putative binding sites of Bmlp3 have been analyzed in detail and the electrostatic potential of the protein surface at physiological pH 7.4 conditions has been calculated. The results of these calculations are the starting point for an explanation of the recently reported cell-penetrating properties of the 30-kDa lipoproteins.

The promoter of Bmlp3 gene can direct fat body-specific expression in the transgenic silkworm, Bombyx mori

The fat body plays multiple, crucial roles in the life of silkworms. Targeted expression of transgenes in the fat body of the silkworm, Bombyx mori, is important not only for clarifying the function of endogenous genes expressed in this tissue, but also for producing valuable recombinant proteins. However, fat body-specific gene expression remains difficult due to a lack of suitable tissue-specific promoters. Here we report the isolation of the fat body-specific promoter of Bmlp3, a member of the 30K protein family of silkworms. The 1.1 kb fragment from −374 to +738 of Bmlp3 displayed strong promoter activity in the cell lines BmE and Spli-221. In transgenic silkworms, a DsRed reporter gene controlled by the 1.1 kb Bmlp3 promoter fragment was expressed specifically in the fat body in a stage-specific pattern that was nearly identical to the endogenous Bmlp3 gene. We conclude that the 1.1 kb Bmlp3 promoter fragment is sufficient to direct tissue- and stage-specific expression of transgenes in the fat body of silkworms, highlighting the potential use of this promoter for both functional genomics research and biotechnology applications.

The synthesis, transportation and degradation of BmLP3 and BmLP7, two highly homologous Bombyx mori 30K proteins

The 30K proteins comprise about 35% of the total embryo yolk proteins and function as storage proteins during embryonic development of the domesticated silkworm Bombyx mori. The most abundant components of hemolymph are 30K proteins in the early and middle pupal stages. In the present study, the 30K protein BmLP7 was purified from larval hemolymph by chromatography. We prepared the antibody of this protein and found that it could bind to both BmLP3 and BmLP7. We used western blotting to analyze the dynamic change of BmLP3 and BmLP7 proteins in the hemolymph during development and found their concentration decreased dramatically from day 4 pupae, which appears to be linked to their accumulation in the oocyte for forming yolk granule since then. We found BmLP3 and BmLP7 proteins reduced significantly in day 10 eggs (the day before hatching). The crude extract of the newly hatched larvae showed proteolytic activity against BmLP3 and BmLP7 and immunohistochemistry showed BmLP3 and BmLP7 were degraded in the embryonic gut lumen in day 10 eggs. These systematic studies of BmLP3 and BmLP7 reveal their synthesis, transportation and degradation, which could represent the experience of all 30K proteins.