Proteome Analysis of Silkworm, Bombyx mori, Larval Gonads: Characterization of Proteins Involved in Sexual Dimorphism and Gametogenesis

Expression of the gonad-specific small heat shock protein, CfHSP20.2, in the spruce budworm, Choristoneura fumiferana (Clem.)

Small heat shock proteins (sHSPs) play important roles in insect development and stress resistance. However, the in vivo functions and mechanisms of action remain largely unknown or unclear for most members of the sHSPs in insects. This study investigated the expression of CfHSP20.2 in the spruce budworm, Choristoneura fumiferana (Clem.) under normal and heat-stress conditions. Under normal conditions, CfHSP20.2 transcript and protein were highly and constantly expressed in the testes of male larvae, pupae and young adults and in the ovaries of female late-stage pupae and adults. After adult eclosion, CfHSP20.2 remained highly and almost constantly expressed in the ovaries, but in contrast, was downregulated in the testes. Upon heat stress, CfHSP20.2 was upregulated in the gonads and non-gonadal tissues in both sexes. These results indicate that CfHSP20.2 expression is gonad-specific and heat-inducible. This provides evidence that the CfHSP20.2 protein plays important roles during reproductive development under normal environmental conditions, while under heat-stress conditions, it may also enhance the thermal tolerance of the gonads and non-gonadal tissues.

Construction and analysis of the protein-protein interaction network for the olfactory system of the silkworm Bombyx mori

Olfaction plays an essential role in feeding and information exchange in insects. Previous studies on the olfaction of silkworms have provided a wealth of information about genes and proteins, yet, most studies have only focused on a single gene or protein related to the insect's olfaction. The aim of the current study is to determine key proteins in the olfactory system of the silkworm, and further understand protein-protein interactions (PPIs) in the olfactory system of Lepidoptera. To achieve this goal, we integrated Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and network analyses. Furthermore, we selected 585 olfactory-related proteins and constructed a (PPI) network for the olfactory system of the silkworm. Network analysis led to the identification of several key proteins, including GSTz1, LOC733095, BGIBMGA002169-TA, BGIBMGA010939-TA, GSTs2, GSTd2, Or-2, and BGIBMGA013255-TA. A comprehensive evaluation of the proteins showed that glutathione S-transferases (GSTs) had the highest ranking. GSTs also had the highest enrichment levels in GO and KEGG. In conclusion, our analysis showed that key nodes in the biological network had a significant impact on the network, and the key proteins identified via network analysis could serve as new research targets to determine their functions in olfaction.

Comparative proteomic analysis of sex-biased proteins in ovary and testis at different stages of Spodoptera litura

Sex-biased protein is thought to be able to drive the phenotypic differences in males and females in insects. In this study, 1385 and 1727 proteins were identified as differentially accumulated proteins (DAPs) by comparing the protein abundances at pupae stage with those at adult stage in ovary and testis of S.litura, respectively. And among which, 548 DAPs were showed to be expressed in both ovary and testis, and 837 and 1179 proteins were considered as ovary-specific and testis-specific DAPs, respectively. To further identify DAPs related to gonad development and sex dimorphism, a total of 320 DAPs were selected and defined as "proteins of specific interest" based on several selecting criteria. Sex dimorphism is a complex and dynamic developmental progress, and these identified DAPs were suggested to be involved in multiple functions such as organonitrogen compound catabolic process, glycosylation, proteasome, N-Glycan biosynthesis and other reproduction-related processes. Overall, our results highlighted these sexual-biased, gonad development related and sexual dimorphism related DAPs, and their abundance variations along with development were also examined, which could provide important information for their functional analysis in reproduction and potential biomarkers for developing useful strategies against S. litura and other orthologous pests. BIOLOGICAL SIGNIFICANCE: Sex dimorphism entails the differentiation of two sexual functions, resulting in sexually phenotypic differences and leading to the development of female and male morphologies and behaviors. However, sex dimorphism related proteins remain to be identified in many non-model insects. In this study, iTRAQ-based proteomic analysis was applied to examine the variations of protein abundances at pupae stage and adult stage in ovary and testis of S.litura, respectively. Reproduction and sex dimorphism related proteins were further identified as "proteins of specific interest". These identified candidate proteins provided valuable information for their further functional analysis in reproduction and could serve as potential biomarkers for developing useful strategies against S. litura and other orthologous pests.

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.

Shotgun proteomic analysis of Bombyx mori brain: emphasis on regulation of behavior and development of the nervous system

The insect brain plays crucial roles in the regulation of growth and development and in all types of behavior. We used sodium dodecyl sulfate polyacrylamide gel electrophoresis and high-performance liquid chromatography - electron spray ionization tandem mass spectrometry (ESI-MS/MS) shotgun to identify the proteome of the silkworm brain, to investigate its protein composition and to understand their biological functions. A total of 2210 proteins with molecular weights in the range of 5.64-1539.82 kDa and isoelectric points in the range of 3.78-12.55 were identified. These proteins were annotated according to Gene Ontology Annotation into the categories of molecular function, biological process and cellular component. We characterized two categories of proteins: one includes behavior-related proteins involved in the regulation of behaviors, such as locomotion, reproduction and learning; the other consists of proteins related to the development or function of the nervous system. The identified proteins were classified into 283 different pathways according to KEGG analysis, including the PI3K-Akt signaling pathway which plays a crucial role in mediating survival signals in a wide range of neuronal cell types. This extensive protein profile provides a basis for further understanding of the physiological functions in the silkworm brain.

Integrative Proteomics and Metabolomics Analysis of Insect Larva Brain: Novel Insights into the Molecular Mechanism of Insect Wandering Behavior

Before metamorphosis, most holometabolous insects, such as the silkworm studied here, undergo a special phase called the wandering stage. Insects in this stage often display enhanced locomotor activity (ELA). ELA is vital because it ensures that the insect finds a safe and suitable place to live through the pupal stage. The physiological mechanisms of wandering behavior are still unclear. Here, we integrated proteomics and metabolomics approaches to analyze the brain of the lepidopteran insect, silkworm, at the feeding and wandering stages. Using LC-MS/MS and GC-MS, in all we identified 3004 proteins and 37 metabolites at these two stages. Among them, 465 proteins and 22 metabolites were changed. Neural signal transduction proteins and metabolites, such as neurofilament, dopaminergic synapse related proteins, and glutamic acid, were significantly altered, which suggested that active neural conduction occurred in the brain at the wandering stage. We also found decreased dopamine degradation at the wandering stage. The proposed changes in active neural conduction and increased dopamine concentration might induce ELA. In addition, proteins involved in the ubiquitin proteasome system and lysosome pathway were upregulated, revealing that the brain experiences morphological remodeling during metamorphosis. These findings yielded novel insights into the molecular mechanism underlying insect wandering behavior.

Transgenic characterization of two testis-specific promoters in the silkworm, Bombyx mori

Sex-specific regulatory elements are key components for developing insect genetic sexing systems. The current insect genetic sexing system mainly uses a female-specific modification system whereas little success was reported on male-specific genetic modification. In the silkworm Bombyx mori, a lepidopteran model insect with economic importance, a transgene-based, female-specific lethality system has been established based on sex-specific alternative splicing factors and a female-specific promoter BmVgp (vitellogenin promoter) has been identified. However, no male-specific regulatory elements have yet been identified. Here we report the transgenic identification of two promoters that drive reporter gene expression in a testis-specific manner in B. mori. Putative promoter sequences from the B. mori Radial spoke head 1 gene (BmR1) and beta-tubulin 4 gene (Bmβ4) were introduced using piggybac-based germline transformation. In transgenic silkworms, expression of the reporter gene enhanced green fluorescent protein (EGFP) directed by either BmR1 promoter (BmR1p) or Bmβ4p showed precisely testis-specific manners from the larval to adult stage. Furthermore, EGFP expression of these two transgenic lines showed different localization in the testis, indicating that BmR1p or Bmβ4p might be used as distinct regulatory elements in directing testis-specific gene expression. Identification of these testis-specific promoters not only contributes to a better understanding of testis-specific gene function in insects, but also has potential applications in sterile insect techniques for pest management.

Next-generation proteomics: toward customized biomarkers for environmental biomonitoring

Because of their ecological representativeness, invertebrates are commonly employed as test organisms in ecotoxicological assessment; however, to date, biomarkers employed for these species were the result of a direct transposition from vertebrates, despite deep evolutionary divergence. To gain efficiency in the diagnostics of ecosystem health, specific biomarkers must be developed. In this sense, next-generation proteomics enables the specific identification of proteins involved in key physiological functions or defense mechanisms, which are responsive to ecotoxicological challenges. However, the analytical investment required restricts use in biomarker discovery. Routine biomarker validation and assays rely on more conventional mass spectrometers. Here, we describe how proteomics remains a challenge for ecotoxicological test organisms because of the lack of appropriate protein sequences databases, thus restricting the analysis on conserved and ubiquitous proteins. These limits and some strategies used to overcome them are discussed. These new tools, such as proteogenomics and targeted proteomics, should result in new biomarkers specific to relevant environmental organisms and applicable to routine ecotoxicological assessment.

Shotgun proteomic analysis of wing discs from the domesticated silkworm (Bombyx mori) during metamorphosis

Proteomic profiles from the wing discs of silkworms at the larval, pupal, and adult moth stages were determined using shotgun proteomics and MS sequencing. We identified 241, 218, and 223 proteins from the larval, pupal, and adult moth stages, respectively, of which 139 were shared by all three stages. In addition, there were 55, 37, and 43 specific proteins identified at the larval, pupal, and adult moth stages, respectively. More metabolic enzymes were identified among the specific proteins expressed in the wing disc of larvae compared with pupae and moths. The identification of FKBP45 and the chitinase-like protein EN03 as two proteins solely expressed at the larval stage indicate these two proteins may be involved in the immunological functions of larvae. The myosin heavy chain was identified in the pupal wing disc, suggesting its involvement in the formation of wing muscle. Some proteins, such as proteasome alpha 3 subunits and ribosomal proteins, specifically identified from the moth stage may be involved in the degradation of old cuticle proteins and new cuticle protein synthesis. Gene ontology analysis of proteins specific to each of these three stages enabled their association with cellular component, molecular function, and biological process categories. The analysis of similarities and differences in these identified proteins will greatly further our understanding of wing disc development in silkworm and other insects.