Isolation and comparison of different ecdysone-responsive cuticle protein genes in wing discs of Bombyx mori

Cuticle thickening mediates insecticide penetration resistance in Spodoptera litura

INTRODUCTION

Long-term and extensive use of chemical pesticides has led to the development of resistance in many important agricultural pests. The mechanisms of resistance formation in pests are complex and variable, and unraveling the resistance mechanisms is the key to control resistant pests. Insect cuticle, as the first line of defense for insecticides, plays a non-negligible role in insecticide penetration resistance. Although penetration resistance is widespread in insects, the multiple molecular mechanisms that impede insecticide penetration are unclear, especially in Spodoptera litura.

OBJECTIVES

This study aims to reveal the molecular mechanisms of insecticide penetration resistance in S. litura.

METHODS

The structure and thickness of cuticle were analyzed by TEM, and the role of cuticle in penetration resistance was determined by different application methods. The molecular mechanism of cuticular proteins overexpression was analyzed using RNAi, TEM, dual-luciferase assay and EMSA from cis- and trans-acting factors. In addition, the relationship between the chitin synthetic pathway and insecticide resistance was explored through enzyme activity, inhibitor assay, molecular docking and RNAi. Furthermore, the role of 20E in penetration resistance was analyzed.

RESULTS

The cuticle of the resistant populations was significantly thickened and accompanied by extrusion, which contributed significantly to indoxacarb resistance. Constitutive upregulation of trans-acting factor SlituFTZ-F1 co-regulates the overexpression of SlituCP26 with cis-acting elements in the SlituCP26 promoter (74 bp insertion), affecting the cuticle thickness‑mediated indoxacarb penetration resistance. Meanwhile, the overexpression of key genes in the chitin synthesis pathway increased the chitin content, which combined with SlituCP26 to participate in indoxacarb resistance. Moreover, 20E affected the SlituFTZ-F1-mediated regulatory pathway and chitin biosynthesis pathway in indoxacarb resistance.

CONCLUSION

This study comprehensively elucidated the molecular mechanism of cuticle thickening mediating penetration resistance to indoxacarb and confirmed its existence in the field populations of S. litura.

Ecdysone and gene expressions for chromatin remodeling, histone modification, and Broad Complex in relation to pupal commitment in Bombyx mori

In the present study, we tried to clarify when and how pupal commitment (PT) better to use PC occurs and what is involved in the PT of Bombyx mori. To clarify this, we examined the responsiveness of a wing disc to ecdysone, referring to metamorphosis-related BR-C, development-related Myc and Wnt, and chromatin remodeling-related genes at around the predicted PT stage of the Bombyx wing disc. Wing disc responsiveness to juvenile hormone (JH) and ecdysone was examined using Methoprene and 20-hydroxyecdysone (20E) in vitro. The body weight of B. mori increased after the last larval ecdysis, peaked at Day 5 of the fifth larval instar (D5L5), and then decreased. The responsiveness of the wing disc to JH decreased after the last larval ecdysis up to D3L5. Bmbr-c (the Broad Complex of B. mori) showed enhanced expression in D4L5 wing discs with 20E treatment. Some chromatin remodeler and histone modifier genes (Bmsnr1, Bmutx, and Bmtip60) showed upregulation after being cultured with 20E in D4L5 wing discs. A low concentration of 20E is suggested to induce responsiveness to 20E in D4L5 wing discs. Bmbr-c, Bmsnr1, Bmutx, and Bmtip60 were upregulated after being cultured with a low concentration of 20E in D4L5 wing discs. The expression of Bmmyc and Bmwnt1 did not show a change after being cultured with or without 20E in D4L5 wing discs, while enhanced expression was observed with 20E in D5L5 wing discs. From the present results, we concluded that PT of the wing disc of B. mori occurred beginning on D4L5 with the secretion of low concentrations of ecdysteroids. Bmsnr1, Bmutx, Bmtip60, and BR-C are also involved.

Establishment and application of a silkworm CRISPR/Cas9 tool for conditionally manipulating gene disruption in the epidermis

Spatial or temporal specific gene knockout system is a valuable tool for studying the molecular mechanisms underlying developmental processes. The integument is essential for insect fitness and survival, but tools for dissecting function of genes in this tissue are lacking. In this study, we firstly identified an epidermis specifically expressed gene of the domesticated silkworm, BmCPG25, by comparative transcriptomic analysis. Furthermore, a transgenic silkworm expressing the RNA dependent CRISPR-Cas9 protein driven by the regulatory region of the BmCPG25 was established. Immunochemistry analysis showed the endonuclease was specifically expressed in the nuclear of epidermal cells. We also validated the efficiency of this system by disrupting the function of an epidermis specifically expressed cuticular protein gene (Cpr21) and a ubiquitously expressed cuticular gene (Cph18), respectively. In summary, we successfully constructed a conditional knockout toolkit to manipulate the gene editing in epidermal cells, which provides a valuable approach to study the molecular mechanism of integument development.

iTRAQ Proteomic Analysis of Interactions Between 20E and Phospholipase C in Apolygus lucorum (Meyer-Dür)

Polyphagous Apolygus lucorum has become the dominant insect in Bacillus thuringiensis (Bt) cotton fields. Hormone 20-hydroxyecdysone (20E) regulates multiple insect development and physiology events. 20E responses are controlled by pathways triggered by phospholipase C (PLC)-associated proteins. However, 20E-modulated genes and related proteins that can be affected by PLC still remain unknown. Here, isobaric tag for relative and absolute quantitation (iTRAQ) and immunoblotting techniques were used to compare differentially expressed proteins (DEPs) in A. lucorum in response to the treatment of 20E and the PLC inhibitor U73122 as well as their combination. A total of 1,624 non-redundant proteins and 97, 248, 266 DEPs were identified in the 20E/control, U73122/control, and 20E + U73122/control groups, respectively. Only 8 DEPs, including pathogenesis-related protein 5-like, cuticle protein 19.8, trans-sialidase, larval cuticle protein A2B-like, cathepsin L1, hemolymph juvenile hormone-binding protein, ATP-dependent RNA helicase p62-like, and myosin-9 isoform X1, were detected in all three groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEPs were involved in diverse signaling pathways. The results were validated by immunoblotting, which highlighted the reliability of proteomics analysis. These findings provided novel insights into the function of PLC in 20E signaling pathway in A. lucorum.

BR-C Z4 and FoxJ interact to regulate expression of a chitin synthase gene CHSA-2b in the pupal wing discs of the silkworm, Bombyx mori

Elaborate regulation of tissue- and stage-specific expression of genes is prerequisite for insect development. The hormone 20-hydroxyecdysone (20E) initiates metamorphosis by regulating the expression of a series of genes. However, how 20E orderly regulates the pupa-specific expression of genes remains unclear. In this study, we report a regulatory mechanism for the pupa-specific expression of chitin synthase A 2b (CHSA-2b) in Bombyx mori. We found that Broad-Complex Z4 (BR-C Z4) was up-regulated by 20E just before pupation, while transcription factor FoxJ and CHSA-2b were up-regulated during the pupal stage. There is a Fox cis-regulatory element in the CHSA-2b promoter region, and FoxJ protein bound to this element, enhancing the CHSA-2b transcription during the pupal stage. In addition to CHSA-2b, FoxJ also up-regulated the expression of 16 out of 19 pupa-specific genes tested. However, at the prepupal stage, 20E-induced BR-C Z4 inhibited the FoxJ transcription, indirectly inhibiting the CHSA-2b transcription. These data suggest that at the pre-pupation stage, 20E-induced BR-C Z4 inhibited the expression of pupa-stage genes like CHSA-2b by inhibiting the expression of FoxJ; by the pupal stage, the expression of BR-C Z4 decreased, releasing its inhibition on FoxJ, which then up-regulated the expression of the pupa-specific genes. This study explains the elaborate regulation of the pupa-specific gene expression during metamorphosis in B. mori.

CRISPR Disruption of BmOvo Resulted in the Failure of Emergence and Affected the Wing and Gonad Development in the Silkworm Bombyx mori

The domesticated silkworm is an economically important insect that is widely used as a lepidopteran insect model. Although somatic sex determination in the silkworm is well characterized, germline sex determination is not. Here, we used the transgenic-based CRISPR/Cas9 genome editing system to study the function of the Ovo gene in Bombyx mori. BmOvo is the homolog of a factor important in germline sex determination in Drosophila melanogaster. BmOvo mutants had abnormally shaped eggs that were disordered in the ovarioles, and gonad development was abnormal. Interestingly, wing discs and wings did not develop properly, and most of the mutants failed to eclose. Gene expression analyses by qRT-PCR showed that BmOvo gene was highly expressed in the wing disc and epidermis. Genes involved in the WNT signaling pathway and wing development genes BmWCP10 and BmE74 were downregulated in the BmOvo mutants when compared with wild-type animals. These results demonstrate that the BmOvo gene product plays an important role in wing metamorphosis. Thus, this study provides new insights into the multiple functions of BmOvo beyond germline sex determination.

Microscopic cuticle structure comparison of pupal melanic and wild strain of Spodoptera exigua and their gene expression profiles in three time points

The beet armyworm, Spodoptera exigua (Hubner), is one of the major crop pests and is a target for current pest control approaches using insecticides. S. exigua melanic mutants (SEM) spontaneously occurred in the S. exigua wild type (SEW) strain and have been maintained under laboratory conditions on an artificial diet. Scanning electron microscopy showed that the inner cuticle of the SEM had a denser and less orderly structure. We investigated the cuticle protein genes using RNA-seq at three different developmental stages of both SEM and SEW. Comparison of cDNA libraries showed that 7257 CPs were significantly up-regulated and 664 genes were significantly downregulated in SEM at the developmental stage of 46-h in the fifth instar. In addition, 460 genes were significantly up-regulated and 439 genes were significantly down-regulated in the SEM at the development stage of 4-h before pupation. Moreover, 162 genes were significantly up-regulated and 293 genes were significantly downregulated in the SEM, just after pupation. Two genes CPR63 and CPR97 were identified from RNA sequences to verify the differentially expressed gene (DEG) results through quantitative real-time PCR (qRT-PCR). The results show that expression of both CPR63 and CPR97 structural cuticular proteins were significantly different between SEM and SEW. This functional analysis may help in understanding the role that these genes play in the cuticle pattern of the SEM.

BmCHSA-2b, a Lepidoptera specific alternative splicing variant of epidermal chitin synthase, is required for pupal wing development in Bombyx mori

Insect chitin synthase A (CHSA) is an epidermis-specific enzyme that plays an essential role in insect development. In this study, the function and regulation of CHSA-2b, an alternative splicing variant of Bombxy mori CHSA that is discovered only in Lepidopteran insects, were investigated. Analysis of mRNA level showed that BmCHSA-2b was responsive to 20-hydroxyecdysone (20E) in pupal wing unlike BmCHSA-2a, which shares almost the identical sequence as BmCHSA-2b except the first 31 amino acids, suggesting that the expression of these two alternative splicing variants is driven by different promoters of CHSA gene. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis showed that BmCHSA-2b was up-regulated in the wing of mid-pupa unlike BmCHSA-2a, which was up-regulated in epidermis and wing disc at the beginning and end of pupal stage. Further analysis reveals that the up-regulations of BmCHSA-2a and BmCHSA-2b in pupal wing were consistent with the increase of chitin content and wing area at the same stages, respectively. Furthermore, the higher transcription level of BmCHSA-2b in the mid-pupal wing of male than that in female was consistent with the chitin content of pupal wing between genders. Injection of double-stranded RNAs of BmCHSA-2b resulted in the decrease in the area and chitin content of the wing, and irregular and crimpled vein. All these results together suggest that B. mori evolves an extra promoter in CHSA gene to activate BmCHSA-2b expression in the wing of mid-pupal stage in response to 20E, and BmCHSA-2b is required for the wing development in the mid-pupa of B. mori.

piRNA-3878 targets P450 (CpCYP307B1) to regulate pyrethroid resistance in Culex pipiens pallens

Piwi-interacting RNAs (piRNAs) are a novel class of noncoding single-strand RNAs. They play an important role in the germ cell maintenance, brain development, epigenetic regulation of cancer, and antiviral function. However, little is known about the relationship between the piRNAs and insecticide resistance in mosquitoes. In this study, we reported that piRNA-3878 was related with pyrethroid resistance in Culex pipiens pallens. The expression level of piRNA-3878 was lower in both laboratory and field-collected deltamethrin-resistant (DR) strains. Overexpression of piRNA-3878 increased the susceptibility of the DR strain, while inhibiting the expression of piRNA-3878 in DS strain made the mosquitoes more resistant to deltamethrin. Furthermore, we identified that CpCYP307B1 was the target of piRNA-3878. The mosquito mortality rate was increased after downregulating the expression of CpCYP307B1. These findings revealed that piRNA-3878 could target CpCYP307B1 to regulate pyrethroid resistance.

Analysis of expression and chitin-binding activity of the wing disc cuticle protein BmWCP4 in the silkworm, Bombyx mori

The insect exoskeleton is mainly composed of chitin filaments linked by cuticle proteins. When insects molt, the cuticle of the exoskeleton is renewed by degrading the old chitin and cuticle proteins and synthesizing new ones. In this study, chitin-binding activity of the wing disc cuticle protein BmWCP4 in Bombyx mori was studied. Sequence analysis showed that the protein had a conservative hydrophilic "R&R" chitin-binding domain (CBD). Western blotting showed that BmWCP4 was predominately expressed in the wing disc-containing epidermis during the late wandering and early pupal stages. The immunohistochemistry result showed that the BmWCP4 was mainly present in the wing disc tissues containing wing bud and trachea blast during day 2 of wandering stage. Recombinant full-length BmWCP4 protein, "R&R" CBD peptide (CBD), non-CBD peptide (BmWCP4-CBD^- ), four single site-directed mutated peptides (M₁ , M₂ , M₃ and M₄ ) and four-sites-mutated peptide (M_F ) were generated and purified, respectively, for in vitro chitin-binding assay. The results indicated that both the full-length protein and the "R&R" CBD peptide could bind with chitin, whereas the BmWCP4-CBD^- could not bind with chitin. The single residue mutants M₁ , M₂ , M₃ and M₄ reduced but did not completely abolish the chitin-binding activity, while four-sites-mutated protein M_F completely lost the chitin-binding activity. These data indicate that BmWCP4 protein plays a critical role by binding to the chitin filaments in the wing during larva-to-pupa transformation. The conserved aromatic amino acids are critical in the interaction between chitin and the cuticle protein.

Transcriptional response of mysid crustacean, Americamysis bahia, is affected by subchronic exposure to nonylphenol

Nonylphenol (NP) has been classified as an endocrine-disrupting chemical. In this study, we conducted mysid DNA microarray analysis with which has 2240 oligo DNA probes to observe differential gene expressions in mysid crustacean (Americamysis bahia) exposed to 1, 3, 10 and 30 μg/l of NP for 14 days. As a result, we found 31, 27, 39 and 68 genes were differentially expressed in the respective concentrations. Among these genes, the expressions of five particular genes were regulated in a similar manner at all concentrations of the NP exposure. So, we focused on one gene encoding cuticle protein, and another encoding cuticular protein analogous to peritrophins 1-H precursor. These genes were down-regulated by NP exposure in a dose-dependent manner, and it suggested that they were related in a reduction of the number of molting in mysids. Thus, they might become useful molecular biomarker candidates to evaluate molting inhibition in mysids.

Mutation of a Cuticle Protein Gene, BmCPG10, Is Responsible for Silkworm Non-Moulting in the 2nd Instar Mutant

In the silkworm, metamorphosis and moulting are regulated by ecdysone hormone and juvenile hormone. The subject in the present study is a silkworm mutant that does not moult in the 2^nd instar (nm2). Genetic analysis indicated that the nm2 mutation is controlled by a recessive gene and is homozygous lethal. Based on positional cloning, nm2 was located in a region approximately 275 kb on the 5^th linkage group by eleven SSR polymorphism markers. In this specific range, according to the transcriptional expression of thirteen genes and cloning, the relative expression level of the BmCPG10 gene that encodes a cuticle protein was lower than the expression level of the wild-type gene. Moreover, this gene’s structure differs from that of the wild-type gene: there is a deletion of 217 bp in its open reading frame, which resulted in a change in the protein it encoded. The BmCPG10 mRNA was detectable throughout silkworm development from the egg to the moth. This mRNA was low in the pre-moulting and moulting stages of each instar but was high in the gluttonous stage and in newly exuviated larvae. The BmCPG10 mRNA showed high expression levels in the epidermis, head and trachea, while the expression levels were low in the midgut, Malpighian tubule, prothoracic gland, haemolymph and ventral nerve cord. The ecdysone titre was determined by ELISA, and the results demonstrated that the ecdysone titre of nm2 larvae was lower than that of the wild-type larvae. The nm2 mutant could be rescued by feeding 20-hydroxyecdysone, cholesterol and 7—dehydrocholesterol (7dC), but the rescued nm2 only developed to the 4^th instar and subsequently died. The moulting time of silkworms could be delayed by BmCPG10 RNAi. Thus, we speculated that the mutation of BmCPG10 was responsible for the silkworm mutant that did not moult in the 2^nd instar.

Cuticular protein and transcription factor genes expressed during prepupal-pupal transition and by ecdysone pulse treatment in wing discs of Bombyx mori

We aimed to understand the underlying mechanism that regulates successively expressed cuticular protein (CP) genes around pupation in Bombyx mori. Quantitative PCR was conducted to clarify the expression profile of CP genes and ecdysone-responsive transcription factor (ERTF) genes around pupation. Ecdysone pulse treatment was also conducted to compare the developmental profiles and the ecdysone induction of the CP and ERTF genes. Fifty-two CP genes (RR-1 13, RR-2 18, CPG 8, CPT 3, CPFL 2, CPH 8) in wing discs of B. mori were examined. Different expression profiles were found, which suggests the existence of a mechanism that regulates CP genes. We divided the genes into five groups according to their peak stages of expression. RR-2 genes were expressed until the day of pupation and RR-1 genes were expressed before and after pupation and for longer than RR-2 genes; this suggests different construction of exo- and endocuticular layers. CPG, CPT, CPFL and CPH genes were expressed before and after pupation, which implies their involvement in both cuticular layers. Expression profiles of ERTFs corresponded with previous reports. Ecdysone pulse treatment showed that the induction of CP and ERTF genes in vitro reflected developmental expression, from which we speculated that ERTFs regulate CP gene expression around pupation.

20-Hydroxyecdysone (20E) Primary Response Gene E93 Modulates 20E Signaling to Promote Bombyx Larval-Pupal Metamorphosis

As revealed in a previous microarray study to identify genes regulated by 20-hydroxyecdysone (20E) and juvenile hormone (JH) in the silkworm, Bombyx mori, E93 expression in the fat body was markedly low prior to the wandering stage but abundant during larval-pupal metamorphosis. Induced by 20E and suppressed by JH, E93 expression follows this developmental profile in multiple silkworm alleles. The reduction of E93 expression by RNAi disrupted 20E signaling and the 20E-induced autophagy, caspase activity, and cell dissociation in the fat body. Reducing E93 expression also decreased the expression of the 20E-induced pupal-specific cuticle protein genes and prevented growth and differentiation of the wing discs. Importantly, the two HTH domains in E93 are critical for inducing the expression of a subset of 20E response genes, including EcR, USP, E74, Br-C, and Atg1. By contrast, the LLQHLL and PLDLSAK motifs in E93 inhibit its transcriptional activity. E93 binds to the EcR-USP complex via a physical association with USP through its LLQHLL motif; and this association is enhanced by 20E-induced EcR-USP interaction, which attenuates the transcriptional activity of E93. E93 acts through the two HTH domains to bind to GAGA-containing motifs present in the Atg1 promoter region for inducing gene expression. In conclusion, E93 transcriptionally modulates 20E signaling to promote Bombyx larval-pupal metamorphosis.

Transcriptomic analysis of developmental features of Bombyx mori wing disc during metamorphosis

Background

Wing discs of B. mori are transformed to pupal wings during the larva-to-pupa metamorphosis with dramatic morphological and structural changes. To understand these changes at a transcriptional level, RNA-seq of the wing discs from 6-day-old fifth instar larvae (L5D6), prepupae (PP) and pupae (P0) was performed.

Results

In total, 12,254 transcripts were obtained from the wing disc, out of which 5,287 were identified to be differentially expressed from L5D6 to PP and from PP to P0. The results of comprehensive analysis of RNA-seq data showed that during larvae-to-pupae metamorphosis, many genes of 20E signaling pathway were up-regulated and those of JH signaling pathway were down-regulated. Seventeen transcription factors were significantly up-regulated. Cuticle protein genes (especially wing cuticle protein genes), were most abundant and significantly up-regulated at P0 stage. Genes responsible for the degradation and de novo synthesis of chitin were significantly up-regulated. There were A and B two types of chitin synthases in B. mori, whereas only chitin synthase A was up-regulated. Both trehalose and D-fructose, which are precursors of chitin synthesis, were detected in the hemolymph of L5D6, PP and P0, suggesting de novo synthesis of chitin. However, most of the genes that are related to early wing disc differentiation were down-regulated.

Conclusions

Extensive transcriptome and DGE profiling data of wing disc during metamorphosis of silkworm have been generated, which provided comprehensive gene expression information at the transcriptional level. These results implied that during the larva-to-pupa metamorphosis, pupal wing development and transition might be mainly controlled by 20E signaling in B. mori. The 17 up-regulated transcription factors might be involved in wing development. Chitin required for pupal wing development might be generated from both degradation of componential chitin and de novo synthesis. Chitin synthase A might be responsible for the chitin synthesis in the pupal wing, while both trehalose and D-fructose might contribute to the de novo synthesis of chitin during the formation of pupal wing.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-820) contains supplementary material, which is available to authorized users.

Cloning, expression patterns, and preliminary characterization of AccCPR24, a novel RR-1 type cuticle protein gene from Apis cerana cerana

Cuticular proteins (CPs) are key components of insect cuticle, a structure that plays a pivotal role in insect development and defense. In this study, we cloned the full-length cDNA of a CP gene from Apis cerana cerana (AccCPR24). An amino acid sequence alignment indicated that AccCPR24 contains the conserved Rebers and Riddiford consensus sequence and shares high similarity with the genes from other hymenopteran insects. We then isolated the genomic DNA and found that the first intron, which is present in other CP genes, is absent in AccCPR24. Real-time quantitative polymerase chain reaction (qPCR) analysis revealed that AccCPR24 is highly expressed in the late pupal stage and midgut. Expression was inhibited by an exogenous ecdysteroid in vitro but was enhanced by this hormone in vivo; environmental stressors, such as heavy metals and pesticides, also influenced gene expression. In addition, a disc diffusion assay showed that AccCPR24 enhanced the ability of bacterial cells to resist multiple stresses. We infer from our results that AccCPR24 acts in honeybee development and in protecting these insects from abiotic stresses.

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.

Effects of BmKIT 3 R gene transfer on pupal development of Bombyx mori Linnaeus using a Gal4/UAS binary transgenic system

The pupal stage of the silkworm Bombyx mori Linnaeus lasts for approximately two weeks. However, prolongation of pupal duration would reduce the labor required to process and dry fresh cocoons. This study investigated the effects of BmKIT(3)(R) gene (from the Chinese scorpion Buthus martensii Karsch) transfer on the pupal development of B. mori using a Gal4/UAS binary transgenic system. Gal4 driven by a pupa-specific promoter BmWCP4 (from a B. mori wing-cuticle protein gene) or PDP (from a B. mori cocoonase gene), and BmKIT(3)(R) driven by a UAS cis-acting element were used to construct novel piggyBac-derived plasmids containing a neomycin-resistance gene (neo) controlled by the Bombyx mori nucleopolyhedrovirus (BmNPV) ie-1 (immediate-early gene) promoter and a green fluorescent protein gene (gfp) under the control of the B. mori actin 3 (A3) promoter. The vector was transferred into silkworm eggs by sperm-mediated gene transfer. Transgenic silkworms were produced after screening for neo and gfp genes, and gene transfer was verified by polymerase chain reaction and dot-blot hybridization. The larval development of the hybrid progeny of Gal4- and UAS-transgenic silkworms was similar to that of normal silkworms, but some pupae failed to metamorphose into moths, and the development of surviving pupae was arrested as a result of BmKIT(3)(R) expression. Moreover, Gal4 driven by the BmWCP4 promoter delayed pupal development more effectively than that driven by the PDP promoter in the Gal4/UAS binary transgenic system. Pupal durations of hybrid transgenic silkworm progeny with BmWCP4 and PDP promoters were approximately 5, 2, and 4 days longer, respectively, compared to corresponding normal silkworms, BmWCP4/Gal4, and UAS/BmKIT(3)(R) transgenic silkworms, respectively. These results suggest new avenues of research for prolonging the pupal duration of silkworms.

Determination of mRNA expression of DMRT93B, vitellogenin, and cuticle 12 in Daphnia magna and their biomarker potential for endocrine disruption

We explored the use of molecular genetic biomarkers for endocrine disruption in Daphnia magna after the exposure to fenoxycarb (FOC), a model juvenile hormone analog. For this purpose, the mRNA expression patterns of DMRT93B (DMRT, sex determination), cuticle 12 (CUT, molting), and vitellogenin (VTG, embryo development) were determined in D. magna. Furthermore, these results were compared with developmental abnormality and reproduction performance. The fold changes of CUT and VTG mRNA expression showed significant dose-response relationship with FOC exposure. Relative mRNA expressions of DMRT and CUT showed notable changes at as low as 1 ng/l FOC. After chronic exposure FOC significantly delayed the first day of reproduction and decreased the number of young and growth rate even at 10 ng/l FOC. A concentration-dependant trend in reproduction effect was also observed. Developmental abnormality such as poorly developed second antennae and curved or unextended shell spines were observed. These results suggest that the three mRNAs, i.e., DMRT, CUT, and VTG can be used as biomarkers of endocrine disrupting effects in D. magna.

Transcription factors BmPOUM2 and BmβFTZ-F1 are involved in regulation of the expression of the wing cuticle protein gene BmWCP4 in the silkworm, Bombyx mori

In Bombyx mori, the wing cuticle protein gene BmWCP4 is expressed specifically in the epidermis at the onset and mid-stage of pupation and is responsible for the formation of the pupal cuticle during the larval-pupal metamorphosis. The gene consists of four exons and three introns and is present as a single copy in the genome. Its expression was up-regulated by 20-hydroxyecdysone (20E) and the 20E-induced expression was suppressed by juvenile hormone (JH) III. The upstream regulatory sequence region of the BmWCP4 gene was cloned and the regulatory elements responsible for 20E induction were identified. Two cis-regulatory elements (CREs) bound by the transcription factors BmPOUM2 and BmβFTZ-F1 were identified that mediated 20E-regulated expression of this gene. An electrophoretic mobility shift assay detected two nuclear proteins isolated from the epidermis and the BmN cell line that specifically bound to the POU and βFTZ-F1 CREs, respectively. BmPOUM2 recombinant protein explicitly bound to the POU CRE. Developmental and 20E-induced expression of the BmWCP4, BmPOUM2 and BmβFTZ-F1 genes showed that BmPOUM2 and BmβFTZ-F1 were initially expressed, followed by BmWCP4. These data suggest that the 20E-induced expression of BmWCP4 is mediated by the transcription factors BmPOUM2 and BmβFTZ-F1 binding to their CREs in the regulatory sequence region of the BmWCP4 gene.

Ecdysone directly and indirectly regulates a cuticle protein gene, BMWCP10, in the wing disc of Bombyx mori

The hormonal regulation of cuticle protein genes is a good model to study the molecular mechanism of signaling by ecdysteroids, which initiates each of the major developmental transitions in insects. This study was conducted to clarify the regulation of the expression of an ecdysone-inducible cuticle protein gene, BMWCP10. Induction of the BMWCP10 transcript by ecdysone was partly inhibited in the presence of cycloheximide, which implies that the BMWCP10 promoter is directly and indirectly activated by ecdysone. Using electrophoretic mobility shift analysis and a competition experiment, we identified a putative ecdysone response element (EcRE1) located at positions -93 to -81 relative to the transcription start site. Site-directed mutagenesis of this site, followed by introduction into wing discs, dramatically abolished the reporter activity. This EcRE1 is necessary for the activation of the promoter by 20-hydroxyecdysone (20E) in the wing disc, since the mutation of EcRE1 caused loss of responsiveness to 20E. Collectively, the data obtained in our current and previous work indicate that ecdysone receptor and Broad-Complex Z2 (BR-Z2) are required for maximal BMWCP10 expression in wing disc.

Microarray analysis of the gene expression profile in the midgut of silkworm infected with cytoplasmic polyhedrosis virus

In order to obtain an overall view on silkworm response to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection, a microarray system comprising 22,987 oligonucluotide 70-mer probes was employed to compare differentially expressed genes in the midguts of BmCPV-infected and normal silkworm larvae. At 72 h post-inoculation, 258 genes exhibited at least 2.0-fold differences in expression level. Out of these, 135 genes were up-regulated, while 123 genes were down-regulated. According to gene ontology (GO), 140 genes were classified into GO categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates that 35 genes were involved in 10 significant (P<0.05) KEGG pathways. The expressions of genes related to valine, leucine, and isoleucine degradation, retinol metabolism, and vitamin B6 metabolism were all down-regulated. The expressions of genes involved in ribosome and proteasome pathway were all up-regulated. Quantitative real-time polymerase chain reaction was performed to validate the expression patterns of 13 selected genes of interest. The results suggest that BmCPV infection resulted in the disturbance of protein and amino acid metabolism and a series of major physiological and pathological changes in silkworm. Our results provide new insights into the molecular mechanism of BmCPV infection and host cell response.

The regulation of expression of insect cuticle protein genes

The exoskeleton of insects (cuticle) is an assembly of chitin and cuticle proteins. Its physical properties are determined largely by the proteins it contains, and vary widely with developmental stages and body regions. The genes encoding cuticle proteins are therefore good models to study the molecular mechanisms of signalling by ecdysteroids and juvenile hormones, which regulate molting and metamorphosis in insects. This review summarizes the studies of hormonal regulation of insect cuticle protein genes, and the recent progress in the analysis of the regulatory sequences and transcription factors important for their expression.

betaFTZ-F1 and Broad-Complex positively regulate the transcription of the wing cuticle protein gene, BMWCP5, in wing discs of Bombyx mori

The present study was undertaken to clarify the mechanism regulating cuticle protein gene expression. Expression of BMWCP5 was strong at around pupation and weak at the mid-pupal stage in wing tissues of Bombyx mori. We analyzed the upstream region of the BMWCP5 gene using a transient reporter assay with a gene gun system to identify the regulatory elements responsible for its unique expression pattern. We identified two betaFTZ-F1 binding sites to be important cis-acting elements for the transcription activation of the luciferase reporter gene by an ecdysone pulse. Site-directed mutagenesis of these sites, followed by introduction into wing discs, significantly decreased the reporter activity. We also found that the regions carrying the binding sites for the ecdysone-responsive factor BR-C Z4 (BR-Z4) were responsible for the hormonal enhancement of the reporter gene activity in wing discs. Mutation of the BR-Z4 binding sites decreased the reporter activity. The nuclear proteins that bound to these betaFTZ-F1 and BR-Z4 sites were identified by an electrophoretic mobility shift assay (EMSA). The results demonstrate for the first time that the BR-Z4 isoform can bind to the upstream region of the cuticle protein gene, BMWCP5, and activate its expression. The results also suggest that the BMWCP5 transcription is primarily regulated by the ecdysone pulse through betaFTZ-F1, and the stage-specific enhancement is brought about through BR-Z4.

Activation of BMWCP10 promoter and regulation by BR-C Z2 in wing disc of Bombyx mori

The cuticle protein gene BMWCP10 is transcriptionally upregulated by ecdysone during development. In the present study, using a transient reporter assay, the activity of various genomic segments at the 5'-flanking region of the BMWCP10 gene in driving gene expression and their involvement in ecdysone-mediated activation were assessed in the Bombyx wing disc. The promoter activity of BMWCP10 was responsive to 20-hydroxyecdysone (20E) in a dose-dependent manner, and the highest luciferase activity was observed in the presence of 2 microg/ml 20E. Furthermore, the upstream BMWCP10 promoter was activated by 20E in a stage-specific manner, and the 2.9-kb promoter contained essential elements for the temporal regulation of BMWCP10 in the Bombyx wing disc. Deletion studies revealed that the -598/-387 bp region was required for high-level transcription. In this region, a BR-C Z2 binding element was identified by electrophoretic mobility shift assay (EMSA). Site-directed mutagenesis of this element in the context of the 598-bp promoter fragment significantly decreased the reporter activity in response to ecdysone treatment. The results confirmed the role of BmBR-C Z2 in the transcription regulation of BMWCP10 and suggested the contribution of BmBR-C Z2 to BMWCP10 induction by 20E.

Genome-wide identification of cuticular protein genes in the silkworm, Bombyx mori

Many kinds of cuticular proteins are found in a single insect species and their numbers and features are diversified among insects. Because there are so many cuticular proteins and so much sequence variation among them, an overview of cuticular protein gene is needed. Recently, a complete silkworm genome sequence was obtained through the integration of data from two whole genome sequence projects performed independently in 2004. To identify cuticular protein genes in the silkworm Bombyx mori exhaustively, we searched both the Bombyx whole genome sequence as well as various EST libraries, and found 220 putative cuticular protein genes. We also revised the annotation of the gene model, and named each identified cuticular protein based on its motif. The phylogenetic tree of cuticular protein genes among B. mori, Drosophila melanogaster, and Apis mellifera revealed that duplicate cuticular protein clusters have evolved independently among insects. Comparison of EST libraries and northern blot analyses showed that the tissue- and stage-specific expression of each gene was intricately regulated, even between adjacent genes in the same gene cluster. This study reveals many novel cuticular protein genes as well as insights into cuticular protein gene regulation.

From genome to proteome: great progress in the domesticated silkworm (Bombyx mori L.)

As the only truly domesticated insect, the silkworm not only has great economic value, but it also has value as a model for genetics and molecular biology research. Genomics and proteomics have recently shown vast potential to be essential tools in domesticated silkworm research, especially after the completion of the Bombyx mori genome sequence. This paper reviews the progress of the domesticated silkworm genome, particularly focusing on its genetic map, physical map and functional genome. This review also presents proteomics, the proteomic technique and its application in silkworm research.

Regulation of 20-hydroxyecdysone on the larval pigmentation and the expression of melanin synthesis enzymes and yellow gene of the swallowtail butterfly, Papilio xuthus

The swallowtail butterfly, Papilio xuthus, changes its larval body pattern dramatically during the fourth ecdysis. Cuticular pigmentation occurs with precise timing just before ecdysis. We previously found that the cuticular pigmentation was regulated by three melanin synthesis genes, tyrosine hydroxylase (TH), dopa decarboxylase (DDC), and ebony. We discovered that yellow is strongly expressed in the presumptive black markings earlier than TH and DDC. Because the ecdysis is triggered by 20-hydroxyecdysone (20E), the effects of 20E on the pigmentation and expression of the melanin synthesis genes were examined. Here, we established a method for the topical application of 20E to molting specimens, so that 20E has only a partial effect, resulting in successful ecdysis. When we applied 20E during the mid-phase of the molting period, when the 20E titer is declining, cuticular pigmentation was completely inhibited. The cessation of hormonal treatments caused delayed pigmentation. yellow expression was promoted by a high titer of 20E, whereas the expression of TH, DDC, and ebony was suppressed, suggesting that a decline in the 20E concentration is necessary for the induction of the expression of the latter three genes. These results indicate that cuticular pigmentation is controlled by the exposure to 20E and its removal.

Daphnia magna and ecotoxicogenomics: gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries

In the present study, the existing life stage-specific cDNA library was extended with energy- and molting-related genes using Suppression Subtractive Hybridization PCR and a microarray for the aquatic test organism Daphnia magna was created. A gene set of 2455 fragments was produced belonging to different pathways such as carbohydrate and lipid metabolism, O2 transport and heme metabolism, immune response, embryo development, cuticula metabolism and visual perception pathways. Using this custom microarray, gene expression profiles were generated from neonates exposed to three concentrations of the anti-ecdysteroidal fungicide fenarimol (0.5, 0.75, 1 microg/ml) during 48 h and 96 h. In total, 59 non-redundant genes were differentially expressed, of which more genes were down- than up-regulated. The gene expression data indicated a main effect on molting specific pathways. At the highest concentration, a set of proteolytic enzymes - including different serine proteases and carboxypeptidases - were induced whereas different cuticula proteins were down-regulated (48 h). Moreover, effects on embryo development were demonstrated at the gene expression as well as at the organismal level. The embryo development related gene vitellogenin was differentially expressed after 96 h of exposure together with a significant increase in embryo abnormalities in the offspring. This study suggests that this Daphnia magna microarray is of great further value for the elucidation of molecular mechanisms of toxicity and for the future development of specific biomarkers for hazard characterization.

Glycine-rich protein genes, which encode a major component of the cuticle, have different developmental profiles from other cuticle protein genes in Bombyx mori

Three types of GRP (glycine-rich proteins) cDNAs were identified in the EST database of Bombyx mori. These came from 21 ESTs in the W3-stage wing disc EST library. We named them BmGRP1, BmGRP2 and BmGRP3. BmGRP1 and BmGRP2 had 57% identity in deduced amino acid sequences. Expression of all BmGRPs was observed in the epidermis at the fourth molting stage, and in the wing at pupation and mid-pupal stage. It is suggested that BmGRPs contribute to larval, pupal and adult cuticles together with other cuticle proteins. Transcripts of BmGRP2 increased after 7 days of pupal stage. BmGRP2 is suggested to construct adult trachea in the wing. Hormonal response of BmGRPs was compared with that of another group of cuticular protein genes, BMWCPs. BmGRPs were induced by a pulse of 20E. Induction of BmGRP3 was observed in W1 wing discs in the presence of JHA which was added with 20E, whereas that of BMWCP2 was inhibited in the presence of JHA. Induction of BmGRPs was observed in the wing discs of V3 and W1 stages, while that of BMWCP2 was not observed in the V3 wing discs. These differences between BMWCPs and BmGRPs in response to hormones at different developmental stages are discussed.

Novel macula-like virus identified in Bombyx mori cultured cells

We identified a novel, 6,513-bp-long RNA, termed Bombyx mori macula-like latent virus (BmMLV) RNA, which abundantly expressed in B. mori cultured BmN cells. BmMLV RNA potentially encodes two proteins, putative RNA replicase and coat protein, which share structural features and sequence similarities with those of a plant RNA virus, the genus Maculavirus. Northern blot analysis showed that two transcripts were expressed in BmN cells: a 6.5-kb-long RNA, which contains both putative RNA replicase and coat protein genes, and a 1.2-kb-long RNA, which contains only a coat protein gene. Southern blot analysis showed that BmMLV RNA is not carried by the B. mori genome. RT-PCR analysis also revealed the presence of BmMLV RNA in several B. mori cell lines other than BmN cells, suggesting that BmMLV RNA latently exists in B. mori cultured cells. Infection studies showed that BmMLV virions were able to infect BmMLV-negative Spodoptera frugiperda Sf-9 cells and B. mori larvae. Electron microscopy and Northern blot analysis of a purified BmMLV revealed that isometric virions appear to be 28 to 30 nm in diameter and contain a 6.5-kb genomic RNA. These results showed that BmMLV is a novel macula-like virus infectious to and replicable in B. mori-derived cells.

Change in the expressed gene patterns of the wing disc during the metamorphosis of Bombyx mori

The present study was conducted to clarify what occurs during the metamorphosis of the imaginal disc in insects. To understand the metamorphosis on a molecular level, the changes in expression profiles in the imaginal disc during metamorphosis were investigated. For this purpose, we constructed cDNA libraries from four different stages of wing discs of Bombyx mori, sequenced about 1000 cDNAs randomly collected from each library, and constructed a database of expressed sequence tags (EST). The morphological changes and expression profiles from EST were compared during those four stages. Microarray analysis was applied to quantify the expression of each gene in each stage in order to confirm whether the expression of the genes identified from EST was induced by 20-hydroxyecdysone (20E) in a stage-specific manner. Wing discs showed dynamic morphogenesis in 4-5 days during the preparatory stage of metamorphosis, which was under the control of an ecdysteroid. Different expressed profiles were observed in each of the four different stages by comparison of each EST clone. These profiles reflected the morphological changes of the Bombyx wing disc during metamorphosis. The results of expression profiles from the four stages suggested that the V4 stage was cell proliferating; W0, proliferating and the beginning of differentiation; W2, morphologically changing; W3, cuticle secreting. Microarray analysis showed the effectiveness of its application on 20E induction of genes in wing discs. The wing disc of B. mori is an exceptionally suitable system for understanding the relationship between morphological changes and the distribution of mRNA.

The genetics and genomics of the silkworm, Bombyx mori

We review progress in applying molecular genetic and genomic technologies to studies in the domesticated silkworm, Bombyx mori, highlighting its use as a model for Lepidoptera, and in sericulture and biotechnology. Dense molecular linkage maps are being integrated with classical linkage maps for positional cloning and marker-assisted selection. Classical mutations have been identified by a candidate gene approach. Cytogenetic and sequence analyses show that the W chromosome is composed largely of nested full-length long terminal repeat retrotransposons. Z-chromosome-linked sequences show a lack of dosage compensation. The downstream sex differentiation mechanism has been studied via the silkworm homolog of doublesex. Expressed sequence tagged databases have been used to discover Lepidoptera-specific genes, provide evidence for horizontal gene transfer, and construct microarrays. Physical maps using large-fragment bacterial artificial chromosome libraries have been constructed, and whole-genome shotgun sequencing is underway. Germline transformation and transient expression systems are well established and available for functional studies, high-level protein expression, and gene silencing via RNA interference.

Expression profiling of baculovirus genes in permissive and nonpermissive cell lines

The baculoviruses Bombyx mori nucleopolyhedrovirus (BmNPV) and Autographa californica multicapsid NPV (AcMNPV) are highly homologous at the genomic level, but they have essentially nonoverlapping host ranges. In order to characterize baculovirus replication in permissive and nonpermissive cell lines, the expression profiles of baculovirus-specific genes (at 2, 6, 12, 24, 36, 48 or 72 h post-infection) were examined in BmN (BmNPV-permissive) or Sf-9 (AcMNPV-permissive) cells that were inoculated with BmNPV or AcMNPV. Surprisingly, nearly all of the 154 genes of AcMNPV appeared to be expressed in both Sf-9 and BmN cells although the peak expression levels of these genes were delayed by roughly 12 h in the nonpermissive BmN cells. In addition, the expression levels of the very late AcMNPV polyhedrin and p10 genes were dramatically reduced in BmN cells, which presumably led to the inability of AcMNPV to form polyhedral inclusion bodies in BmN cells. Nearly all of the 136 genes of BmNPV appeared to be expressed in BmN cells, however, BmNPV gene expression was dramatically reduced in Sf-9 cells inoculated with BmNPV. Experiments in which BmNPV DNAs were transfected to Sf-9 cells suggested that this dramatic reduction in gene expression was not the result of poor attachment, penetration or uncoating of the BmNPV virion into Sf-9 cells. In conclusion, we established a system to monitor global gene expression patterns during baculovirus infection in permissive and nonpermissive cell lines. This system was used to identify global trends in the transcription of baculovirus genes during productive and nonproductive infection.

A functional analysis of ACP-20, an adult-specific cuticular protein gene from the beetle Tenebrio: role of an intronic sequence in transcriptional activation during the late metamorphic period

A gene encoding the adult cuticular protein ACP-20 was isolated in Tenebrio. It consists of three exons interspersed by two introns, intron 1 interrupting the signal peptide. To understand the regulatory mechanisms of ACP-20 expression, ACP-20 promoter-luciferase reporter gene constructs were transfected into cultured pharate adult wing epidermis. Transfection assays needed the presence of 20-hydroxyecdysone, confirming that ACP-20 is up-regulated by ecdysteroids. Analysis of 5' deletion constructs revealed that three regions are necessary for high levels of transcription. Interaction experiments between intronic fragments and epidermal nuclear proteins confirmed the importance of intron 1 in ACP-20 transcriptional control, which results from the combined activity of regulatory cis-acting elements of the promoter and those of intron 1.

CYP306A1, a Cytochrome P450 Enzyme, Is Essential for Ecdysteroid Biosynthesis in the Prothoracic Glands of Bombyx and Drosophila

Ecdysteroids mediate a wide variety of developmental and physiological events in insects. In the postembryonic development of insects, ecdysone is synthesized in the prothoracic gland (PG). Although many studies have revealed the biochemical and physiological properties of the enzymes for ecdysteroid biosynthesis, most of the molecular identities of these enzymes have not been elucidated. Here we describe an uncharacterized cytochrome P450 gene, designated Cyp306a1, that is essential for ecdysteroid biosynthesis in the PGs of the silkworm Bombyx mori and fruit fly Drosophila melanogaster. Using the microarray technique for analyzing gene expression profiles in PG cells during Bombyx development, we identified two PG-specific P450 genes whose temporal expression patterns are correlated with changes in ecdysteroid titer during development. Amino acid sequence analysis showed that one of the Bombyx P450 genes belongs to the CYP306A1 subfamily. The temporal and spatial expression pattern of the Drosophila Cyp306a1 homolog is essentially the same as that of Bombyx Cyp306a1. We also found that Drosophila Cyp306a1 is disrupted in the phantom (phm) mutant, known also as the Halloween mutant. The morphological defects and decreased expression of ecdysone-inducible genes in phm suggest that this mutant cannot produce a high titer of ecdysone. Finally we demonstrate that S2 cells transfected with Cyp306a1 convert ketodiol to ketotriol via carbon 25 hydroxylation. These results strongly suggest that CYP306A1 functions as a carbon 25 hydroxylase and has an essential role in ecdysteroid biosynthesis during insect development.

Microarray analysis of gene expression profiles in wing discs of Bombyx mori during pupal ecdysis

Wing discs of holometabolous insects undergo dramatic morphological changes during metamorphosis, a process that is controlled by the actions of hundreds of gene products. Using cDNA microarrays constructed from 5086 ESTs, we monitored the gene expression profiles in wing discs of Bombyx mori at 13 time points during pupal ecdysis (day-4 fifth instar larvae to day-0 pupae). Of the 5086 ESTs on the microarrays, 2998 ESTs had significant signals in more than half of the experiments. Of the 2998 ESTs, genes represented by 683 ESTs showed significant perturbations during pupal ecdysis. Genes previously known to be induced during metamorphosis were identified, including E75, Urbain, Chitinases, and cuticle proteins. The expressions of genes represented by 59 ESTs induced at the beginning of wandering contained genes predicted to be involved in protein degradation, amino acid metabolism, and amino acid transport. The expressions of genes represented by 147 ESTs induced after the ecdysteroid peak had a role in cuticle synthesis, pigmentation, ion transport, protein transport, and transcription regulation. The expressions of genes represented by 85 ESTs repressed after the ecdysteroid peak were predicted to be involved in nucleotide and nucleic acid metabolism and cell cycle. This indicates the involvement of several biological processes in wing disc development during metamorphosis.

The construction of an EST database for Bombyx mori and its application

To build a foundation for the complete genome analysis of Bombyx mori, we have constructed an EST database. Because gene expression patterns deeply depend on tissues as well as developmental stages, we analyzed many cDNA libraries prepared from various tissues and different developmental stages to cover the entire set of Bombyx genes. So far, the Bombyx EST database contains 35,000 ESTs from 36 cDNA libraries, which are grouped into approximately 11,000 nonredundant ESTs with the average length of 1.25 kb. The comparison with FlyBase suggests that the present EST database, SilkBase, covers >55% of all genes of Bombyx. The fraction of library-specific ESTs in each cDNA library indicates that we have not yet reached saturation, showing the validity of our strategy for constructing an EST database to cover all genes. To tackle the coming saturation problem, we have checked two methods, subtraction and normalization, to increase coverage and decrease the number of housekeeping genes, resulting in a 5-11% increase of library-specific ESTs. The identification of a number of genes and comprehensive cloning of gene families have already emerged from the SilkBase search. Direct links of SilkBase with FlyBase and WormBase provide ready identification of candidate Lepidoptera-specific genes.