Drosophila cuticular proteins with the R&R Consensus: annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences

Pupal cuticle protein is abundant during early adult diapause in the mosquito Culex pipiens

Using a proteomics approach, we identified 13 differentially abundant proteins in heads of nondiapause, early, and mid-diapause Culex pipiens L. adult females. Three proteins that were more abundant during early diapause showed highest identities to pupal cuticle protein (PCP). The majority of less abundant proteins were involved in energy metabolism and cytoskeletonal reorganization. The increase of PCP in early diapause may be involved in enhancing stress resistance in the cuticle, a response akin to the general enhancement of stress resistance associated with overwintering insects. PCP also may have utility as a biomarker for early diapause in this species.

Annotation and analysis of low-complexity protein families of Anopheles gambiae that are associated with cuticle

We have characterized four new families of homologous genes of the mosquito, Anopheles gambiae, all of which include members shown by previous work to be cuticular in nature. The CPLCG, CPLCW, CPLCP, and CPLCA families (where CPLC is 'cuticular protein of low complexity') encode proteins with a high proportion of low-complexity sequence. We have also annotated the An. gambiae Tweedle genes, a family of cuticular protein genes first described in Drosophila, and additional ungrouped An. gambiae cuticular proteins identified by proteomics. Our annotations reveal multiple gene-family expansions that are specific to Diptera or Culicidae. The CPLCG and CPLCW families occur within a large and dynamic tandem array on chromosome 3R that includes sets of concertedly evolving genes. Most gene families exhibit two or more different expression profiles during development.

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.

Drosophila DHR38 nuclear receptor is required for adult cuticle integrity at eclosion

DHR38 is the only Drosophila member of the NR4A subclass of vertebrate nuclear receptors, which have been implicated in multiple biological pathways, including neuronal function, apoptosis, and metabolism. Although an earlier study identified three point mutations in DHR38, none of these were shown to be a null allele for the locus, leaving it unclear whether a complete loss of DHR38 function might uncover novel roles for the receptor. Here we show that a specific DHR38 null allele, DHR38(Y214), leads to fully penetrant pharate adult lethality, similar to the most severe phenotype associated with the EMS-induced mutations. DHR38(Y214) mutants display minor effects on ecdysone-regulated transcription at the onset of metamorphosis. In contrast, cuticle gene expression is significantly reduced in DHR38(Y214) mutant pupae. These studies define the essential functions of DHR38 and provide a genetic context for further characterization of its roles during development.

New insights into peritrophic matrix synthesis, architecture, and function

The peritrophic matrix (PM) is a chitin and glycoprotein layer that lines the invertebrate midgut. Although structurally different, it is functionally similar to the mucous secretions of the vertebrate digestive tract. The PM is a physical barrier, protecting the midgut epithelium from abrasive food particles, digestive enzymes, and pathogens infectious per os. It is also a biochemical barrier, sequestering and, in some cases, inactivating ingested toxins. Finally, the PM compartmentalizes digestive processes, allowing for efficient nutrient acquisition and reuse of hydrolytic enzymes. The PM consists of an organized lattice of chitin fibrils held together by chitin binding proteins. Glycans fill the interstitial spaces, creating a molecular sieve, the properties of which are dependent on the immediate ion content and pH. In this review, we have integrated recent structural and functional information to create a holistic model for the PM. We also show how this information may generate novel technologies for use in insect pest management.

The genome of a lepidopteran model insect, the silkworm Bombyx mori

Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of approximately 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a GLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific tRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes.

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.

Catalogue of epidermal genes: genes expressed in the epidermis during larval molt of the silkworm Bombyx mori

BACKGROUND

The insect cuticle is composed of various proteins and formed during the molt under hormonal regulation, although its precise composition and formation mechanism are largely unknown. The exhaustive catalogue of genes expressed in epidermis at the molt constitutes a massive amount of information from which to draw a complete picture of the molt and cuticle formation in insects. Therefore, we have catalogued a library of full-length cDNAs (designated epM) from epidermal cells during the last larval molt of Bombyx mori.

RESULTS

Of the 10,368 sequences in the library, we isolated 6,653 usable expressed sequence tags (ESTs), which were categorized into 1,451 nonredundant gene clusters. Seventy-one clusters were considered to be isoforms or premature forms of other clusters. Therefore, we have identified 1,380 putative genes. Of the 6,653 expressed sequences, 48% were derived from 92 cuticular protein genes (RR-1, 24; RR-2, 17; glycine-rich, 29; other classes, 22). A comparison of epM with another epidermal EST data set, epV3 (feeding stage: fifth instar, day 3), showed marked differences in cuticular protein gene. Various types of cuticular proteins are expressed in epM but virtually only RR-1 proteins were expressed in epV3. Cuticular protein genes expressed specifically in epidermis, with several types of expression patterns during the molt, suggest different types of responses to the ecdysteroid pulse. Compared with other Bombyx EST libraries, 13 genes were preferentially included in epM data set. We isolated 290 genes for proteins other than cuticular proteins, whose amino acid sequences retain putative signal peptides, suggesting that they play some role in cuticle formation or in other molting events. Several gene groups were also included in this data set: hormone metabolism, P450, modifier of cuticular protein structure, small-ligand-binding protein, transcription factor, and pigmentation genes.

CONCLUSION

We have identified 1,380 genes in epM data set and 13 preferentially expressed genes in epidermis at the molt. The comparison of the epM and other EST libraries clarified the totally different gene expression patterns in epidermis between the molting and feeding stages and many novel tissue- and stage-specifically expressed epidermal genes. These data should further our understanding of cuticle formation and the insect molt.

Extensive gene amplification and concerted evolution within the CPR family of cuticular proteins in mosquitoes

Annotation of the Anopheles gambiae genome has revealed a large increase in the number of genes encoding cuticular proteins with the Rebers and Riddiford Consensus (the CPR gene family) relative to Drosophila melanogaster. This increase reflects an expansion of the RR-2 group of CPR genes, particularly the amplification of sets of highly similar paralogs. Patterns of nucleotide variation indicate that extensive concerted evolution is occurring within these clusters. The pattern of concerted evolution is complex, however, as sequence similarity within clusters is uncorrelated with gene order and orientation, and no comparable clusters occur within similarly compact arrays of the RR-1 group in mosquitoes or in either group in D. melanogaster. The dearth of pseudogenes suggests that sequence clusters are maintained by selection for high gene-copy number, perhaps due to selection for high expression rates. This hypothesis is consistent with the apparently parallel evolution of compact gene architectures within sequence clusters relative to single-copy genes. We show that RR-2 proteins from sequence-cluster genes have complex repeats and extreme amino-acid compositions relative to single-copy CPR proteins in An. gambiae, and that the amino-acid composition of the N-terminal and C-terminal sequence flanking the chitin-binding consensus region evolves in a correlated fashion.

Proteomic analysis of the honey bee worker venom gland focusing on the mechanisms of protection against tissue damage

Honey bee workers use venom for the defence of the colony and themselves when they are exposed to dangers and predators. It is produced by a long thin, convoluted, and bifurcated gland, and consists of several toxic proteins and peptides. The present study was undertaken in order to identify the mechanisms that protect the venom gland secretory cells against these harmful components. Samples of whole venom glands, including the interconnected reservoirs, were separated by two-dimensional gel electrophoresis and the most abundant protein spots were subjected to mass spectrometric identification using MALDI TOF/TOF-MS and LC MS/MS. This proteomic study revealed four antioxidant enzymes: CuZn superoxide dismutase (SOD1), glutathione-S-transferase sigma 1 isoform A (GSTS1), peroxiredoxin 2540 (PXR2540) and thioredoxin peroxidase 1 isoform A (TPX1). Although glutathione-S-transferase (GST) has also been associated with xenobiotic detoxification, the protein we found belongs to the GST Sigma class which is known to protect against oxidative stress only. Moreover, we could demonstrate that the GST and SOD activity of the venom gland was low and moderate, respectively, when compared to other tissues from the adult honey bee. Several proteins involved in other forms of stress were likewise found but it remains uncertain what their function is in the venom gland. In addition to major royal jelly protein 9 (MRJP9), already found in a previous proteomic study, we identified MRJP8 as second member of the MRJP protein family to be associated with the venom gland. Transcripts of both MRJPs were amplified and sequenced. Two endocuticular structural proteins were abundantly present in the 2D-gel and most probably represent a structural component of the epicuticular lining that protects the secretory cells from the toxins they produce.

Developmental expression patterns of cuticular protein genes with the R&R Consensus from Anopheles gambiae

CPR proteins are the largest cuticular protein family in arthropods. The whole genome sequence of Anopheles gambiae revealed 156 genes that code for proteins with the R&R Consensus and named CPRs. This protein family can be divided into RR-1 and RR-2 subgroups, postulated to contribute to different regions of the cuticle. We determined the temporal expression patterns of these genes throughout post-embryonic development by means of real-time qRT-PCR. Based on expression profiles, these genes were grouped into 21 clusters. Most of the genes were expressed with sharp peaks at single or multiple periods associated with molting. Genes coding for RR-1 and RR-2 proteins were found together in several co-expression clusters. Twenty-five genes were expressed exclusively at one metamorphic stage. Five out of six X-linked genes showed equal expression in males and females, supporting the presence of a gene dosage compensation system in A. gambiae. Many RR-2 genes are organized into sequence clusters whose members are extremely similar to each other and generally closely associated on a chromosome. Most genes in each sequence cluster are expressed with the same temporal expression pattern and at the same level, suggesting a shared mechanism to regulate their expression.

Annotation and analysis of a large cuticular protein family with the R&R Consensus in Anopheles gambiae

BACKGROUND

The most abundant family of insect cuticular proteins, the CPR family, is recognized by the R&R Consensus, a domain of about 64 amino acids that binds to chitin and is present throughout arthropods. Several species have now been shown to have more than 100 CPR genes, inviting speculation as to the functional importance of this large number and diversity.

RESULTS

We have identified 156 genes in Anopheles gambiae that code for putative cuticular proteins in this CPR family, over 1% of the total number of predicted genes in this species. Annotation was verified using several criteria including identification of TATA boxes, INRs, and DPEs plus support from proteomic and gene expression analyses. Two previously recognized CPR classes, RR-1 and RR-2, form separate, well-supported clades with the exception of a small set of genes with long branches whose relationships are poorly resolved. Several of these outliers have clear orthologs in other species. Although both clades are under purifying selection, the RR-1 variant of the R&R Consensus is evolving at twice the rate of the RR-2 variant and is structurally more labile. In contrast, the regions flanking the R&R Consensus have diversified in amino-acid composition to a much greater extent in RR-2 genes compared with RR-1 genes. Many genes are found in compact tandem arrays that may include similar or dissimilar genes but always include just one of the two classes. Tandem arrays of RR-2 genes frequently contain subsets of genes coding for highly similar proteins (sequence clusters). Properties of the proteins indicated that each cluster may serve a distinct function in the cuticle.

CONCLUSION

The complete annotation of this large gene family provides insight on the mechanisms of gene family evolution and clues about the need for so many CPR genes. These data also should assist annotation of other Anopheles genes.