Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels

The Acute and Chronic Effects of a Sediment-Bound Synthetic Musk, Galaxolide, on Hyalella azteca, Chironomus dilutus, and Lumbriculus variegatus

Galaxolide is one of the most frequently used synthetic polycyclic musks on the market and is commonly detected in aquatic waterways. Previous studies have mainly evaluated the toxicity of this emerging contaminant using water-only exposures; however, its high Log K_ow (5.9) suggests that this compound is likely to partition to sediments. Three benthic invertebrates, Chironomus dilutus, Hyalella azteca, and Lumbriculus variegatus, were exposed to sediment-bound Galaxolide using both acute (10 d; survival) and chronic (28 d; survival and growth) bioassays. The acute and chronic LC50s for Galaxolide ranged from 238 to 736 mg/kg sediment (2400-7430 µg/g organic carbon [OC]) for all three species, which were above concentrations commonly detected in the environment (< 2.5 mg/kg). Growth effects (i.e., weight and/or length) were noted in two of the three organisms (with C. dilutus being the exception); however, these effects were also noted at concentrations above those that are environmentally relevant. Molecular level evaluations were conducted with surviving L. variegatus and C. dilutus collected from treatments near the LC50 value. Markers of oxidative stress (glutathione-s-transferase) and endocrine disruption (estrogen-related receptor) in C. dilutus were significantly decreased in the treatment group compared to controls by 0.7-fold and 1.9-fold, respectively. Although acute and chronic effects were largely absent at environmentally relevant concentrations, changes in endocrine response suggest that more sensitive endocrine-based endpoints, such as emergence (for C. dilutus) and molting (for H. azteca), are needed to ensure that the risk of this emerging contaminant is low at environmentally relevant concentrations.

Profilin is associated with transcriptionally active genes

We have raised antibodies against the profilin of Chironomus tentans to study the location of profilin relative to chromatin and to active genes in salivary gland polytene chromosomes. We show that a fraction of profilin is located in the nucleus, where profilin is highly concentrated in the nucleoplasm and at the nuclear periphery. Moreover, profilin is associated with multiple bands in the polytene chromosomes. By staining salivary glands with propidium iodide, we show that profilin does not co-localize with dense chromatin. Profilin associates instead with protein-coding genes that are transcriptionally active, as revealed by co-localization with hnRNP and snRNP proteins. We have performed experiments of transcription inhibition with actinomycin D and we show that the association of profilin with the chromosomes requires ongoing transcription. However, the interaction of profilin with the gene loci does not depend on RNA. Our results are compatible with profilin regulating actin polymerization in the cell nucleus. However, the association of actin with the polytene chromosomes of C. tentans is sensitive to RNase, whereas the association of profilin is not, and we propose therefore that the chromosomal location of profilin is independent of actin.

Analysis of expressed sequence tags and characterization of a novel gene, Slmg7, in the midgut of the common cutworm, Spodoptera litura

BACKGROUND

Out of total 3,081 assembled expressed sequence tags (ESTs) sequences representing 6,815 high-quality ESTs identified in three cDNA libraries constructed with RNA isolated from the midgut of Spodoptera litura, 1,039 ESTs showed significant hits and 1,107 ESTs did not show significant hits in BLAST searches. It is of interest to clarify whether or not these ESTs that did not show hits function in S. Litura.

RESULTS

Twenty "no-hit" ESTs containing at least one putative open reading frame were selected for further expression analysis. The results from northern blot analysis showed that six of the selected ESTs are expressed in the larval midgut of this insect at different levels, suggesting that these ESTs represent true mRNA products, whereas the other 14 ESTs could not be detected. Homologues of the four larval midgut-predominant genes (Slmg2, Slmg7, Slmg9 and Slmg17) were detected in the genomes of other lepidopteran insects but not in Drosophila melanogaster. A novel gene, Slmg7, is expressed at a high level specifically in the midgut during each of the larval stages. Slmg7 is a single copy gene and encodes a 143-amino acids protein. The SLMG7 protein was localized to the cytoplasm of Spli-221 cells.

CONCLUSIONS

Six ESTs from the no hit list are transcribed into mRNA and are mainly expressed in the midgut of S. litura. Slmg7 is a novel gene that is localized to the cytoplasm.

Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective

OBJECTIVES

Chironomus riparius, a non-biting midge (Chironomidae, Diptera), is extensively used as a model organism in aquatic ecotoxicological studies, and considering the potential of C. riparius larvae as a bio-monitoring species, little is known about its genome sequences. This study reports the results of an Expressed Sequence Tags (ESTs) sequencing project conducted on C. riparius larvae using 454 pyrosequencing.

METHODS

To gain a better understanding of C. riparius transcriptome, we generated ESTs database of C. ripairus using pyrosequencing method.

RESULTS

Sequencing runs, using normalized cDNA collections from fourth instar larvae, yielded 20,020 expressed sequence tags, which were assembled into 8,565 contigs and 11,455 singletons. Sequence analysis was performed by BlastX search against the National Center for Biotechnology Information (NCBI) nucleotide (nr) and uniprot protein database. Based on the gene ontology classifications, 24% (E-value ≤1(-5)) of the sequences had known gene functions, 24% had unknown functions and 52% of sequences did not match any known sequences in the existing database. Sequence comparison revealed 81% of the genes have homologous genes among other insects belonging to the order Diptera providing tools for comparative genome analyses. Targeted searches using these annotations identified genes associated with essential metabolic pathways, signaling pathways, detoxification of toxic metabolites and stress response genes of ecotoxicological interest.

CONCLUSIONS

The results obtained from this study would eventually make ecotoxicogenomics possible in a truly environmentally relevant species, such as, C. riparius.

The association of Brahma with the Balbiani ring 1 gene of Chironomus tentans studied by immunoelectron microscopy and chromatin immunoprecipitation

Many steps of gene expression take place during transcription, and important functional information can thus be obtained by determining the distribution of specific factors along a transcribed gene. The Balbiani ring (BR) genes of the dipteran Chironomus tentans constitute a unique system for mapping the association of specific factors along a eukaryotic gene using immuno-electron microscopy (immuno-EM). The chromatin immunoprecipitation (ChIP) technique has provided an alternative, more general method for studying the association of proteins with specific genomic sequences. The immuno-EM and the ChIP methods suffer from different limitations, and thus a combination of both is advantageous. We have established optimal conditions for ChIP on chromatin extracted from the salivary glands of C. tentans , and we have analyzed the association of the SWI/SNF chromatin remodelling factor Brahma (Brm) with the BR1 gene by combined immuno-EM and ChIP. We show that Brm is not restricted to the promoter of the BR1 gene but is also associated with sequences in the middle and distal portions of the gene, which suggests that Brm has additional roles apart from regulating transcription initiation.

Transcriptomic profiles of Drosophila melanogaster third instar larval midgut and responses to oxidative stress

Oligoarray analysis was used to determine the number and nature of genes expressed in third instar Drosophila melanogaster larval midguts. The majority of transcripts were associated with protein synthesis and metabolism. Serine proteases were the main proteolytic enzymes detected. Some 40% of the cytochrome P450 genes and 74% of the glutathione S transferases (GSTs) in the genome of D. melanogaster were observed to be expressed in the midgut by oligoarray analysis. We also identified potential transcription factor binding motifs (TFBMs) of P450s, GSTs and carboxylesterases. Many of the midgut-expressed GST genes contained candidate TFBMs homologous to TFBMs in mammals that have been associated with responses to oxidative stress. We also investigated the response of GSTs in the midgut to dietary H2O2, which showed a dosage-based differential response.

Exploring the midgut transcriptome of Phlebotomus papatasi: comparative analysis of expression profiles of sugar-fed, blood-fed and Leishmania-major-infected sandflies

Background

In sandflies, the blood meal is responsible for the induction of several physiologic processes that culminate in egg development and maturation. During blood feeding, infected sandflies are also able to transmit the parasite Leishmania to a suitable host. Many blood-induced molecules play significant roles during Leishmania development in the sandfly midgut, including parasite killing within the endoperitrophic space. In this work, we randomly sequenced transcripts from three distinct high quality full-length female Phlebotomus papatasi midgut-specific cDNA libraries from sugar-fed, blood-fed and Leishmania major-infected sandflies. Furthermore, we compared the transcript expression profiles from the three different cDNA libraries by customized bioinformatics analysis and validated these findings by semi-quantitative PCR and real-time PCR.

Results

Transcriptome analysis of 4010 cDNA clones resulted in the identification of the most abundant P. papatasi midgut-specific transcripts. The identified molecules included those with putative roles in digestion and peritrophic matrix formation, among others. Moreover, we identified sandfly midgut transcripts that are expressed only after a blood meal, such as microvilli associated-like protein (PpMVP1, PpMVP2 and PpMVP3), a peritrophin (PpPer1), trypsin 4 (PpTryp4), chymotrypsin PpChym2, and two unknown proteins. Of interest, many of these overabundant transcripts such as PpChym2, PpMVP1, PpMVP2, PpPer1 and PpPer2 were of lower abundance when the sandfly was given a blood meal in the presence of L. major.

Conclusion

This tissue-specific transcriptome analysis provides a comprehensive look at the repertoire of transcripts present in the midgut of the sandfly P. papatasi. Furthermore, the customized bioinformatic analysis allowed us to compare and identify the overall transcript abundance from sugar-fed, blood-fed and Leishmania-infected sandflies. The suggested upregulation of specific transcripts in a blood-fed cDNA library were validated by real-time PCR, suggesting that this customized bioinformatic analysis is a powerful and accurate tool useful in analysing expression profiles from different cDNA libraries. Additionally, the findings presented in this work suggest that the Leishmania parasite is modulating key enzymes or proteins in the gut of the sandfly that may be beneficial for its establishment and survival.

Characterization and expression during development and under environmental stress of the genes encoding ribosomal proteins L11 and L13 in Chironomus riparius

The Chironomus riparius gene sequences encoding ribosomal proteins L11 and L13 were characterized and their expression analysed during development, and under different types of cellular stress. A comparative and phylogenetic study among different orders of insects was carried out by analysis of sequence databases. L11 is highly conserved, both at the level of DNA and protein, and it shares over 90% amino acid identity with homologous sequences from other insects. Interestingly, the changes are mainly concentrated in the C-terminal domain of the protein. Conversely, L13 shows a lower degree of homology, around 60% amino acid identity, and the changes were dispersed throughout the length of the polypeptide. Surprisingly, when comparing L13 nucleotide sequences, only a very low or no homology was found even among diptera. These results are helpful for defining the structural and, therefore, evolutionary constraints of these proteins. Studies of gene expression by RT-PCR showed that they are differentially expressed in distinct stages of development. Both L11 and L13 were significantly upregulated during embryogenesis. The expression profiles of the transcripts were also analysed after a general stress, such as heat shock, as well as after a specific stress, such as acute cadmium treatment. In both conditions, no significant differences to controls were detected in L11 and L13 transcripts, in spite of the drastic changes observed in the stress-induced gene HSP70, and the inhibitory effect on rRNA transcription. These data confirm that both genes are equally robust against harmful environmental conditions, suggesting that they could be used as a control for environmentally responsive genes in Chironomus. Overall, our results show a coordinated expression of both the L11 and the L13 genes, but not a coordinated regulation of rRNA and ribosomal protein production.