Differential transcriptome analysis of the common shrimp Crangon crangon: special focus on the nuclear receptors and RNAi-related genes.

The decapod Crangon crangon is one of the most valuable European fisheries commodities. Despite its economic importance, little sequence data is available for this shrimp species. In this paper, we report the transcriptome sequencing for five different stages of C. crangon (early embryo, late embryo, larva, female adults and male adults) and the annotation and stage-specific expression analysis of nuclear receptors (NRs) and RNA interference (RNAi)-related genes. The NRs are transcription factors that play an essential role in growth, development, cell differentiation, molting/metamorphosis and reproduction, while the RNAi-related genes are very important for internal gene expression regulation and in antiviral defense. We discovered a NR in the female C. crangon which is either a very rapidly evolved homolog of HR10, or a novel NR altogether. This new NR could act as a biological marker for sex determination as it is not expressed in male adults. Most RNAi-related genes were present in C. crangon, proving that the requirements for successful RNAi is present in this decapod shrimp. RNAi-based applications in Crangon such as its use in functional genomics or as antiviral therapeutics could become very important in the near future.

The heterodimeric ecdysteroid receptor complex in the brown shrimp Crangon crangon: EcR and RXR isoform characteristics and sensitivity towards the marine pollutant tributyltin.

Decapod crustaceans are characterized by multiple ecdysteroid receptor (EcR) and retinoid-X-receptor (RXR) isoforms, which likely exhibit variant dimerization and transactivation interactions. In the brown shrimp C. crangon we cloned C-terminally truncated CrcEcR and CrcRXR isoforms and isoforms exhibiting deletions within the hinge region. For the former, in silico modeling of the CrcEcR indicated that, where the conserved helices H10 and H11 of the ligand-binding domain (LBD) are missing, an alternative C-terminal α-helix repairs the ligand-binding pocket (LBP). The truncated CrcRXR isoforms lack a major part of the LBD (H4-H12), thereby compromising ligand binding and dimerization. Through an in vitro ecdysteroid responsive reporter assay, we showed that these natural receptor variations do not impair receptor functioning but probably alter the receptor dimerization preferences. By the same in vitro assay, using full-length CrcEcR and CrcRXR, the effect of tributyltin (TBT) on ecdysteroid-induced transactivation was evaluated. The transactivation by 10nM PonA was reduced with 64% by 20 nM TBT. In silico modeling confirmed that TBT fits in the full-length CrcRXR-LBD. Furthermore, semi-quantitative PCR indicated altered expression of CrcEcR and CrcRXR isoforms after in vivo acute exposure to TBT, especially in the ovaries.

Molecular aspects of lipid metabolism in the midgut gland of the brown shrimp Crangon crangon.

The brown shrimp, Crangon crangon, is well adapted to the variable environmental conditions in the southern North Sea. It is very abundant, has high reproduction rates, and holds a key position in coastal ecosystems. This species has very low lipid deposits in the midgut gland, suggesting that the main function of the midgut gland is metabolic turnover rather than energy storage. Based on seasonal gene expression studies and established transcriptome data, we investigated key components of lipid metabolic pathways. Gene expression of triacylglycerol lipase, phospholipase, and fatty acid desaturase were analyzed and compared with that of other digestive enzymes involved in lipid, carbohydrate, and protein catabolism. Our results suggest that gene expression of digestive enzymes involved in lipid metabolism is modulated by the lipid content in the midgut gland and is related to food availability. Brown shrimp seem to be capable of using cellular phospholipids during periods of food paucity but high energetic (lipid) requirements. Two of three isoforms of fatty acid binding proteins (FABPs) from the midgut gland involved in fatty acid transport showed specific mutations of the binding site. We hypothesize that the mutations in FABPs and deficiencies in anabolic pathways limit lipid storage capacities in the midgut gland of C. crangon. In turn, food utilization, including lipid catabolism, has to be efficient to fulfill the energetic requirements of brown shrimp.

Transcriptome analysis of the midgut gland of the brown shrimp Crangon crangon indicates high polymorphism in digestive enzymes.

Tolerance of organisms towards heterogeneous and variable environments is highly related to physiological flexibility. An effective strategy to enhance physiological flexibility is the expression of polymorphic enzymes. This seems to be the case in the brown shrimp Crangon crangon. It shows high reproduction rates, feeds opportunistically on endo- and epibenthic organisms, and is apparently well adapted to variable environmental conditions. Previous electrophoretic studies revealed a high level of polymorphism and no consistent phenotype of digestive enzymes between individuals. In order to understand the underlying biochemical processes, we carried out a transcriptome-based study of digestive enzymes of C. crangon. Detailed sequence analyses of triacylglycerol lipase, phospholipase A2, alpha amylase, chitinase, trypsin and cathepsin L were performed to identify putative isoforms. The number of isoforms, and thus the degree of polymorphism varied among enzymes: lipases and carbohydrases showed higher numbers of isoforms in enzymes that besides their extracellular function also have diverse intracellular functions. Furthermore, cysteine proteinases showed a lower polymorphism than serine proteinases. We suggest that the expression of enzyme isoforms improves the efficiency of C. crangon in gaining energy from different food sources.