Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

Abstract

High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts.

Sodium salt medium-chain fatty acids andBacillus-based probiotic strategies to improve growth and intestinal health of gilthead sea bream (Sparus aurata)

“…Absorption of lipids occurs mostly in the first segments of fish intestines, where bile salts are secreted to hydrolyze triglycerides to free fatty-acids and glycerol ( Sundell & Rønnestad, 2011 ) resembling mammalian small intestines. In accordance, expression of fabp6 , involved in reabsorption of bile acids and exclusively expressed in mammalian ileums ( Besnard et al, 2002 ), can only be found in the posterior intestinal segment of GSB and other fish species ( Alves-Costa et al, 2008 ; Pérez-Sánchez et al, 2015 ; Calduch-Giner, Sitjà-Bobadilla & Pérez-Sánchez 2016 ). FABP2, involved in regulation of the intracellular concentration of free fatty acids, preferentially binds long-chain fatty acids (LCFAs) ( Lowe et al, 1987 ), but can also bind MCFAs ( Huang et al, 2002 ).…”

The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract

“…Similarly, over 1,900 DEGs (fold-change cutoff of 2) were observed between anterior-middle and posterior-intestinal segments (including the rectum) in a carnivorous fish, European sea bass ( Dicentrarchus labrax ) using a custom oligo microarray. 58 Using a cluster analysis of the DEGs, we extracted expression patterns that are characteristic of the three tissue types ( Supplementary Fig. S3 ).…”

“…4 ). Calduch-Giner et al 58 suggested that fish intestine transcriptomes are not static, but change spatially, seasonally and with diet. Since the samples of GI tract examined were obtained from cultured yellowtail maintained under the same conditions and sampled at the same time, our study suggests that the expression of proteolytic enzymes also varies between individuals, and that such differences may cause different physiological conditions in individuals.…”

Fish Transcriptomics: Applied to Our Understanding of Aquaculture

“…Apolipoproteins are vital in lipid transport and uptake in vertebrates and has been shown to be synthesized primarily in the intestine and liver of most teleost. As a caveat, it has been suggested that the fish intestine transcriptomes are plastic, in which they can change spatially, seasonally, and with diet (Calduch-Giner et al 2016). This provides a key detail of matching the available digestive enzymes present within the aquaculture species with the corresponding diet presented.…”