Gene structure and promoter function of a teleost ribosomal protein: a tilapia (Oreochromis mossambicus) L18 gene

Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes

Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.

Identification of 5'-upstream region of pufferfish ribosomal protein L29 gene as a strong constitutive promoter to drive GFP expression in zebrafish

The genomic structure of Tetraodon fluviatilis L29 gene was determined and its promoter activity was analyzed in COS-1 cells and zebrafish embryos. The TfL29 gene comprises four exons and three introns, spanning approximately 1.7kb. The 5(')-upstream 2.2-kb of the first exon contains 10 E-boxes and many putative binding motifs for transcription factors GATA-1, AML-1a, c-Myb, Oct-1, CdxA, and NRF-2. Promoter activity assay showed that the distal 2.2-kb fragment not only had high luciferase activity in COS-1 cells, but also strong and ubiquitous GFP expression in a variety of tissues in zebrafish embryos. On the other hand, there are no TATA or CAAT boxes within a 300-bp region upstream from the transcription initiation site. Although this region has high luciferase activity in COS-1 cells, it is not sufficient to drive GFP expression in zebrafish embryos. In this proximal 300-bp region, there are two E-boxes, two CdxA sites, and one NRF-2 site that is immediately downstream of the transcription start site.

Application of comparative genomics in fish endocrinology

This review discusses the ways in which comparative genomics can contribute to the study of fish endocrinology. First, the phylogenetic position of fish and an overview of their specific endocrine systems are presented. The emphasis will be on teleosts because they are the most abundant fishes and because most data are available for this group. Second, the complexity of fish genomics is reviewed. With the vast array of genome sizes and ploidy levels, assignment of gene orthology is more difficult in fish, but this is an absolute prerequisite in functional analysis and it is important to be aware of such genome plasticity when cloning genes. The ease with which a gene is cloned at the genomic level is directly related to genome size and complexity, a factor that is not known in the majority of fish species. Finally, the methodology is presented along with specific examples of parathyroid hormone-related protein (PTHrP) (a previously unidentified hormone in fish), calcium-sensing receptor, and calcitonin (with a duplication of this particular ligand in Fugu rubripes). Preliminary data also suggest that there are further duplicated genes in the calcium regulatory system. Comparative genomics has provided a valuable approach for isolating and characterizing a range of fish genes involved in calcium regulation. However, for understanding the physiology and endocrine regulation of this system, particularly with regard to gene duplication, an alternative approach is required in which conventional endocrinology techniques will play a significant role.

Transgenic tilapia and the tilapia genome

The tilapia fish (Oreochromis niloticus) has an important place in the aquaculture of the developing world. It is also a very useful laboratory animal, and readily lends itself to the transgenic technology. Through the use of reporter genes, a range of potential gene promoters have been tested in tilapia, both through transient and stable expression of the reporter construct. Using the transgenic technology, growth enhanced lines of tilapia have been produced. These fish have no abnormalities and offer a considerable growth advantage for future exploitation. It is however crucial that transgenic fish, to be exploited in aquaculture, be sterile, and various methods of achieving sterility are considered. These include triploidy, gene knock out of crucial hormone encoding genes via homologous recombination, and knock down of the function of the same genes via ribozyme or antisense technologies. Transgenic tilapia also offer the potential for exploitation as biofactories in the production of valuable pharmaceutical products, and this is also discussed.

Gene structure of the carp fish ribosomal protein L41: seasonally regulated expression

The seasonal acclimatization of the carp fish demands physiological compensatory responses. The process involves profound nucleolar adjustments and remarkable changes in rRNA synthesis, which affect ribosomal biogenesis. We have documented that protein kinase CK2, whose activity is related to ribosomal protein L41 and the regulation of rRNA synthesis, was expressed in notably higher amounts in summer-acclimatized carp compared to the cold-season adapted fish. Thus, we approached the study of the functional genomics of carp L41 protein. We report the first cloning of a fish L41 gene encoding the highly conserved 25 amino acids, including approximately 1700 bp regulatory upstream region and the 3(') polyadenylation signal, plus the isolation and characterization of two different L41 cDNAs. We found a clear differential expression of L41, which follows the same pattern as protein kinase CK2beta that transcribes at higher levels in the summer-acclimatized carp than it does in the winter-adapted fish.