Molecular cloning and expression of caspase-3 in the protandrous cinnamon clownfish, Amphiprion melanopus, during sex change

Anemonefishes: A model system for evolutionary genomics

Anemonefishes are an iconic group of coral reef fish particularly known for their mutualistic relationship with sea anemones. This mutualism is especially intriguing as it likely prompted the rapid diversification of anemonefish. Understanding the genomic architecture underlying this process has indeed become one of the holy grails of evolutionary research in these fishes. Recently, anemonefishes have also been used as a model system to study the molecular basis of highly complex traits such as color patterning, social sex change, larval dispersal and life span. Extensive genomic resources including several high-quality reference genomes, a linkage map, and various genetic tools have indeed enabled the identification of genomic features controlling some of these fascinating attributes, but also provided insights into the molecular mechanisms underlying adaptive responses to changing environments. Here, we review the latest findings and new avenues of research that have led to this group of fish being regarded as a model for evolutionary genomics.

Identification and functional characterization of three caspases in Takifugu obscurus in response to bacterial infection

Caspases are evolutionarily conserved proteases, which are inextricably linked with the apoptosis and immune system in mammals. However, the expression pattern and function of some caspases remain largely unknown in pufferfish. In this study, three different pufferfish caspases (caspase-2 (Pfcasp-2), caspase-3 (Pfcasp-3), and caspase-8 (Pfcasp-8)) were characterized, and their expression patterns and functions were determined following Aeromonas hydrophila infection. The open reading frames of Pfcasp-2, -3, and -8 are 1,320, 846, and 1455 bp, respectively. Analyses of sequence alignment and phylogenetic tree showed that casp-2, -3, and -8 share 52%-65%, 33%-40%, 63%-78% overall sequence identities with those of other vertebrates, respectively. 3D structures of Pfcasp-2, -3, and -8 enjoy conservation in core area together, while each owns a distinctive profile. Comparisons of deduced amino acid sequences indicated that Pfcaspases possessed the caspase domain and conserved active sites like 'HG' and 'QACXG' (X for R or G). qRT-PCR results revealed that Pfcasp-2, -3, and -8 were expressed constitutively in a wide range of organs, especially in immune-related organs including whole blood and kidney. In vitro, the expressions of the three caspases (Pfcasp-2, 3, and -8) and immune-related genes (IgM and IL-8) were significantly up-regulated in kidney leukocytes after A. Hydrophila challenge and inhibitors treatment. The expressions of Pfcasp-2 and Pfcasp-3 were successfully inhibited in the kidney leukocytes by Ac-DEVD-CHO (an inhibitor to caspase-3), but the expression of Pfcasp-8 was not affected. Cellular localization analysis showed that the distribution of Pfcasp-2, -3, and -8 was in cytoplasm. Further, overexpression of Pfcasp-2, -3, or -8 was found to cause DNA damage and apoptosis, suggesting that three caspases may be related to apoptosis and mediate different apoptosis pathways in pufferfish. Moreover, the expressions of these caspases were also up-regulated in whole blood and kidney after A. hydrophila challenge, indicating their possible involvement in the immune response against A. hydrophia stimulation. Taken together, the results of this study suggest that the caspase-2,-3, and -8 may play an important role in the apoptosis and immune response in pufferfish.

First draft genome of an iconic clownfish species (Amphiprion frenatus)

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare groups to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for advancing studies of the particular life history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation.

Ca(2+) and caspases are involved in hydroxyl radical-induced apoptosis in erythrocytes of Jian carp (Cyprinus carpio var. Jian)

There are young erythrocytes and mature erythrocytes in the peripheral blood of fish. The present study explored the apoptosis in hydroxyl radical ((·)OH)-induced young and mature erythrocytes of Jian carp (Cyprinus carpio var. Jian). Carp erythrocytes from the peripheral blood were separated into the young fraction, the intermediate fraction and the mature fraction using fixed-angle centrifugation. The erythrocytes in three age fractions were treated with the caspase inhibitors (zVAD-fmk) in physiological carp saline (PCS) or Ca(2+)-free PCS in the presence of 40 μM FeSO4/20 μM H2O2. The results showed that the (·)OH-induced reactive oxygen species (ROS) generation, phosphatidylserine (PS) exposure and DNA fragmentation are caspase dependent in carp erythrocytes. Furthermore, the ROS generation, PS exposure and DNA fragmentation in the more young fraction are more dependent on the caspase activity. This suggested that the caspases are involved in the (·)OH-induced apoptosis in the young erythrocytes of fish. Results also indicated that Ca(2+) is involved in (·)OH-induced calpain activation, PS exposure and DNA fragmentation in carp erythrocytes. Moreover, the calpain activation, DNA fragmentation and PS exposure in the more mature fraction are more dependent on the levels of Ca(2+). This revealed that (·)OH-induced apoptosis is Ca(2+) dependent in the mature erythrocytes of fish. Taken together, there might be two apoptosis pathways in fish erythrocytes: one is the caspase-dependent apoptosis in the young erythrocytes and the other is the Ca(2+)-involved apoptosis in the mature erythrocytes.

Cadmium induces liver cell apoptosis through caspase-3A activation in purse red common carp (Cyprinus carpio)

Caspase-3, the essential effector caspase, plays a pivotal role during caspase-dependent apoptosis. In this study, we isolated and characterized caspase-3A gene from common carp. The common carp caspase-3A comprising 273 amino acids showed 71.8% sequence similarity and 59.3% sequence identity to human caspase-3. It exhibited an evolutionarily conserved structure of mammalian caspase-3 genes, including a pro-domain, a large subunit, a small subunit and other motifs such as the pentapeptide active-site motif (QACRG) and the putative cleavage sites at the aspartic acids. Phylogenetic analysis demonstrated that common carp caspase-3A formed a clade with cyprinid fish caspase-3. To assess whether caspase-3A is involved in cadmium (Cd)-induced cell apoptosis in common carp, a Cd exposure experiment was performed. TUNEL analysis showed that Cd triggered liver cell apoptosis; caspase-3A activity was markedly increased; its proenzyme level was significantly decreased, and the levels of its cleaved forms were markedly increased. However, real-time quantitative PCR analysis revealed that the mRNA transcript level of caspase-3A was not significantly elevated. Immunoreactivities were observed in the cytoplasm of hepatocytes by immunohistochemical detection. The findings indicates that Cd can trigger liver cell apoptosis through the activation of caspase-3A. Caspase-3A may play an essential role in Cd-induced apoptosis.