Fish calcitonin genes: primitive bony fish genes have been conserved in some lower vertebrates

Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

Subfunctionalization and evolution of liver-expressed antimicrobial peptide 2 (LEAP2) isoform genes in Siberian sturgeon (Acipenser baerii), a primitive chondrostean fish species

Two liver-expressed antimicrobial peptide 2 (LEAP2) isoforms were characterized in a primitive chondrostean sturgeon species, Acipenser baerii (Acipenseriformes). A. baerii LEAP2 isoforms represented essentially common structures shared by their vertebrate orthologs at both genomic (i.e., tripartite organization) and peptide (two conserved disulfide bonds) levels. A. baerii LEAP2 isoforms (designed LEAP2AB and LEAP2C, respectively) phylogenetically occupy the most basal position in the actinopterygian lineage and represent an intermediate character between teleostean and tetrapodian LEAP2s in the sequence alignment. Molecular phylogenetic analysis including LEAP2s from extant primitive fish species indicated that the evolutionary origin of ancestral LEAP2 in vertebrate groups should date back to earlier than the actinopterygian-sarcopterygian split. Gene expression assays under both basal and stimulated conditions suggested that A. baerii LEAP2 isoforms have undergone substantial subfunctionalization in tissue distribution pattern, developmental/ontogenetic expression, and immune responses. LEAP2AB showed a predominant liver expression, while LEAP2C exhibited the highest level of expression in the intestine. LEAP2C was a more dominantly expressed isoform during embryonic development and prelarval ontogeny. The LEAP2AB isoform is more closely associated with innate immune response to microbial invasion, compared with LEAP2C, as evidenced by results from LPS, poly(I:C) and Aeromonas hydrophila challenges. Synthetic mature peptides of LEAP2AB displayed a more potent antimicrobial activity than did LEAP2C. Data from this study could be useful not only to provide deeper insights into the evolutionary mechanism of LEAP2 in the actinopterygian lineage but also to better understand the innate immunity of this commercially important chondrostean species.

The Calcitonin/Calcitonin Gene-Related Peptide Family in Invertebrate Deuterostomes

Calcitonin (CT)/CT gene-related peptide (CGRP) family peptides (CT/CGRP family peptides) including CT, CGRP, adrenomedullin, amylin, and CT receptor-stimulating peptide have been identified from various vertebrates and perform a variety of important physiological functions. These peptides bind to two types of receptors including CT receptor (CTR) and CTR-like receptor (CLR). Receptor recognition of CT/CGRP family peptides is determined by the heterodimer between CTR/CLR and receptor activity-modifying protein (RAMP). Comparative studies of the CT/CGRP family have been exclusively performed in vertebrates from teleost fishes to mammals and strongly manifest that the CGRP family system containing peptides, their receptors, and RAMPs was derived from a common ancestor. In addition, CT/CGRP family peptides and their receptors are also identified and inferred from various invertebrate species. However, the evolutionary process of the CT/CGRP family from invertebrates to vertebrates remains enigmatic. In this review, I principally summarize the CT/CGRP family peptides and their receptors in invertebrate deuterostomes, highlighting the study of invertebrate chordates including ascidians and amphioxi. The CT/CGRP family peptide that shows similar molecular structure and function with that of vertebrate CT has been identified from ascidian, Ciona intestinalis. Amphioxus, Branchiostoma floridae also possessed three CT/CGRP family peptides, one CTR/CLR receptor, and three RAMP-like proteins. The molecular function of the receptor complex formed by amphioxus CTR/CLR and a RAMP-like protein was clarified. Moreover, CT/CGRP family peptides have been identified in the superphylum Ambulacraria, which is close to Chordata. Finally, this review provides potential hypotheses of the evolution of CGRP family peptides and their receptors from invertebrates to vertebrates.

Sardine procalcitonin amino-terminal cleavage peptide has a different action from calcitonin and promotes osteoblastic activity in the scales of goldfish

The nucleotide sequence of a sardine preprocalcitonin precursor has been determined from their ultimobranchial glands in the present study. From our analysis of this sequence, we found that sardine procalcitonin was composed of procalcitonin amino-terminal cleavage peptide (N-proCT) (53 amino acids), CT (32 amino acids), and procalcitonin carboxyl-terminal cleavage peptide (C-proCT) (18 amino acids). As compared with C-proCT, N-proCT has been highly conserved among teleosts, reptiles, and birds, which suggests that N-proCT has some bioactivities. Therefore, both sardine N-proCT and sardine CT were synthesized, and their bioactivities for osteoblasts and osteoclasts were examined using our assay system with goldfish scales that consisted of osteoblasts and osteoclasts. As a result, sardine N-proCT (10^-7M) activated osteoblastic marker enzyme activity, while sardine CT did not change. On the other hand, sardine CT (10^-9 to 10^-7M) suppressed osteoclastic marker enzyme activity, although sardine N-proCT did not influence enzyme activity. Furthermore, the mRNA expressions of osteoblastic markers such as type 1 collagen and osteocalcin were also promoted by sardine N-proCT (10^-7M) treatment; however, sardine CT did not influence their expressions. The osteoblastic effects of N-proCT lack agreement. In the present study, we can evaluate exactly the action for osteoblasts because our scale assay system is very sensitive and it is a co-culture system for osteoblasts and osteoclasts with calcified bone matrix. Both CT and N-proCT seem to influence osteoblasts and osteoclasts and promote bone formation by different actions in teleosts.

Platypus and opossum calcitonins exhibit strong activities, even though they belong to mammals

In mammalian assay systems, calcitonin peptides of non-mammalian species exhibit stronger activity than those of mammals. Recently, comparative analyses of a wide-range of species revealed that platypus and opossum, which diverged early from other mammals, possess calcitonins that are more similar in amino acid sequence to those of non-mammals than mammals. We herein determined whether platypus and opossum calcitonins exhibit similar biological activities to those of non-mammalian calcitonins using an assay of actin ring formation in mouse osteoclasts. We also compared the dose-dependent effects of each calcitonin on cAMP production in osteoclasts. Consistent with the strong similarities in their primary amino acid sequences, platypus and opossum calcitonins disrupted actin rings with similar efficacies to that of salmon calcitonin. Human calcitonin exhibited the weakest inhibitory potency and required a 100-fold higher concentration (EC₅₀=3×10^-11M) than that of salmon calcitonin (EC₅₀=2×10^-13M). Platypus and opossum calcitonins also induced cAMP production in osteoclast cultures with the same efficacies as that of salmon calcitonin. Thus, platypus and opossum calcitonins exhibited strong biological activities, similar to those of the salmon. In addition, phylogenetic analysis revealed that platypus and opossum calcitonins clustered with the salmon-type group but not human- or porcine-type group. These results suggest that platypus and opossum calcitonins are classified into the salmon-type group, in terms of the biological activities and amino acid sequences.

Fish calcitonin receptor has novel features

Calcitonin (CT), a 32-amino acid peptide, was initially isolated from fish. Fish CT has higher affinity to mammalian CT receptor (CTR), and has activity on calcium homeostasis. Therefore, fish CT has been used as a drug for the treatment of human bone diseases. However, the physiological roles of CT in fish as well as the characteristics of the fish CTR have not been clarified. Here, we cloned and characterized CTR from mefugu (Takifugu obscurus). Full-length cDNA sequencing revealed that mfCTR (mf, mefugu) consists of N-terminal four tandem putative hormone-binding domains (HBDs). Database mining showed that the multiple HBD-containing CTR is a common feature for some other fishes. Detailed pharmacological studies revealed that mfCTR generated cAMP in response to (1) fish CT, (2) calcitonin gene-related peptide (CGRP) in combinations with receptor activity-modifying proteins (mfRAMPs) 1 and 4, and (3) amylin in combinations with mfRAMPs 1-5. Unlike mammalian CTR, mfCTR showed dual affinity sites. Corresponding EC(50) values of those are in close proximity of the in vivo concentration of CT in fish. Analyses of the deletion mutants of mfCTR demonstrated that only the nearmost HBD to the first transmembrane region is functional to the ligands. Although, fish CT has higher affinity to the human CTR, human CT did not bind to the mfCTR. This is the first report that demonstrates the structure and property of fish receptor for CT, CGRP, and amylin. Fish CTR is the first example that has multiple HBD-like sequences.

The Multifunctional Fish Gill: Dominant Site of Gas Exchange, Osmoregulation, Acid-Base Regulation, and Excretion of Nitrogenous Waste

The fish gill is a multipurpose organ that, in addition to providing for aquatic gas exchange, plays dominant roles in osmotic and ionic regulation, acid-base regulation, and excretion of nitrogenous wastes. Thus, despite the fact that all fish groups have functional kidneys, the gill epithelium is the site of many processes that are mediated by renal epithelia in terrestrial vertebrates. Indeed, many of the pathways that mediate these processes in mammalian renal epithelial are expressed in the gill, and many of the extrinsic and intrinsic modulators of these processes are also found in fish endocrine tissues and the gill itself. The basic patterns of gill physiology were outlined over a half century ago, but modern immunological and molecular techniques are bringing new insights into this complicated system. Nevertheless, substantial questions about the evolution of these mechanisms and control remain.

Calcitonin-like immunoreactivity in serum and tissues of the bonnethead shark, Sphyrna tiburo

Calcitonin is a 32-amino acid peptide hormone that is best known for its actions in maintaining skeletal integrity and calcium homeostasis in mammals. Calcitonin also appears to function in regulating certain aspects of animal reproduction, but the nature of this role remains unclear, particularly in nonmammalian vertebrates. The present study investigated the relationship between calcitonin and reproduction in the bonnethead shark (Sphyrna tiburo), a well-studied member of the oldest living vertebrate group (i.e. elasmobranchs) known to possess a calcitonin-producing organ. Serum calcitonin concentrations were measured in 28 reproductively mature female S. tiburo using a heterologous enzyme-linked immunosorbent assay (ELISA) system. Sites of calcitonin immunoreactivity were detected in tissues of mature female and embryonic S. tiburo using immunocytochemistry. Significant increases in serum calcitonin concentrations of mature female S. tiburo occurred during early stages of gestation, a period characterized by yolk-dependency of developing embryos. Immunoreactive calcitonin was detected in the duodenum and pancreas of embryonic S. tiburo sampled during the same period. The results from this study suggest that calcitonin obtained from endogenous and/or maternal sources may function in regulating yolk digestion in embryonic S. tiburo. Therefore, the association between calcitonin and reproduction in elasmobranchs may reflect an important role for this hormone in embryonic development.

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.

The phylogenetic placement of chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.

Cloning of a calcitonin gene-related peptide from genomic DNA and its mRNA expression in flounder, Paralichthys olivaceus

A part of genomic DNA including the calcitonin gene-related peptide (CGRP) gene was cloned from flounder by the genome-walking method. The intron/exon boundary was predicted to occur exactly at the same position as in salmon. The 37-amino acid molecule coded by the region from the intron/exon boundary to the stop codon was preceded by a typical Lys-Arg cleavage signal and included a cleavage/amidation site common to the CGRP of other vertebrates. The predicted amino acid sequence of flounder CGRP had 78%, 78%, 78%, 81%, and 73-78% identity to that of salmon, cod, frog, chicken, and mammalian CGRPs, respectively. Among vertebrates, CGRP is more conserved than calcitonin (CT) because the identity of flounder CT to mammalian CTs is 31-50%. Expression analysis indicated that this hormone is synthesized in the brain, heart, intestine, testis, and ovary. Since we have previously shown that the CGRP receptor is expressed in these tissues, it is suggested that CGRP secreted from each tissue functions in a paracrine or autocrine manner.

Purification and characterization of insulin from the Australian lungfish, Neoceratodus forsteri (Dipnoi)

The Australian lungfish Neoceratodus forsteri, a facultative air breather, is considered to be the most primitive of the extant Dipnoi and so occupies a uniquely important evolutionary position in the transition from fish to tetrapods. Insulin was isolated from an extract of the pancreas of N. forsteri and its primary structure established as: A-Chain, Gly-Ile-Val-Glu-Gln-Cys-Cys-His-Thr-Pro(10)-Cys-Ser-Leu-Tyr-Gln-Leu-G lu-Asn-Tyr-Cys(20)-Asn-Glu-Thr-Glu; B-Chain, Ala-Ala-Val-Asn-Gln-His-Leu-Cys-Gly-Ser(10)-His-Leu-Val-Glu-Ala-Leu- Tyr-Phe-Val-Cys(20)-Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Leu-Pro- Lys(30)-Gly. This amino acid sequence is more similar to that of human insulin than to insulins from present-day amphibians. All the residues in human insulin that are considered to be important in receptor binding, dimerization, and hexamerization are conserved in lungfish insulin except for the substitution (Leu --> Phe) at the position corresponding to B17 in human insulin. Consistent with the assertion that the Dipnoi is a monophyletic group, insulins from N. forsteri and from the African lungfish Protopterus annectens contain extensions to the C-terminus of the A-chain and to the N-terminus of the B-chain that have not been found in other sarcopterygian species. However, the unusual amino acid substitutions found in insulin from P. annectens (e.g., GlyB21 --> Ala, GluB22 --> Asp, and ArgB23 --> Asn) are not present in N. forsteri insulin, suggesting that they occurred in the Protopterus lineage after divergence of the genera.