Extensive expansion and diversification of the chemokine gene family in zebrafish: Identification of a novel chemokine subfamily CX

<p>Abstract</p> <p>Background</p> <p>The chemokine family plays important roles in cell migration and activation. In humans, at least 44 members are known. Based on the arrangement of the four conserved cysteine residues, chemokines are now classified into four subfamilies, CXC, CC, XC and CX3C. Given that zebrafish is an important experimental model and teleost fishes constitute an evolutionarily diverse group that forms half the vertebrate species, it would be useful to compare the zebrafish chemokine system with those of mammals. Prior to this study, however, only incomplete lists of the zebrafish chemokine genes were reported.</p> <p>Results</p> <p>We systematically searched chemokine genes in the zebrafish genome and EST databases, and identified more than 100 chemokine genes. These genes were CXC, CC and XC subfamily members, while no CX3C gene was identified. We also searched chemokine genes in pufferfish fugu and <it>Tetraodon</it>, and found only 18 chemokine genes in each species. The majority of the identified chemokine genes are unique to zebrafish or teleost fishes. However, several groups of chemokines are moderately similar to human chemokines, and some chemokines are orthologous to human homeostatic chemokines CXCL12 and CXCL14. Zebrafish also possesses a novel species-specific subfamily consisting of five members, which we term the CX subfamily. The CX chemokines lack one of the two N-terminus conserved cysteine residues but retain the third and the fourth ones. (Note that the XC subfamily only retains the second and fourth of the signature cysteines residues.) Phylogenetic analysis and genome organization of the chemokine genes showed that successive tandem duplication events generated the CX genes from the CC subfamily. Recombinant CXL-chr24a, one of the CX subfamily members on chromosome 24, showed marked chemotactic activity for carp leukocytes. The mRNA was expressed mainly during a certain period of the embryogenesis, suggesting its role in the zebrafish development.</p> <p>Conclusion</p> <p>The phylogenic and genomic organization analyses suggest that a substantial number of chemokine genes in zebrafish were generated by zebrafish-specific tandem duplication events. During such duplications, a novel chemokine subfamily termed CX was generated in zebrafish. Only two human chemokines CXCL12 and CXCL14 have the orthologous chemokines in zebrafish. The diversification observed in the numbers and sequences of chemokines in the fish may reflect the adaptation of the individual species to their respective biological environment.</p

Fingerprinting of hatchery haplotypes and acquisition of genetic information by whole-mitogenome sequencing of masu salmon, Oncorhynchus masou masou, in the Kase River system, Japan.

Stocking hatchery fish can lead to disturbance and extinction of the local indigenous population. Masu salmon Oncorhynchus masou masou, which is endemic across Japan, is a commonly stocked fish for recreational fishing in Japan. To conserve the indigenous resource, their genetic information is required, however, especially on Kyushu Island, the paucity of genetic information for this species has hindered proper resource management. Here, to identify hatchery mitogenome haplotypes of this species, stocked in the Kase River system, Kyushu Island, Japan, and to provide mitogenomic information for the resource management of this species, we analyzed the whole-mitogenome of masu salmon in this river system and several hatcheries potentially used for stocking. Whole-mitogenome sequencing clearly identified hatchery haplotypes, like fingerprints: among the 21 whole-mitogenome haplotypes obtained, six were determined to be hatchery haplotypes. These hatchery haplotypes were distributed in 13 out of 17 sites, suggesting that informal stocking of O. m. masou has been performed widely across this river system. The population of no hatchery haplotypes mainly belonged to clade I, a clade not found in Hokkaido Island in previous studies. Sites without hatchery haplotypes, and the non-hatchery haplotypes in clade I might be candidates for conservation as putative indigenous resources. The whole-mitogenome haplotype analysis also clarified that the same reared strain was used in multiple hatcheries. Analysis of molecular variance suggested that stocked hatchery haplotypes reduce the genetic variation among populations in this river system. It will be necessary to pay attention to genetic fluctuations so that the resources of this river system will not deteriorate further. The single nucleotide polymorphism data obtained here could be used for resource management in this and other rivers: e.g., for monitoring of informal stocking and stocked hatchery fishes, and/or putative indigenous resources

Identification of Immune Relevant Genes Using Expressed Sequence Tags (ESTs) in Common carp (Cyprinus carpio) Gills and Intestine

Identification of immune related molecules that function in fish organs is important for better understanding of the host defense mechanisms in fish. Expressed sequence tags (ESTs) represent the expressed portion of a genome, so they have proven to be useful tool for gene identification and confirmation of gene predictions. In the present study, a transcriptome analysis of carp gill and intestine EST libraries have been done as an attempt to identify the immune relevant genes expressed in those organs. A total of 2148 EST clones were generated from the two libraries: 1099 clones from gill library in which 632 clones were matched with functional proteins and 1049 clones from intestine library in which 559 clones were matched with functional proteins. The results of gill EST library has more frequency of innate immune–molecules containing MHC class I and MHC class II, which showed 18.3% of the immune molecules than those in intestine library which represents 10.8% only. The gill library also showed higher frequency of the cytokines and chemokine molecules and/or their receptors compared to the intestine library

The binding spectra of carp C3 isotypes against natural targets independent of the binding specificity of their thioester

The central component of complement, C3, plays a versatile role in innate immune defense of vertebrates and some invertebrates. A notable molecular characteristic of this component is an intra-chain thioester site that enables C3 to bind covalently to its target. It has been reported that the binding preference of the thioester to hydroxyl or amino groups is primarily defined by presence or absence of the catalytic histidine residue at position 1126 in human C3. In teleosts, a unique C3 (non-His type) has been found, in addition to the common His type C3. These distinct C3 isoforms may provide diversity in the target-binding attributable to the different binding specificities of their thioesters. In the present study, we examine the hypothesized correlation of the catalytic histidine with the binding spectra of two major C3 isotypes of carp towards various model and natural targets. The results reveal that non-His type C3, rather than His type C3, has a wider range of binding spectrum, despite the binding specificity of its thioester being limited to amino groups. It is therefore hypothesized that the binding spectra of C3 isotypes are not defined by the binding specificity of the thioester but is more affected by differences in microbe-associated molecular patterns that activate complement. Overall, the present data imply that non-His type C3 plays a significant role against bacterial infections in the fish defense system.Published version is available for viewing only. (See "Related DOI")「関連DOI」より出版社版の閲覧専用ページへリン