Molecular cloning, characterization and expression analysis of a miiuy croaker (Miichthys miiuy) CXC chemokine gene resembling the CXCL9/CXCL10/CXCL11.

Chemokines are a large family of chemotactic cytokines playing crucial roles in the innate immune response. In the present study, we report the cloning of a CXC chemokine gene resembling the closely related CXCL9/CXCL10/CXCL11 from the miiuy croaker Miichthys miiuy (MimiCXC). Both 5'-RACE and 3'-RACE were carried out in order to obtain the complete cDNA, which consists of a 73 bp 5'-UTR, a 369 bp open reading frame encoding 122 amino acids and a 715 bp 3'-UTR. The deduced MimiCXC contains a 19-aa signal peptide and a 103-aa mature polypeptide, which possesses the typical arrangement of four cysteines as found in other known CXC chemokines. It shares 4.8%-65.6% sequence identities to mammalian CXC chemokines and the highest sequence identity of 65.6% is between MimiCXC and CXCL10 chemokine. Three exons and two introns were identified in MimiCXC gene. The MimiCXC gene was constitutively expressed in all tissues tested, although at different levels. Upon induction with Vibrio anguillarum, MimiCXC gene expression was up-regulated in kidney and spleen, however, down-regulated in liver. These results indicate that MimiCXC may be involved in immune responses as well as homeostatic processes in miiuy croaker.

The complete mitochondrial genome of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae): genome characterization and phylogenetic considerations.

The complete mitochondrial genome sequence of the marbled rockfish Sebastiscus marmoratus (Scorpaeniformes, Scorpaenidae) was determined and phylogenetic analysis was conducted to elucidate the evolutionary relationship of the marbled rockfish with other Sebastinae species. This mitochondrial genome, consisting of 17301 bp, is highly similar to that of most other vertebrates, containing the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and one putative control region. Most of the genes are encoded on the H-strand, while the ND6 and seven tRNA genes (for Gln, Ala, Asn, Tyr, Ser (UCA), Glu, and Pro) are encoded on the L-strand. The reading frame of two pairs of genes overlapped on the same strand (the ATPase 8 and 6 genes overlapped by ten nucleotides; ND4L and ND4 genes overlapped by seven nucleotides). The possibly nonfunctional light-strand replication origin folded into a typical stem-loop secondary structure and a conserved motif (5'-GCCGG-3') was found at the base of the stem within the tRNA(Cys) gene. An extent termination-associated sequence (ETAS) and conserved sequence blocks (CSB) were identified in the control region, except for CSB-1; unusual long tandem repeats were found at the 3' end of the control region. Phylogenetic analyses supported the view that Sebastinae comprises four genera (Sebates, Hozukius, Helicolenus, and Sebasticus).

Sequence and expression analysis of cathepsin S gene in the miiuy croaker Miichthys miiuy.

Cathepsin S (CTSS) is a lysosomal cysteine endopeptides of the papain family. In the present study, CTSS gene was isolated from miiuy croaker (Miichthys miiuy) by expressed sequence tag analysis. The complete miiuy croaker CTSS cDNA comprised 1,454 nucleotides, including 56 bp at the 5'-UTR and 394 bp at the 3'-UTR. The open reading frame is 1,017 bp, and it encodes 338 amino acid residues with a calculated molecular weight of 37.1 kDa. BLAST analysis revealed that miiuy croaker cathepsin S shared high similarity with other known cathepsin S, and it showed significant homology with that of Japanese flounder, the degree of conservation of the miiuy croaker CTSS nucleotide sequence in comparison with other teleost species ranged from 63.0 to 81.7%. The N-linked glycosylation sites and catalytic sites are conserved in miiuy croaker CTSS. The CTSS transcript was expressed in all tissues examined; high levels of transcripts of CTSS were detected liver, muscle, and fin. These results provide important information for further exploring the roles of cathepsin S in antigen processing.

Molecular characterization of miiuy croaker CC chemokine gene and its expression following Vibrio anguillarum injection.

A CC chemokine gene was isolated from miiuy croaker (Miichthys miiuy) by expressed sequence tag analysis. The Mimi-CC cDNA contains an open reading frame of 429 nucleotides encoding 142 amino acid residues. The deduced Mimi-CC possesses the typical arrangement of four cysteines as found in other known CC chemokines (C³¹, C³², C56, and C7°). It shares 15.3%-37.4% identity to CC chemokines of mammal and teleost. Phylogenetic analysis showed that miiuy croaker was most closely related to Atlantic cod. Genomic analysis revealed that Mimi-CC gene consists of four exons and three introns, which is not typical of CC chemokines but resembles that of CXC chemokines. Real-time quantitative RT-PCR demonstrated that Mimi-CC is constitutively expressed in most tissues including lymphoid organs, and the highest expression of Mimi-CC transcripts in normal tissues was observed in muscle. Challenge of miiuy croaker with Vibrio anguillarum resulted in significant changes in the expression of CC chemokine transcripts in four tissues, especially in kidney and spleen.

Genomic sequences comparison and differential expression of miiuy croaker MHC class I gene, after infection by Vibrio anguillarum.

Major histocompatibility complex (MHC) has a central role in the adaptive immune system by presenting foreign peptide to the T-cell receptor. MHC gene family contains two main subgroups of immunologically active molecules. In order to study the molecular function and genomic characteristic of class I gene in teleost, the full lengths of MHC class Iα cDNA and genomic sequence were cloned from miiuy croaker (Miichthys miiuy). Seven exons and six introns were identified in miiuy croaker class Iα gene. This genomic structural feature of miiuy croaker is similar to that present in some fishes such as Japanese flounder and Atlantic salmon, but different from that present in some other fishes such as half-smooth tongue sole and channel catfish. The deduced amino acid sequence of class Iα gene had 25.9-54.1% identity with those of mammal and teleost. Real-time quantitative RT-PCR demonstrated that the MHC class Iα gene was ubiquitously expressed in 10 normal tissues; expression levels of MHC Iα gene were found first upregulated and then downregulated throughout the pathogenic bacteria infection process in spleen and kidney.

The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations.

Sciaenidae is a diverse, commercially important family. To understand the phylogenetic position of Collichthys niveatus in this family, we present its complete mitochondrial genome sequence. The genome is 16469 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Further sequencing for the complete control region was performed on Collichthys lucida. Although the conserved sequence domains such as extend termination associated sequence (ETAS) and conserved sequence block domains (CSB-1, CSB-2 and CSB-3) are recognized in the control region of the two congeneric species, the typical central conserved blocks (CSB-F, CSB-E and CSB-D) could not be detected, while they are found in Miichthys miiuy and Cynoscion acoupa of Sciaenidae and other Percoidei fishes. Phylogenetic analyses do not support the monophyly of Pseudosciaeniae, which is against with the morphological results. C. niveatus is most closely related to Larimichthys polyactis, and Collichthys and Larimichthys may be merged into one genus, based on the current datasets.