Cloning and sequence analysis of cDNA for the proteasome activator PA28-beta subunit of flounder (Paralichthys olivaceus)

Antigen Presentation and Autophagy in Teleost Adaptive Immunity

Infectious diseases are a burden for aquaculture. Antigen processing and presentation (APP) to the immune effector cells that fight pathogens is key in the adaptive immune response. At the core of the adaptive immunity that appeared in lower vertebrates during evolution are the variable genes encoding the major histocompatibility complex (MHC). MHC class I molecules mainly present peptides processed in the cytosol by the proteasome and transported to the cell surface of all cells through secretory compartments. Professional antigen-presenting cells (pAPC) also express MHC class II molecules, which normally present peptides processed from exogenous antigens through lysosomal pathways. Autophagy is an intracellular self-degradation process that is conserved in all eukaryotes and is induced by starvation to contribute to cellular homeostasis. Self-digestion during autophagy mainly occurs by the fusion of autophagosomes, which engulf portions of cytosol and fuse with lysosomes (macroautophagy) or assisted by chaperones (chaperone-mediated autophagy, CMA) that deliver proteins to lysosomes. Thus, during self-degradation, antigens can be processed to be presented by the MHC to immune effector cells, thus, linking autophagy to APP. This review is focused on the essential components of the APP that are conserved in teleost fish and the increasing evidence related to the modulation of APP and autophagy during pathogen infection.

Transcriptome Analysis of Paralichthys olivaceus Erythrocytes Reveals Profound Immune Responses Induced by Edwardsiella tarda Infection

Unlike mammalian red blood cells (RBCs), fish RBCs are nucleated and thus capable of gene expression. Japanese flounder (Paralichthys olivaceus) is a species of marine fish with important economic values. Flounder are susceptible to Edwardsiella tarda, a severe bacterial pathogen that is able to infect and survive in flounder phagocytes. However, the infectivity of and the immune response induced by E. tarda in flounder RBCs are unclear. In the present research, we found that E. tarda was able to invade and replicate inside flounder RBCs in both in vitro and in vivo infections. To investigate the immune response induced by E. tarda in RBCs, transcriptome analysis of the spleen RBCs of flounder challenged with E. tarda was performed. Six sequencing libraries were constructed, and an average of 43 million clean reads per library were obtained, with 85% of the reads being successfully mapped to the genome of flounder. A total of 1720 differentially expressed genes (DEGs) were identified in E. tarda-infected fish. The DEGs were significantly enriched in diverse Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially those associated with immunity, disease, and infection. Ninety-one key DEGs involved in 12 immune-related pathways were found to form extensive interaction networks. Twenty-one genes that constituted the hub of the networks were further identified, which were highly regulated by E. tarda and involved in a number of immune processes, notably pathogen recognition and signal transduction, antigen processing and presentation, inflammation, and splicing. These results provide new insights into the immune role of flounder RBCs during bacterial infection.

Transcriptome Analysis Shows That IFN-I Treatment and Concurrent SAV3 Infection Enriches MHC-I Antigen Processing and Presentation Pathways in Atlantic Salmon-Derived Macrophage/Dendritic Cells

Type I interferons (IFNs) have been shown to play an important role in shaping adaptive immune responses in addition to their antiviral properties in immune cells. To gain insight into the impact of IFN-I-induced pathways involved in early adaptive immune responses, i.e., antigen-presenting pathways, in an Atlantic salmon-derived (Salmo salar L.) macrophage cell line (TO-cells), we used a comparative de novo transcriptome analysis where cells were treated with IFN-I or kept untreated and concurrently infected with salmonid alphavirus subtype 3 (SAV3). We found that concurrent treatment of TO-cells with IFN-I and SAV3 infection (SAV3/IFN⁺) significantly enriched the major histocompatibility complex class I (MHC-I) pathway unlike the non-IFN-I treated TO-cells (SAV3/IFN⁻) that had lower expression levels of MHC-I pathway-related genes. Genes such as the proteasomal activator (PA28) and β-2 microglobulin (β2M) were only differentially expressed in the SAV3/IFN⁺ cells and not in the SAV3/IFN⁻ cells. MHC-I pathway genes like heat shock protein 90 (Hsp90), transporter of antigen associated proteins (TAPs) and tapasin had higher expression levels in the SAV3/IFN⁺ cells than in the SAV3/IFN⁻ cells. There were no MHC-II pathway-related genes upregulated in SAV3/IFN⁺-treated cells, and cathepsin S linked to the degradation of endosomal antigens in the MHC-II pathway was downregulated in the SAV3/IFN⁻ cells. Overall, our findings show that concurrent IFN-I treatment of TO-cells and SAV3 infection enriched gene expression linked to the MHC-I antigen presentation pathway. Data presented indicate a role of type I IFNs in strengthening antigen processing and presentation that may facilitate activation particularly of CD8+ T-cell responses following SAV3 infection, while SAV3 infection alone downplayed MHC-II pathways.

Molecular characterization and expressional affirmation of the beta proteasome subunit cluster in rock bream immune defense

Immunoproteasomes are primarily induced upon infection and formed by replacing constitutive beta subunits with inducible beta subunits which possess specific cleavage properties that aid in the release of peptides necessary for MHC class I antigen presentation. In this study, we report the molecular characterization and expression analysis of the inducible immunosubunits PSMB8, PSMB9, PSMB9-L, and PSMB10 from rock bream, Oplegnathus fasciatus. The three subunits shared common active site residues and were placed in close proximity to fish homologues in the reconstructed phylogenetic tree, in which the mammalian homologues formed separate clades, indicating a common ancestral origin. The rock bream immunosubunits possessed higher identity and similarity with the fish homologues. RbPSMB8, RbPSMB9, RbPSMB9-L, and RbPSMB10 were multi-exonic genes with 6, 6, 7 and 8 exons, respectively. These four genes were constitutively expressed in all the examined tissues. Immunostimulants such as lipopolysaccharide and poly I:C induced RbPSMB8, RbPSMB9, RbPSMB9-L, and RbPSMB10 in liver and head kidney, suggesting their possible involvement in immune defense in rock bream.

Genomic structural characterization and transcriptional expression analysis of proteasome activator PA28α and PA28β subunits from Oplegnathus fasciatus

Proteasomes are multicatalytic subunit complexes involved in the degradation of cytosolic proteins and antigen presentation. In this study, we have characterized the alpha and beta subunits of proteasome activator complex from rock bream at the molecular level. RbPA28α and RbPA28β possessed the characteristic features of the subunits identified from mammals and teleosts. The RbPA28α and RbPA28β proteasome subunits contained a proline-rich motif (Region A), subunit-specific insert in the region corresponding to the KEKE motif of the known PA28α (Region B), conserved activation loop (Region C), a potential protein kinase C recognition site (Region D) and a highly homologous C-terminal region (Region E) among all three PA28 subunits. Multiple sequence alignment and pairwise alignment revealed that RbPA28α and RbPA28β proteins shared high homology with the teleosts and mammals. RbPA28α and RbPA28β genome possessed 11 exons interrupted by 10 introns. In silico promoter analysis of RbPA28α and RbPA28β revealed various transcription factor-binding sites displaying their regulation under various stress conditions. Tissue distribution profiling showed a higher expression in blood and gills. Transcriptional expression analysis of RbPA28α and RbPA28β showed up-regulation in the immune tissues following LPS and poly I:C challenges, providing further evidence for the immunological role of RbPA28α and RbPA28β.

Molecular mechanisms of IFN-gamma to up-regulate MHC class I antigen processing and presentation

IFN-gamma up-regulates MHC class I expression and antigen processing and presentation on cells, since IFN-gamma can induce multiple gene expressions that are related to MHC class I antigen processing and presentation. MHC class I antigen presentation-associated gene expression is initiated by IRF-1. IRF-1 expression is initiated by phosphorylated STAT1. IFN-gamma binds to IFN receptors, and then activates JAK1/JAK2/STAT1 signal transduction via phosphorylation of JAK and STAT1 in cells. IFN-gamma up-regulates MHC class I antigen presentation via activation of JAK/STAT1 signal transduction pathway. Mechanisms of IFN-gamma to enhance MHC class I antigen processing and presentation were summarized in this literature review.

Molecular and functional characterization of a cystatin analogue in large yellow croaker (Pseudosciaena crocea)

The cDNA of a cystatin analogue was isolated from the spleen Smart cDNA library of large yellow croaker Pseudosciaena crocea (Lyccys). The open reading frame (ORF) of 354 nucleotides (nt) of Lyccys encodes a protein of 118 amino acids (aa), containing a 21-aa signal peptide and a 97-aa mature polypeptide. The deduced Lyccys possessed structural features of the Family II cystatins, including three evolutionally conserved motifs known to interact with the active sites of cysteine peptidases: Gly at the N-terminus (Gly(25)), Gln-X-Val-X-Gly motif (Q(69)LVAG(73)) and Pro-Try pair at the C-terminus (P(106)W(107)). Genomic analysis revealed that Lyccys gene, spanning 2297 nt, consisted of three exons and two introns. The Lyccys gene was constitutively expressed in all eight tissues examined although at different levels. Real-time PCR analysis revealed that Lyccys transcript in spleen and kidney was obviously up-regulated by poly(I:C) or inactivated trivalent bacterial vaccine, while in blood its expression was down-regulated. Immuno-electron microscopy showed that Lyccys was mainly localized to the rough endoplasmic reticulum (rER) or in the vesicular structures in spleen and kidney cells. Recombinant Lyccys protein fused with glutathione S-transferase (rLyccys) was shown to have remarkable protease-inhibitory activity and well affinity binding to papain (with a K(i) of 1.3x10(-13) M). An in vivo administration of rLyccys could significantly up-regulate the expression levels of large yellow croaker tumor necrosis factor-alpha2 (TNF-alpha2) and interleukin-10 in spleen and kidney, but to a lesser extent increase TNF-alpha1 expression. These results suggest that the Lyccys is a secreted inhibitor of cysteine proteinases, which may have an immunomodulatory function in inflammation response.

Molecular cloning of proteasome activator PA28-beta subunit of large yellow croaker (Pseudosciana crocea) and its coordinated up-regulation with MHC class I alpha-chain and beta 2-microglobulin in poly I:C-treated fish

Antigenic peptides presented on MHC class I molecules to cytotoxic T-cells are generated in the cytosol by the 20S proteasome. Two activators PA28-alpha and PA28-beta, which are inducible by interferon-gamma (IFN-gamma), activate the latent 20S proteasome, thus playing an important role in the processing of MHC class I antigen. Molecular properties and function in the MHC class I antigen processing of PA28 have been well studied and documented in mammals while little is known in fish. In the present study, we reported the cloning of a PA28-beta gene homologue from the spleen of large yellow croaker (Pseudosciana crocea), an economically important marine fish (LycPA28-beta). The full-length cDNA of LycPA28-beta is 1133 nucleotides (nt) encoding a protein of 245 amino acids (aa), with a putative molecular weight of 27.7 kDa. The deduced protein shares 76, 69, 61, 60, 59, 57 and 57% sequence identity to sequences found in zebrafish, flounder, pig, rat, mouse, cattle and human, respectively. The deduced LycPA28-beta contains a PA28-beta subunit-specific insert in the region corresponding to the KEKE motif of the known PA28-alpha (Region B), a conserved activation loop (Region C) and a highly homologous C-terminal region among all three PA28 subunits (Region E), and a characteristic proline-rich motif (Region A) and a potential protein kinase C recognition site (Region D). Western blot analysis of various tissues indicated that LycPA28-beta was constitutively expressed in kidney, liver, spleen and intestine, and weakly expressed in muscle tissue, but not detected in gills, heart and brain. The LycPA28-beta expression was significantly up-regulated in kidney, liver, spleen, intestine and muscle tissues, and also induced in gills after 72 h of treatment with a viral micmic, polyinosinic polycytidynic acid (poly I:C). The transcriptional analysis of LycPA28-beta and MHC class I alpha-chain (alpha-chain) and beta(2)-microglobulin (beta(2)m) in spleens of poly I:C-induced large yellow croaker was further performed by RT-PCR. The results showed that the expression of LycPA28-beta and class I alpha-chain and beta(2)m genes was coordinately up-regulated by poly I:C, suggesting that induction of the MHC class I antigen processing and presentation pathway may be required for the antiviral immune response triggered poly I:C in large yellow croaker.

Cloning and sequence analysis of the beta2-microglobulin transcript from flounder, Paralichthys olivaceous

Beta2-microglobulin (beta2M) is a protein found free-form in the serum or on the cell surface non-covalently associated with the alpha-chain of the class I major histocompatibility (MHC-I) complex. The full-length cDNA containing beta2M was cloned from flounder, Paralichthys olivaceous. The transcript consists of 1610 nucleotides (nts), including an open reading frame (ORF) of 384 nts encoding a polypeptide of 128 amino acids. The amino acid sequence of beta2M in flounder is 59, 57, 56, and 48% conserved in catfish, rainbow trout, zebrafish, and humans, respectively. Genomic Southern hybridization suggested the presence of a single copy of beta2M in the flounder genome, and reverse transcription-polymerase chain reaction (RT-PCR) and Northern blot analysis detected the beta2M transcript in the head kidney, spleen, body kidney, liver, and muscle tissues of the flounder. PCR amplification and sequence analysis revealed the lack of an intron in the beta2M gene. The phylogenetic analysis confirmed the evolutionary diversion of the beta2M protein among warm-blooded vertebrates and fish, and the separation between freshwater and seawater fish.

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform

Background

Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps.

Results

Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data.

Conclusion

The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

Salmon spawning migration and muscle protein metabolism: the August Krogh principle at work

The August Krogh principle, stating that for any particular question in biology, nature holds an ideal study system, was applied by choosing the anorexic, long-distance migration of salmon as a model to analyze protein degradation and amino acid metabolism. Reexamining an original study done over 20 years ago on migrating sockeye salmon (Oncorhynchus nerka), data on fish migration and starvation are reviewed and a general model is developed on how fish deal with muscle proteolysis. It is shown that lysosomal activation and degradation of muscle protein by lysosomal cathepsins, especially cathepsin D and sometimes cathepsin L, are responsible for the degradation of muscle protein during fish migration, maturation and starvation. This strategy is quite the opposite to mammalian muscle wasting, including starvation, uremia, cancer and others, where the ATP-ubiquitin proteasome in conjunction with ancillary systems, constitutes the overwhelming pathway for protein degradation in muscle. In mammals, the lysosome plays a bit part, if any. In contrast, the proteasome plays at best a subordinate role in muscle degradation in piscine systems. This diverging strategy is put into the context of fish metabolism in general, with its high amino acid turnover, reliance on amino acids as oxidative substrates and flux of amino acids from muscle via the liver into gonads during maturation. Brief focus is placed on structure, function and evolution of the key player in fishes: cathepsin D. The gene structure of piscine cathepsin D is outlined, focusing on the existence of duplicate, paralogous, cathepsin D genes in some species and analyzing the relationship between a female and liver-specific aspartyl protease and fish cathepsin Ds. Evolutionary relationships are developed between different groups of piscine cathepsins, aspartyl proteases and other cathepsins. Finally, based on specific changes in muscle enzymes in fish, including migrating salmon, common strategies of amino acid and carbon flux in fish muscle are pointed out, predicting some metabolic concepts that would make ideal application grounds for the August Krogh principle.