Cathepsins in the kidney of olive flounder, Paralichthys olivaceus, and their responses to bacterial infection

Whole genome identification of olive flounder (Paralichthys olivaceus) cathepsin genes: Provides insights into its regulation on biotic and abiotic stresses response

Cathepsins are major lysosomal enzymes involved in essential physiological processes, including protein degradation, tissue differentiation, and innate or adaptive responses. Several kinds of cathepsins have been reported in teleost fishes, but no characterization have been performed for the inflammatory response of cathepsin family in olive flounder until now. In our current study, a total of 17 cathepsins in olive flounder were systematically identified and characterized. Phylogenetic analysis clearly indicated that the cathepsin genes was highly conserved. Analysis of structure and motifs exhibited high sequence similarity of cathepsin genes in olive flounder. Expression profiles of cathepsin genes in different tissues and developmental stages showed that cathepsins were temporally and spatially specific. RNA-seq analysis of bacteria and temperature stresses revealed that members of cathepsin were involved in inflammatory responses. Collectively, our findings would provide a further reference for understanding the molecular mechanisms of cathepsins in olive flounder.

Cathepsin D Plays a Vital Role in Macrobrachium nipponense of Ovary Maturation: Identification, Characterization, and Function Analysis

The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction in resilience, a low survival rate, and an increased risk of hypoxia, this in turn, seriously affects the economic benefits of prawn farming. Cathepsin D is a lysosomal protease involved in the ovarian maturation of M. nipponense. In the current study, the cDNA of the gene encoding cathepsin D (Mn-CTSD) was cloned from M. nipponense. The total length was 2391 bp and consisted of an open reading frame (ORF) of 1158 bp encoding 385 amino acids. Sequence analysis confirmed the presence of conserved N-glycosylation sites and characteristic sequences of nondigestive cathepsin D. The qPCR analysis indicated that Mn-CTSD was highly expressed in all tissues tested, most significantly in the ovaries, whereas in situ hybridization showed that expression occurred mainly in oocyte nuclei. Analysis of its expression during development showed that Mn-CTSD peaked during the O-IV stage of ovarian maturation. For the RNAi interference experiment, female M. nipponense specimens in the ovary stage I were selected. Injection of Mn-CTSD double-stranded (ds)RNA into female M. nipponense decreased the expression of Mn-CTSD in the ovaries, such that the Gonad Somatic Index (GSI) of the experimental group was significantly lower than that of the control group (1.79% versus 4.57%; p < 0.05). Ovary development reached the O-III stage in 80% of the control group, compared with 0% in the experimental group. These results suggest that Mn-CTSD dsRNA inhibits ovarian maturation in M. nipponense, highlighting its important role in ovarian maturation in this species and suggesting an approach to controlling ovarian maturation during M. nipponense aquaculture.

Transcriptomic Analysis of Fish Hosts Responses to Nervous Necrosis Virus

Nervous necrosis virus (NNV) has been responsible for mass mortalities in the aquaculture industry worldwide, with great economic and environmental impact. The present review aims to summarize the current knowledge of gene expression responses to nervous necrosis virus infection in different fish species based on transcriptomic analysis data. Four electronic databases, including PubMed, Web of Science, and SCOPUS were searched, and more than 500 publications on the subject were identified. Following the application of the appropriate testing, a total of 24 articles proved eligible for this review. NNV infection of different host species, in different developmental stages and tissues, presented in the eligible publications, are described in detail, revealing and highlighting genes and pathways that are most affected by the viral infection. Those transcriptome studies of NNV infected fish are oriented in elucidating the roles of genes/biomarkers for functions of special interest, depending on each study’s specific emphasis. This review presents a first attempt to provide an overview of universal host reaction mechanisms to viral infections, which will provide us with new perspectives to overcome NNV infection to build healthier and sustainable aquaculture systems.

Proteome profile of spleen in rock bream (Oplegnathus fasciatus) naturally infected with rock bream iridovirus (RBIV)

BACKGROUND

Rock bream iridovirus (RBIV) is one of the most dangerous pathogens that causes the highest mortality in the aquaculture of rock bream (Oplegnathus fasciatus). Even though RBIV infection leads to huge economic loss, proteome studies on RBIV-infected rock bream have not been conducted to provide information about the differential protein expression pattern by the host protection system.

OBJECTIVE

The purpose of this study was to investigate the protein expression patterns in spleens of rock bream olive after infection by RBIV or mixed infection by RBIV and bacteria.

METHODS

Depending on the infection intensity and sampling time point, fish were divided into five groups: uninfected healthy fish at week 0 as the control (0C), heavily infected fish at week 0 (0H), heavily mixed RBIV and bacterial infected fish at week 0 (0MH), uninfected healthy fish at week 3 (3C), and lightly infected fish at week 3 (3L). Proteins were extracted from the spleens of infected rock bream. We used 2-DE analysis with LC-MS/MS to investigate proteome changes in infected rock bream.

RESULTS

The results of the LC-MS/MS analyses showed different protein expression profiles after infection. Proteins related to oxygen transport and energy generation, such as hemoglobin, beta-globin, and ATP synthase, were mostly expressed in the infected spleen. Whereas proteins involved in structure and cell movement, such as tubulin, myosin, actin binding proteins, and intermediate filament proteins, were down-regulated in the infected spleens. The protein expression profiles between infection by RBIV and mixed infection by RBIV and bacteria showed similar patterns.

CONCLUSIONS

Our results indicated that infection by RBIV or mixed infection by RBIV and bacteria triggered energy generation and oxygen-transport, but cell migration and constructional changes in the spleen were extremely decreased.

Differential proteome profile of gill and spleen in three pathogen-infected Paralichthys olivaceus

BACKGROUND

Olive flounder (Paralichthys olivaceus) is one of the major cultured fish species in Asia including Korea. However, the mass mortality of olive flounder caused by various pathogens leads to huge economic loss. The pathogens that lead to fish mortality include parasites, bacteria, and viruses that can cause various kinds of diseases.

OBJECTIVE

The purpose of this study was to investigate the protein expression patterns in the gills and spleens of olive flounder after artificial infection. We hypothesized that proteomics levels in gills and spleen may be differentially expressed depending on infectious agents.

METHODS

To investigate the expression pattern of proteins in gills and spleens, olive flounders were experimentally infected with VHSV (virus), S. parauberis (bacteria), or M. avidus (pathogenic ciliate). Proteins were extracted from the gills and spleens of infected olive flounder. We used 2-DE analysis with LC-MS/MS to investigate proteome changes in infected olive flounders.

RESULTS

The results of the LC-MS/MS analyses showed different protein expression profiles depending on pathogenic sources and target organs. Proteins related to cytoskeletal structure like keratin, calmodulin and actin were mostly expressed in the infected gills. Proteins involved in the metabolism pathway like glycolysis were expressed mainly in the spleens. The protein profiles of S. parauberis and VHSV infection groups had many similarities, but the profile of the M. avidus infection group was greatly different in the gill and spleen.

CONCLUSION

Our results indicate that measures according to the characteristics of each pathogen are necessary for disease prevention and treatment of farmed fish.

Role of major histocompatibility complex II antigen-presentation pathway genes in orange-spotted grouper infected with Cryptocaryon irritans

Cryptocaryon irritans, a pathogen model for fish mucosal immunity, causes skin mucosal and systematic humoral immune response. Where and how MHC II antigen presentation occurs in fish infected with C. irritans remain unknown. In this study, the full-length cDNA of the grouper cysteine protease CTSS was cloned. The expression distributions of six genes (CTSB, CTSL, CTSS, GILT, MHC IIA and MHC IIB) involved in MHC II antigen presentation pathway were tested. These genes were highly expressed in systematic immune tissues and skin and gill mucosal-associated immune tissues. All six genes were upregulated in skin at most time points. Five genes expected CTSS was upregulated in spleen at most time points. CTSB, CTSL and MHC IIA were upregulated in the gill and head kidney at some time points. These results indicate that the presentation of MHC II antigen intensively occurred in local infected skin and gill. Spleen, not head kidney, had the most extensive systematic antigen presentation. In skin, six genes most likely peaked at day 2, earlier than in spleen (5-7 days), marking an earlier skin antibody peak than any recorded in serum previously. This significant and earlier mucosal antigen presentation indicates that specific immune response occurs in local mucosal tissues.

Gene expression profiles alteration after infection of virus, bacteria, and parasite in the Olive flounder (Paralichthys olivaceus)

Olive flounder (Paralichthys olivaceus) is one of economically valuable fish species in the East Asia. In comparison with its economic importance, available genomic information of the olive flounder is very limited. The mass mortality caused by variety of pathogens (virus, bacteria and parasites) is main problem in aquaculture industry, including in olive flounder culture. In this study, we carried out transcriptome analysis using the olive flounder gill tissues after infection of three types of pathogens (Virus; Viral hemorrhagic septicemia virus, Bacteria; Streptococcus parauberis, and Parasite; Miamiensis avidus), respectively. As a result, we identified total 12,415 differentially expressed genes (DEG) from viral infection, 1,754 from bacterial infection, and 795 from parasite infection, respectively. To investigate the effects of pathogenic infection on immune response, we analyzed Gene ontology (GO) enrichment analysis with DEGs and sorted immune-related GO terms per three pathogen groups. Especially, we verified various GO terms, and genes in these terms showed down-regulated expression pattern. In addition, we identified 67 common genes (10 up-regulated and 57 down-regulated) present in three pathogen infection groups. Our goals are to provide plenty of genomic knowledge about olive flounder transcripts for further research and report genes, which were changed in their expression after specific pathogen infection.

Identification of transposable elements fused in the exonic region of the olive flounder genome

Transposable elements (TEs) are mobile genetic sequences that comprise a large portion of vertebrate genomes. The olive flounder (Paralichthys olivaceus) is a valuable marine resource in East Asia. The scope of most genomic studies on the olive flounder is limited to its immunology as their focus is the prevention of mass mortality of this species. Thus, for a broader understanding of the species, its genomic information is consistently in demand. Transcripts sequences were acquired from transcriptome analysis using gill tissues of 12 olive flounders. Distribution of TEs inserted in exonic region of the olive flounder genome was analyzed using RepeatMasker ( http://www.repeatmasker.org/ ). We found 1140 TEs in the exonic region of the genome and long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs) insertions occurred with forward orientation preferences. Transposons belonging to the hAt, Gypsy, and LINE 1 (L1) subfamilies were the most abundant DNA transposons, LTRs, and long interspersed elements (LINEs), respectively. Finally, we carried out a gene ontology analysis to determine the function of TE-fused genes. These results provide some genomic information about TEs that is useful for future research on changes in properties and functions of genes by TEs in the olive flounder genome.

Trancriptome profiles of Amur sturgeon spleen in response to Yersinia ruckeri infection

Yersinia ruckeri (YR) is the causative agent of yersiniosis which has caused significant economic losses in fish culture worldwide, including in Amur sturgeon (Acipenser schrenckii) culture. To better understand the mechanism of the immune responses to YR in Amur sturgeon, the transcriptomic profiles of the spleens from YR-infected and non-infected groups were obtained using RNA-seq techniques. The de novo assemblies yielded totally 145 670 unigenes from the two libraries. The total numbers of transcripts in YR-infected and non-infected groups were from 110 893 to 147 336, with the mean length varying from 560 to 631 (N50: from 882 to 1083). GO analysis revealed that 10 038 unigenes were categorized into 26 biological processes subcategories, 17 cellular components subcategories and 19 molecular functions subcategories. A total of 59 487 unigenes were annotated in the KEGG pathway and 20 pathways were related to the immune system. 1465 differently expressed genes (DEGs) were identified, including 377 up-regulated genes and 1088 down-regulated genes. 125 DEGs were found to be related to immune responses of Amur sturgeon and further divided into 16 immune-related KEGG pathways, including antigen processing and presentation, complement and coagulation cascades, T cell receptor signaling pathway, B cell receptor signaling pathway, NOD-like receptor signaling pathway, chemokine signaling pathway, etc. Eight of the DEGs were further validated by qRT-PCR. Altogether, the results obtained in this study will provide insight into the immune response of Amur sturgeon against Y. ruckeri infection.

Cathepsin B Regulates Collagen Expression by Fibroblasts via Prolonging TLR2/NF-κB Activation

Fibroblasts are essential for tissue repair due to producing collagens, and lysosomal proteinase cathepsin B (CatB) is involved in promoting chronic inflammation. We herein report that CatB regulates the expression of collagens III and IV by fibroblasts in response to a TLR2 agonist, lipopolysaccharide from Porphyromonas gingivalis (P.g. LPS). In cultured human BJ fibroblasts, mRNA expression of CatB was significantly increased, while that of collagens III and IV was significantly decreased at 24 h after challenge with P.g. LPS (1 μg/mL). The P.g. LPS-decreased collagen expression was completely inhibited by CA-074Me, the specific inhibitor of CatB. Surprisingly, expression of collagens III and IV was significantly increased in the primary fibroblasts from CatB-deficient mice after challenge with P.g. LPS. The increase of CatB was accompanied with an increase of 8-hydroxy-2′-deoxyguanosine (8-OHdG) and a decrease of IκBα. Furthermore, the P.g. LPS-increased 8-OHdG and decreased IκBα were restored by CA-074Me. Moreover, 87% of CatB and 86% of 8-OHdG were colocalized with gingival fibroblasts of chronic periodontitis patients. The findings indicate the critical role of CatB in regulating the expression of collagens III and IV by fibroblasts via prolonging TLR2/NF-κB activation and oxidative stress. CatB-specific inhibitors may therefore improve chronic inflammation-delayed tissue repair.

Genome-wide identification and transcript profile of the whole cathepsin superfamily in the intertidal copepod Tigriopus japonicus

Modulation of expression of cathepsins in innate immune response has previously been reported in mollusks and large crustaceans including crabs, lobsters, and shrimps in response to immune challenges. However, similar responses in copepods and the related cathepsin members remain under-investigated. To understand molecular and innate immune responses in the intertidal copepod Tigriopus japonicus, we identified the full spectra of cathepsin members (2 aspartyl proteases, 18 cysteine proteases, and 4 serine proteases) and also analyzed transcriptional expression of cathepsin (Tj-cathepsin) genes in developmental stages, lipopolysaccharide (LPS)- and two Vibrio species-exposed T. japonicus. The transcriptional levels of most Tj-cathepsin genes were highly increased during the molting transition from the nauplius to the copepodid stages. LPS treatment induced innate immune response via significant transcriptional increase of serine cathepsin (e.g., cathepsin As) members with induction of several cysteine cathepsin genes. However, Tj-aspartyl cathepsin E-like and a novel cysteine cathepsin were slightly reduced in response to LPS exposure. Interestingly, Vibrio species showed very low transcriptional sensitivity in the expression of entire cathepsins, while LPS induced several cathepsin gene-involved primitive immune responses in T. japonicus. In this paper, we discuss how whole cathepsin expression profiling can be linked to host defense mechanism to better understand and uncover the underlying mechanism of copepods' innate immunity.

Molecular characterization of the cathepsin B of turbot (Scophthalmus maximus)

Cathepsin B is an enzymatic protein belonging to the peptidase C1 family. It is involved in diverse physiological and pathological functions that include immune response. In this study, we identified and characterized a cathepsin B homolog (SmCatB) from turbot (Scophthalmus maximus). SmCatB is composed of 330 amino acid residues and possesses typical domain architecture of cathepsin B, which contains a propeptide region and a cysteine protease domain, and the latter processes four conserved residues (Q101, C107, H277, and N297) in the active site. SmCatB shares 80.6-87.6% overall sequence identities with the cathepsin B of a number of teleost. SmCatB expression was detected in a wide range of tissues and upregulated by bacterial infection in a time-dependent manner. Recombinant SmCatB (rSmCatB-WT) purified from Escherichia coli exhibited apparent protease activity, which was optimal at 50 °C and pH 5.5. Compared to rSmCatB-WT, the mutant proteins rSmCatB-C107S, rSmCatB-H277A, and rSmCatB-N297A, which bear C107S, H277A, and N297A mutations, respectively, were significantly reduced in protease activity, with the highest reduction observed with rSmCatB-N297A. These results indicate that SmCatB is a bioactive protease that depends on the conserved structural features and that SmCatB is involved in pathogen-induced immune response.

A developmental hepatotoxicity study of dietary bisphenol A in Sparus aurata juveniles

Previous studies in rats have indicated that a diet enriched with Bisphenol A adversely effects metabolism and reproductive success. In rats exposed to BPA by maternal gavage, alteration in the developmental programming, higher obesity rates and reproductive anomalies were induced. Starting with this evidence, the aim of this study was to provide important insights on the effects induced by a BPA enriched diet, on the reproductive physiology and metabolism of juvenile fish, simulating the scenario occurring when wild fish fed on prey contaminated with environmental BPA. Seabream was chosen as model, as it is one of the primary commercial species valued by consumers and these results could provide important findings on adverse effects that could be passed on to humans by eating contaminated fish. A novel method for measuring BPA in the food and water by affinity chromatography was developed. Analysis of signals involved in reproduction uncovered altered levels of vtg and Zp, clearly indicating the estrogenic effect of BPA. Similarly, BPA up-regulated catd and era gene expression. A noteworthy outcome from this study was the full length cloning of two vtg encoding proteins, namely vtgA and vtgB, which are differently modulated by BPA. Cyp1a1 and EROD activity were significantly downregulated, confirming the ability of estrogenic compounds to inhibit the detoxification process. GST activity was unaffected by BPA contamination, while CAT activity was down regulated. These results collectively confirm the estrogenic effect of BPA and provide additional characterization of novel vtg genes in Sparus aurata.

Cloning, characterisation, and expression analysis of the cathepsin D gene from rock bream (Oplegnathus fasciatus)

Cathepsins are lysosomal cysteine proteases belonging to the papain family, members of which play important roles in normal metabolism for the maintenance of cellular homeostasis. Rock bream (Oplegnathus fasciatus) cathepsin D (RbCTSD) cDNAs were identified by expressed sequence tag analysis of a lipopolysaccharide-stimulated rock bream liver cDNA library. The full-length RbCTSD cDNA (1644 bp) contained an open reading frame of 1191 bp encoding 396 amino acids. Alignment analysis revealed that the active sites and N-glycosylation sites of the deduced protein were well conserved. Phylogenetic analysis revealed that RbCTSD is most closely related to the Mi-iuy croaker (Miichthys miiuy) cathepsin D. RbCTSD was ubiquitously expressed in all the examined tissues, predominantly in muscle and kidneys. RbCTSD mRNA expression was also examined in several tissues under conditions of bacterial and viral challenge. All examined tissues of fish infected with Edwardsiella tarda (E. tarda), Streptococcus iniae (S. iniae), and red sea bream iridovirus (RSIV) showed significant increases in RbCTSD expression compared with the control. In the kidney and spleen, RbCTSD mRNA expression was markedly upregulated following infection with all tested pathogens. These findings indicate that RbCTSD plays an important role in the innate immune response of rock bream. Furthermore, these results provide important information for the identification of other cathepsin D genes in various fish species.

Identification of cathepsin B from large yellow croaker (Pseudosciaena crocea) and its role in the processing of MHC class II-associated invariant chain

In teleost, cathepsin B has been identified from several species and shown to play roles in the host immune response during pathogen challenge. However, the mechanism of how cathepsin B modulates the immune response in teleosts remains poorly understood. In this study, we identified and characterized cathepsin B (LycCatB) and invariant chain (LycIi) from the large yellow croaker (Pseudosciaena crocea). Sequence comparison and phylogenetic analysis indicated that LycCatB and LycIi are highly conserved within teleosts. Quantitative RT-PCR analysis showed that LycCatB mRNA was widely expressed in all examined tissues. We then recombinantly expressed LycCatB and Lyc-TR-Ii (transmembrane domain removed Ii chain) in Pichia pastoris and Escherichiacoli, respectively. The recombinant LycCatB (rLycCatB) can hydrolyze the substrate Z-FR-AMC with a Km value of 40.68μM. Furthermore, co-incubation of rLycCatB with rLyc-TR-Ii led to an efficient cleavage of rLyc-TR-Ii in a time-dependant manner. These results indicated that cathepsin B may be involved in MHC class II-associated Ii processing in large yellow croaker, and provide new information helping to elucidate the immunological functions of teleost cathepsin B.

Characterization of cathepsin B gene from orange-spotted grouper, Epinephelus coioides involved in SGIV infection

The lysosomal cysteine protease cathepsin B of papain family is a key regulator and signaling molecule that involves in various biological processes, such as the regulation of apoptosis and activation of virus. In the present study, cathepsin B gene (Ec-CB) was cloned and characterized from orange-spotted grouper, Epinephelus coioides. The full-length Ec-CB cDNA was composed of 1918 bp and encoded a polypeptide of 330 amino acids with higher identities to cathepsin B of teleosts and mammalians. Ec-CB possessed typical cathepsin B structural features including an N-terminal signal peptide, the propeptide region and the cysteine protease domain which were conserved in other cathepsin B sequences. Phylogenetic analysis revealed that Ec-CB was most closely related to Lutjanus argentimaculatus. RT-PCR analysis showed that Ec-CB transcript was expressed in all the examined tissues which abundant in spleen, kidney and gill. After challenged with Singapore grouper iridovirus (SGIV) stimulation, the mRNA expression of cathepsin B in E. coioides was up-regulated at 24 h post-infection. Subcellular localization analysis revealed that Ec-CB was distributed predominantly in the cytoplasm. When the fish cells (GS or FHM) were treated with the cathepsin B specific inhibitor CA-074Me, the occurrence of CPE induced by SGIV was delayed, and the viral gene transcription was significantly inhibited. Additionally, SGIV-induced typical apoptosis was also inhibited by CA-074Me in FHM cells. Taken together, our results demonstrated that the Ec-CB might play a functional role in SGIV infection.

Identification of cathepsin B in the razor clam Sinonovacula constricta and its role in innate immune responses

Cathepsin B, a lysosomal cysteine protease, has drawn much attention in vertebrates. However, very little is known about the functions of cathepsin B in bivalves. In this study, we identified the cathepsin B gene in the razor clam Sinonovacula constricta. The protein has a typical cysteine protease structure, comprising a 15-residue putative signal peptide, a 75-residue propeptide and a 249-residue mature domain. In the mature domain, there is an occluding loop, an oxyanion hole (Gln) and a catalytic triad (Cys, His and Asn). The cathepsin B gene is expressed in a wide range of tissues but appears to exhibit greatest level of expression in the liver. During the early developmental stages, the transcript could be detected widely. After the clam was infected with Vibrio anguillarum, the expression of the cathepsin B gene showed the most significant up-regulation in the liver and mantle tissues at 8h after infection. The fact that bacterial infection can induce the expression of the cathepsin B transcript suggests that cathepsin B could play an important role in the innate immunity of clams.

Olive flounder (Paralichthys olivaceus) cystatin B: cloning, tissue distribution, expression and inhibitory profile of piscine cystatin B

Among the cystatin superfamily, cystatin B, also known as stefin B, is an intracellular inhibitor that regulates the activities of cysteine proteases, such as papain and cathepsins. In this study, the 536 bp cystatin B cDNA (referred to hereafter as PoCystatin B) was cloned from olive flounder (Paralichthys olivaceus) using a combination of the rapid amplification of cDNA ends (RACE) approach and olive flounder cDNA library screening. To determine the tissue distribution of PoCystatin B mRNA, the expression of PoCystatin B in normal and lipopolysaccharide (LPS)-stimulated flounder tissues were compared with that of the inflammatory cytokines interleukin (IL)-1β, IL-6, and IL-8 by reverse transcription (RT)-polymerase chain reaction (PCR). The results of the RT-PCR analysis revealed ubiquitous PoCystatin B expression in normal and LPS-stimulated tissues. To characterize the enzymatic activity of PoCystatin B protein, recombinant PoCystatin B protein was overexpressed in Escherichia coli BL21(DE3) cells in the pCold™ TF DNA expression vector as a soluble fusion protein of 67-kDa. PoCystatin B inhibited papain cysteine protease, bovine cathepsin B, and fish cathepsins F and X to a greater extent, whereas fish cathepsins L, S, and K were inhibited to a lesser extent. These results indicate that the enzymatic characteristics of the olive flounder cystatin B are similar to those of mammalian cystatin B proteins, and provide a better understanding of the mechanisms of regulation of cathepsins and cystatins in marine organisms.