Expression profiling and microbial ligand binding analysis of high-mobility group box-1 (HMGB1) in turbot (Scophthalmus maximus L.)

Discovery of BbX transcription factor in the patagonian blennie: Exploring expression changes following combined bacterial and thermal stress exposure

High-Mobility Group (HMG) proteins are involved in different processes such as transcription, replication, DNA repair, and immune response. The role of HMG proteins in the immune response of fish has been studied mainly for HMGB1, where its expression can be induced by the stimulation of viral/bacterial PAMPs and can act as a proinflammatory mediator and as a global regulator of transcription in response to temperature. However, for BbX this role remains to be discovered. In this work, we identified the BbX of E. maclovinus and evaluated the temporal expression levels after simultaneous challenge with P. salmonis and thermal stress. Phylogenetic analysis does not significantly deviate from the expected organismal relationships suggesting orthologous relationships and that BbX was present in the common ancestor of the group. BbX mRNA expression levels were very high in the intestinal tissue of E. maclovinus (foregut, midgut, and hindgut). Nevertheless, the protein levels analyzed by WB showed the highest levels of BbX protein in the liver (constitutive expression). On the other hand, the mRNA expression levels of BbX in the liver of E. maclovinus injected with P. salmonis and subjected to thermal stress showed an increase at days 16 and 20 in all treatments applied at 12 °C and 18 °C. Meanwhile, the protein levels quantified by WB showed a statistically significant increase in the HMG-Bbx at all experimental times (4, 8, 12, 16, and 20 dpi). However, at 4 dpi the HMG-Bbx protein levels were much higher than the other days evaluated. The results suggest that BbX protein may be implicated in the response mechanism to temperature and bacterial stimulation in the foregut, midgut, hindgut, and liver, according to our findings at the level of mRNA and protein. Furthermore, our WB analysis suggests an effect of P. salmonis on the expression of this protein that can be observed in condition C+ 12 °C compared to C- 12 °C. Then, there is an effect of temperature that can be evidenced in the condition AM 18 °C and SM 18 °C, compared to AB 18 °C and SB 18 °C at 4, 8, and 12 dpi. We found not differences in the levels of this protein if the thermal stress is achieved through acclimatization or shock. More research is necessary to clarify the importance of this type of HMG in the immune response and thermal tolerance in fish.

Molecular Characterization of High Mobility Group Box 1a (HMGB1a) Gene in Red-Bellied Pacu, Piaractus brachypomus

High mobility group box 1 (HMGB1) is a chromosomal protein in the nucleus and a potent extracellular proinflammatory cytokine, widely described in mammals, nevertheless, with scarce reports in fish. In this study, full open reading frame of HMGB1a gene from Piaractus brachypomus is reported as well as its molecular characterization, including tissue gene expression. At predicted protein level, HMGB1a showed similarities with its orthologs in teleosts and higher vertebrates. The relative gene expression of HMGB1a mRNA was measured in several tissues including the brain, where a differential expression appeared in brain regions, i.e., higher expression in the cerebellum and telencephalon. In addition, in an assay of sublethal exposure to chlorpyrifos, upregulation of HMGB1a was detected in optic chiasm. Furthermore, in a traumatic brain injury model, upregulation of HMGB1a expression was evident 24 hours after lesion and remained higher up to 14 days. These findings suggest a role for HMGB1a in brain damage and its candidature as biomarker of brain injury; however, more studies are required to elucidate the functions of HMGB1a and its regulation in P. brachypomus.

The immune-related circRNA-miRNA-mRNA ceRNA regulatory network in the liver of turbot (Scophthalmus maximus L.) induced by Vibrio anguillarum

Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.

Expression profiling and inflammatory activation analysis of high-mobility group box 1 in Schizothorax prenanti

OBJECTIVE

High-mobility group box 1 (HMGB1) is a highly conserved nuclear protein and participates in the immune response to pathogens in bony fish. In this study, the structure and function of HMGB1 in the cyprinid fish Schizothorax prenanti (SpHMGB1) were investigated.

METHODS

The spatial structure of SpHMGB1 was predicted by CPHmodels. Quantitative reverse transcription PCR was used to detect the mRNA of SpHMGB1 in different tissues and Streptococcus agalactiae infection. The macrophage was treated with synthetic SpHMGB1-B box peptide to analyze the inflammatory activity.

RESULT

Structurally, SpHMGB1 had the conserved A box, B box, and acid tail compared with Zebrafish Danio rerio and mice Mus musculus. SpHMGB1 was universally expressed in various tissues, with the highest expression in the middle kidney. In vivo, SpHMGB1 was significantly induced in response to Streptococcus agalactiae infection in the blood and spleen. Synthetic SpHMGB1-B box peptide activated respiratory burst and up-regulated the messenger RNA expression of interleukin-1β, tumor necrosis factor α, interleukin-10, interferon regulatory factor 1, interferon regulatory factor 7, C-X-C motif chemokine ligand 11-1, C-X-C motif chemokine ligand 11-2, and toll-like receptor 4 in macrophages.

CONCLUSION

This study suggested that SpHMGB1 participated in the response to bacterial pathogens and that SpHMGB1-B box peptide played an important role in mediating the immune response of S. prenanti.

Identification and characterization of high mobility group box 1 and high mobility group box 2 in Siberian sturgeon (Acipenser baerii)

High mobility group box 1 (HMGB1) and high mobility group box 2 (HMGB2) were highly conserved nonhistone chromosomal proteins involved in DNA damage repair, innate immune and inflammatory response. In this study, Acipenser baerii HMGB1 (AbHMGB1) and HMGB 2 (HMGB2) were identified. The open reading frame (ORF) of AbHMGB1 was 621 bp which encoded 206 amino acids, and the ORF of AbHMGB2 was 630 bp encoded 209 amino acids. AbHMGB1 and AbHMGB2 were conserved compared with bony fish by phylogenetic analyzing. qRT-PCR showed that AbHMGB1 and AbHMGB2 were expressed in all examined tissues, AbHMGB1 was expressed abundantly in muscle, followed by head kidney and brain, and AbHMGB2 was highest expressed in gill, followed by brain and muscle. After Streptococcus iniae infection and PAMPs treatment, AbHMGB1 and AbHMGB2 were induced significantly. This study indicated that AbHMGB1 and AbHMGB2 are involved in the process of pathogenic infection and provided a basis for exploring the mechanism of Acipenser baerii enteritis induced by Streptococcus iniae.

Japanese Flounder HMGB1: A DAMP Molecule That Promotes Antimicrobial Immunity by Interacting with Immune Cells and Bacterial Pathogen

High mobility group box (HMGB) proteins are DNA-associated proteins that bind and modulate chromosome structures. In mammals, HMGB proteins can be released from the cell nucleus and serve as a damage-associated molecular pattern (DAMP) under stress conditions. In fish, the DAMP function of HMGB proteins in association with bacterial infection remains to be investigated. In this study, we examined the immunological functions of two HMGB members, HMGB1 and HMG20A, of Japanese flounder. HMGB1 and HMG20A were expressed in multiple tissues of the flounder. HMGB1 was released from peripheral blood leukocytes (PBLs) upon bacterial challenge in a temporal manner similar to that of lactate dehydrogenase release. Recombinant HMGB1 bound to PBLs and induced ROS production and the expression of inflammatory genes. HMGB1 as well as HMG20A also bound to various bacterial pathogens and caused bacterial agglutination. The bacteria-binding patterns of HMGB1 and HMG20A were similar, and the binding of HMGB1 competed with the binding of HMG20A but not vice versa. During bacterial infection, HMGB1 enhanced the immune response of PBLs and repressed bacterial invasion. Collectively, our results indicate that flounder HMGB1 plays an important role in antimicrobial immunity by acting both as a modulator of immune cells and as a pathogen-interacting DAMP.

Interpretation of the Genotype by Tissue Interactions of Four Genes (AFP1, CIRP, YB-1, and HMGB1) in Takifugu rubripes Under Different Low-Temperature Conditions

Background: The differential expression of the same gene in different tissues could be due to the genotype effect, tissue effect, and/or genotype × tissue interactions. However, the genetic mechanisms responsible for this differential expression have not been reported to date.

Methods: Four resistance genes to low temperature, the genes for antifreeze protein (AFP), cold induced RNA binding protein (CIRP), high mobility group protein box-1 (HMGB1), and Y-box binding protein (YB-1), were measured by PCR in the liver, spleen, kidney, brain, heart, intestine, muscle, gonad, and skin of Takifugu rubripes cultured under different temperature conditions (18, 13, 8, and 5°C). Split-split-plot analysis of variance, additive main effects and multiplicative interaction (AMMI) and genotype main effects and genotype × environment interaction (GGE) biplot analysis were used to evaluate the effects of genotype × tissue interactions on gene expression.

Results: The results of split-split-plot analysis of variance showed that water temperature has a significant effect on the expression of T. rubripes cold resistant genes, while tissue × gene interaction has a highly significant effect on it. AMMI analysis showed that the contributions of genotype, tissue, and genotype × tissue interactions to the total variation in gene expression followed two trends: 1) as temperature decreased, the gene effect increased gradually and the genotype × tissue interaction decreased gradually; 2) the gene effect at 18 and 13°C was significantly lower than that at 8 and 5°C, while the interaction at 18 and 13°C was significantly higher than that at 8 and 5°C. GGE analysis showed that: at all temperatures except 8°C, the expression rankings of all four genes were highly positively correlated in all tissues except muscle; the expression stability of the genes was the same at 18°C/13°C and at 8°C/5°C; and AFP1 showed the best expression and stability among the four genes.

Conclusion: 8°C/5°C as the suitable temperature for such experiments for T. rubripes. Among the four antifreeze genes evaluated in this study, AFP1 had the best expression and stability.

Identification of mRNA-miRNA-lncRNA regulatory network associated with the immune response to Aeromonas salmonicides infection in the black rockfish (Sebastes schlegelii)

In aquaculture, Aeromonas salmonicides (A. salmonicida) is a main fish pathogen because of its nearly worldwide distribution, and broad host range. Recently, an increasing number of evidences have uncovered the roles of mRNA-miRNA-lncRNA network in fish diseases. In current study, RNA-seq was conducted in the black rockfish spleen following A. salmonicida infection at 0 h (Sp0 or control) and three different post-infection time-points (2 h: Sp2, 12 h: Sp12 and 24 h: Sp24, respectively) to comprehensively identify differentially expressed (DE) mRNAs, miRNAs and lncRNAs. Enrichment analysis and protein-protein interaction (PPI) analysis of DE mRNAs were performed. Then, expression and correlation analysis for mRNAs and their upstream miRNAs and lncRNAs were conducted. Finally, a total of 1364 mRNAs, 17 miRNAs and 1584 lncRNAs exhibited significantly differential expressions during bacterial infection in the black rockfish spleen. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Amino sugar and nucleotide sugar metabolism, Cell adhesion molecules (CAMs), Neuroactive ligand-receptor interaction, Nicotinate and nicotinamide metabolism, Pentose and glucuronate interconversions, Phagosome, Proteasome, etc. Subsequently, 1091 lncRNA-miRNA-mRNA pathways (323 in Sp2, 609 in Sp12 and 207 in Sp24) were constructed including 400 lncRNAs, 69 miRNAs, and 70 mRNAs. Meanwhile, NLRC3/novel-264/LNC_00116154 pathway demonstrated important immune modulating function in the black rockfish against A. salmonicida infection. Finally, the novel mRNA-miRNA-lncRNA sub-networks were established, among which all mRNAs and ncRNAs possessed significant predictive values for further studies for immune responses in the black rockfish.

Comparative analysis of the miRNA-mRNA regulation networks in turbot (Scophthalmus maximus L.) following Vibrio anguillarum infection

MicroRNAs could not only regulate posttranscriptional silencing of target genes in eukaryotic organisms, but also have positive effect on their target genes as well. These microRNAs have been reported to be involved in mucosal immune responses to pathogen infection in teleost. Therefore, we constructed the immune-related miRNA-mRNA networks in turbot intestine following Vibrio anguillarum infection. In our results, 1550 differentially expressed (DE) genes and 167 DE miRNAs were identified. 113 DE miRNAs targeting 89 DE mRNAs related to immune response were used to construct miRNA-mRNA interaction networks. Functional analysis showed that target genes were associated with synthesis and degradation of ketone bodies, mucin type O-Glycan biosynthesis, homologous recombination, biotin metabolism, and intestinal immune network for IgA production that were equivalent to the function of IgT and IgM in fish intestine. Finally, 10 DE miRNAs and 7 DE mRNAs were selected for validating the accuracy of high-throughput sequencing results by qRT-PCR. The results of this study will provide valuable information for the elucidation of the regulation mechanisms of miRNA-mRNA interactions involved in disease resistance in teleost mucosal immune system.

Promising inhibitors of main protease of novel corona virus to prevent the spread of COVID-19 using docking and molecular dynamics simulation

Coronavirus disease-2019 (COVID-19) is a global health emergency and the matter of serious concern, which has been declared a pandemic by WHO. Till date, no potential medicine/ drug is available to cure the infected persons from SARS-CoV-2. This deadly virus is named as novel 2019-nCoV coronavirus and caused coronavirus disease, that is, COVID-19. The first case of SARS-CoV-2 infection in human was confirmed in the Wuhan city of the China. COVID-19 is an infectious disease and spread from man to man as well as surface to man . In the present work, in silico approach was followed to find potential molecule to control this infection. Authors have screened more than one million molecules available in the ZINC database and taken the best two compounds based on binding energy score. These lead molecules were further studied through docking against the main protease of SARS-CoV-2. Then, molecular dynamics simulations of the main protease with and without screened compounds were performed at room temperature to determine the thermodynamic parameters to understand the inhibition. Further, molecular dynamics simulations at different temperatures were performed to understand the efficiency of the inhibition of the main protease in the presence of the screened compounds. Change in energy for the formation of the complexes between the main protease of novel coronavirus and ZINC20601870 as well ZINC00793735 at room temperature was determined on applying MM-GBSA calculations. Docking and molecular dynamics simulations showed their antiviral potential and may inhibit viral replication experimentally. Communicated by Ramaswamy H. Sarma.

An identified PfHMGB1 promotes microcystin-LR-induced liver injury of yellow catfish (Pelteobagrus fulvidraco)

Microcystin-LR (MC-LR) is a potent hepatotoxin that can cause liver inflammation and injury. However, the mode of action of related inflammatory factors is not fully understood. PfHMGB1 is an inflammatory factor induced at the mRNA level in the liver of juvenile yellow catfish (Pelteobagrus fulvidraco) that were intraperitoneally injected with 50 μg/kg MC-LR. The PfHMGB1 mRNA level was highest in the liver and muscle among 11 tissues examined. The full-length cDNA sequence of PfHMGB1 was cloned and overexpressed in E. coli, and the purified protein rPfHMGB1 demonstrated DNA binding affinity. Endotoxin-free rPfHMGB1 (6-150 μg/mL) also showed dose-dependent hepatotoxicity and induced inflammatory gene expression of primary hepatocytes. PfHMGB1 antibody (anti-PfHMGB1) in vitro reduced MC-LR (30 and 50 μmol/L)-induced hepatotoxicity, suggesting PfHMGB1 is important in the toxic effects of MC-LR. In vivo study showed that MC-LR upregulated PfHMGB1 protein in the liver. The anti-PfHMGB1 blocked its counterpart and reduced ALT/AST activities after MC-LR exposure. Anti-PfHMGB1 partly neutralized MC-LR-induced hepatocyte disorganization, nucleus shrinkage, mitochondria, and rough endoplasmic reticula destruction. These findings suggest that PfHMGB1 promotes MC-LR-induced liver damage in the yellow catfish. HMGB1 may help protect catfish against widespread microcystin pollution.

Characterization and initial functional analysis of cathepsin K in turbot (Scophthalmus maximus L.)

Cathepsins are the best-known group of proteases in lysosomes, playing a significant role in immune responses. Cathepsin K (CTSK) is abundantly and selectively expressed in osteoclasts, dendritic cells and monocyte-derived macrophages, where it is involved in ECM degradation and bone remodeling. A growing body of evidences have indicated the vital roles of cathepsin K in innate immune responses. Here, one CTSK gene was captured in turbot (SmCTSK) with a 993 bp open reading frame (ORF). The genomic structure analysis showed that SmCTSK had 7 exons similar to other vertebrate species. The syntenic analysis revealed that CTSK had the same neighboring genes across all the selected species, which suggested the synteny encompassing CTSK region was conserved during vertebrate evolution. Subsequently, SmCTSK was widely expressed in all the examined tissues, with the highest expression level in spleen and the lowest expression level in liver. In addition, SmCTSK was significantly down-regulated in intestine following Gram-negative bacteria Vibrio anguillarum immersion challenge, but up-regulated in three tissues (gill, skin and intestine) following Gram-positive bacteria Streptococcus iniae immersion challenge. Finally, the rSmCTSK showed strong binding ability to all the examined microbial ligands. Taken together, our results suggested SmCTSK played vital roles in fish innate immune responses against infection. However, the knowledge of SmCTSK is still limited in teleost species, further studies should be carried out to better characterize its comprehensive roles in teleost mucosal immunity.

Heat-Responsive Proteomics of a Heat-Sensitive Spinach Variety

High temperatures seriously limit plant growth and productivity. Investigating heat-responsive molecular mechanisms is important for breeding heat-tolerant crops. In this study, heat-responsive mechanisms in leaves from a heat-sensitive spinach (Spinacia oleracea L.) variety Sp73 were investigated using two-dimensional gel electrophoresis (2DE)-based and isobaric tags for relative and absolute quantification (iTRAQ)-based proteomics approaches. In total, 257 heat-responsive proteins were identified in the spinach leaves. The abundance patterns of these proteins indicated that the photosynthesis process was inhibited, reactive oxygen species (ROS) scavenging pathways were initiated, and protein synthesis and turnover, carbohydrate and amino acid metabolism were promoted in the spinach Sp73 in response to high temperature. By comparing this with our previous results in the heat-tolerant spinach variety Sp75, we found that heat inhibited photosynthesis, as well as heat-enhanced ROS scavenging, stress defense pathways, carbohydrate and energy metabolism, and protein folding and turnover constituting a conservative strategy for spinach in response to heat stress. However, the heat-decreased biosynthesis of chlorophyll and carotenoid as well as soluble sugar content in the variety Sp73 was quite different from that in the variety Sp75, leading to a lower capability for photosynthetic adaptation and osmotic homeostasis in Sp73 under heat stress. Moreover, the heat-reduced activities of SOD and other heat-activated antioxidant enzymes in the heat-sensitive variety Sp73 were also different from the heat-tolerant variety Sp75, implying that the ROS scavenging strategy is critical for heat tolerance.