Analysis and characterization of the head kidney transcriptome from the Antarctic fish Trematomus bernacchii (Teleostea, Notothenioidea): a source for immune relevant genes

Antibacterial and anticancer activity of two NK-lysin-derived peptides from the Antarctic teleost Trematomus bernacchii

The NK-lysin antimicrobial peptide, first identified in mammals, possesses both antibacterial and cytotoxic activity against cancer cell lines. Homologue peptides isolated from different fish species have been examined for their functional characteristics in the last few years. In this study, a NK-lysin transcript was identified in silico from the head kidney transcriptome of the Antarctic teleost Trematomus bernacchii. The corresponding amino acid sequence, slightly longer than NK-lysins of other fish species, contains six cysteine residues that in mammalian counterparts form three disulphide bridges. Real time-PCR analysis indicated its predominant expression in T. bernacchii immune-related organs and tissues, with greatest mRNA abundance detected in gills and spleen. Instead of focusing on the full T. bernacchii derived NK-lysin mature molecule, we selected a 27 amino acid residue peptide (named NKL-WT), corresponding to the potent antibiotic NK-2 sequence found in human NK-lysin. Moreover, we designed a mutant peptide (named NKL-MUT) in which two alanine residues substitute the two cysteines found in the NKL-WT. The two peptides were obtained by solid phase organic synthesis to investigate their functional features. NKL-WT and NKL-MUT displayed antibacterial activity against the human pathogenic bacterium Enterococcus faecalis and the ESKAPE pathogen Acinetobacter baumannii, respectively. Moreover, at the determined Minimum Inhibitory Concentration and Minimum Bactericidal Concentration values against these pathogens, both peptides showed high selectivity as they did not exhibit any haemolytic activity on erythrocytes or cytotoxic activity against mammalian primary cell lines. Finally, the NKL-MUT selectively triggers the killing of the melanoma cell line B16F10 by means of a pro-apoptotic pathway at a concentration range in which no effects were found in normal mammalian cell lines. In conclusion, the two peptides could be considered as promising candidates in the fight against antibiotic resistance and tumour proliferative action, and also be used as innovative adjuvants, either to decrease chemotherapy side effects or to enhance anticancer drug activity.

Temperature effects on teleost immunity in the light of climate change

Temperature is an important environmental modulator of teleost immune activity. Susceptibility of teleosts to temperature variation depends on the species-specific adaptive temperature range, and the activity of the teleost immune system is generally temperature-dependent. Similar to many physiological and metabolic traits of ectotherms, temperature modulates the activity of immune traits. At low temperatures, acquired immunity of many teleost species is down-modulated, and their immuno-competence mainly depends on innate immunity. At intermediate temperatures, both innate and acquired immunity are fully active and provide optimal protection, including long-lasting immunological memory. When temperatures increase and reach the upper permissive range, teleost immunity is compromised. Moreover, temperature shifts may have negative effects on teleost immune functions, in particular if shifts occur rapidly with high amplitudes. On the contrary, short-term temperature increase may help teleost immunity to fight against pathogens transiently. A major challenge to teleosts therefore is to maintain immuno-competence throughout the temperature range they are exposed to. Climate change coincides with rising temperatures, and more frequent and more extreme temperature shifts. Both are likely to influence the immuno-competence of teleosts. Nonetheless, teleosts exist in habitats that differ substantially in temperature, ranging from below zero in the Arctic's to above 40°C in warm springs, illustrating their enormous potential to adapt to different temperature regimes. The present review seeks to discuss how changes in temperature variation, induced by climate change, might influence teleost immunity.

Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective

Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼25 Mya to more than 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans. Thus, notothenioids are models for understanding adaptive radiations, physiological and biochemical adaptations to extreme environments, and genetic mechanisms of human disease. Since 2014, 16 notothenioid genomes have been published, which enable a first-pass holistic analysis of the notothenioid radiation and the genetic underpinnings of novel notothenioid traits. Here, we review the notothenioid radiation from a genomic perspective and integrate our insights with recent observations from other fish radiations. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

F-type lectin from serum of the Antarctic teleost fish Trematomus bernacchii (Boulenger, 1902): Purification, structural characterization, and bacterial agglutinating activity

The increasing availability of sequenced genomes has enabled a deeper understanding of the complexity of fish lectin repertoires involved in early development and immune recognition. The teleost fucose-type lectin (FTL) family includes proteins that preferentially bind fucose and display tandemly arrayed carbohydrate-recognition domains (CRDs) or are found in mosaic combinations with other domains. They function as opsonins, promoting phagocytosis and the clearance of microbial pathogens. The Antarctic fish Trematomus bernacchii is a Perciforme living at extremely low temperatures (-1.68 °C) which is considered a model for studying adaptability to the variability of environmental waters. Here, we isolated a Ca⁺⁺-independent fucose-binding protein from the serum of T. bernacchii by affinity chromatography with apparent molecular weights of 32 and 30 kDa under reducing and non-reducing conditions, respectively. We have characterized its carbohydrate binding properties, thermal stability and potential ability to recognize bacterial pathogens. In western blot analysis, the protein showed intense cross-reactivity with antibodies specific for a sea bass (Dicentrarchus labrax) fucose-binding lectin. In addition, its molecular and structural aspects, showing that it contains two CRD-FTLs confirmed that T. bernacchii FTL (TbFTL) is a bona fide member of the FTL family, with binding activity at low temperatures and the ability to agglutinate bacteria, thereby suggesting it participates in host-pathogen interactions in low temperature environments.

Local immune responses to VAA DNA vaccine against Listonella anguillarum in flounder (Paralichthys olivaceus)

The efficacy of DNA vaccine is associated closely with the expression of the antigen and the intensity of local immune responses. In our previous study, a recombinant DNA plasmid expressing the VAA protein (pVAA) of Listonella anguillarum has been proved to have a good protection against the infection of L. anguillarum. In the present study, the local immune responses eliciting by immunizing flounder with intramuscular (I.M.) injection of pVAA was investigated at the cellular and genetic level, the muscle at the injection site at 7th post vaccination day was sampled and analyzed by hematoxylin-eosin (H&E) staining, immunohistochemistry (IHC), flow cytometry (FCM), RNA sequencing (RNA-Seq)-based transcriptomics and RT-qPCR. Then variations on the specific antibodies in serum at 1st-6th post vaccination week and the relative percent survival rate (RPS) at following 14 days after challenge were measured. The H&E results showed that inflammatory cells and immune cells significantly increased at the injection site. The IHC using monoclonal antibody against T cell markers revealed that both CD4-1⁺ and CD4-2⁺ T lymphocytes were recruited to the injection site and FCM results showed that the proportion of CD4-1⁺ cells in pVAA immunized group was 28.6 %, in the control group was 8.7 %, and that of CD4-2⁺ cells in two groups was 21.2 % and 8.5 %, respectively. These results indicating that the proportion of CD4⁺ cells in the immune group was significantly increased compared with the control group. Moreover, there were 2551 genes differently expressed in pVAA immunized group, KEGG analysis showed the genes involved in the signal transduction and immune system, and surface markers for B-cells genes, T-cells and antigen presenting cells (APCs) genes were highly upregulated, suggesting the activation of the systemic immune responses. Antibody specific anti-L. anguillarum or anti-rVAA antibodies were significantly induced at 2nd post-immunization week, that reached a peak at 4-5th week. RPS in pVAA group was 53.85±3.64 %. In conclusion, pVAA induced effective local immune responses and then the systematic response. This probably is the main contribution of pVAA to effective protection against L. anguillarum.

Cold Adaptation in Antarctic Notothenioids: Comparative Transcriptomics Reveals Novel Insights in the Peculiar Role of Gills and Highlights Signatures of Cobalamin Deficiency

Far from being devoid of life, Antarctic waters are home to Cryonotothenioidea, which represent one of the fascinating cases of evolutionary adaptation to extreme environmental conditions in vertebrates. Thanks to a series of unique morphological and physiological peculiarities, which include the paradigmatic case of loss of hemoglobin in the family Channichthyidae, these fish survive and thrive at sub-zero temperatures. While some of the distinctive features of such adaptations have been known for decades, our knowledge of their genetic and molecular bases is still limited. We generated a reference de novo assembly of the icefish Chionodraco hamatus transcriptome and used this resource for a large-scale comparative analysis among five red-blooded Cryonotothenioidea, the sub-Antarctic notothenioid Eleginops maclovinus and seven temperate teleost species. Our investigation targeted the gills, a tissue of primary importance for gaseous exchange, osmoregulation, ammonia excretion, and its role in fish immunity. One hundred and twenty genes were identified as significantly up-regulated in Antarctic species and surprisingly shared by red- and white-blooded notothenioids, unveiling several previously unreported molecular players that might have contributed to the evolutionary success of Cryonotothenioidea in Antarctica. In particular, we detected cobalamin deficiency signatures and discussed the possible biological implications of this condition concerning hematological alterations and the heavy parasitic loads typically observed in all Cryonotothenioidea.

Whole transcriptome-based miRNA-mRNA network analysis revealed the mechanism of inflammation-immunosuppressive damage caused by cadmium in common carp spleens

Cadmium (Cd) is a well-known environmental pollutant and can damage fish. MicroRNAs (miRNAs) can involve in inflammation and immunosuppression. However, the mechanisms of miRNAs are still unclear in common carp (Cyprinus carpio L.) treated by Cd. In current study, 54 juvenile common carp were randomly divided into the control group and the Cd group (0.26 mg L^-1 Cd) and were cultured for 30 days. The results revealed inflammatory damage in the spleens of common carp after Cd exposure using morphological construction. There were 23 differentially expressed miRNAs including 17 up-regulated differentially expressed miRNAs (miR-1-4-3p, miR-7-1-5p, miR-7-2-5p, miR-10-43-5p, miR-34-3-5p, miR-128-4-3p, miR-128-5-3p, miR-132-2-5p, miR-132-6-5p, miR-216-3-5p, miR-216-4-5p, miR-375-2-3p, miR-375-4-3p, miR-375-5-3p, miR-375-7-3p, miR-375-8-3p, and miR-724-5p) and 6 down-regulated differentially expressed miRNAs (miR-9-6-5p, miR-25-9-3p, miR-31-3-5p, miR-31-12-5p, miR-103-5-5p, and miR-122-1-3p). The 23 miRNAs regulated 2022 target mRNAs. There were 10 pathways and 9 annotation clusters on 2022 target mRNAs using KEGG and GO analysis, respectively. Among them, 5 pathways (NF-κB signaling pathway, Jak-STAT signaling pathway, MAPK signaling pathway, Th1 and Th2 cell differentiation, and Toll-like receptor signaling pathway) and 7 GO terms (negative regulation of immune system process, T cell mediated immunity, regulation of immune response, inflammatory response, positive regulation of inflammatory response, regulation of inflammatory response, and inflammasome complex) were associated with inflammatory response and immunosuppression. miR-375-4-3p, NF-κB, COX-2, PTGES, and IL-4/13A increased and miR-31-12-5p, miR-9-6-5p, MMP9, IL-11, SPI1, and T-Bet decreased using transcriptome sequencing and RT-qPCR in Cd-treated common carp spleens, which revealed that our results were reliable. Our data indicated that miRNAs mediated inflammation-immunosuppressive injury caused by Cd in common carp spleens using whole transcriptome-based miRNA-mRNA network analysis. Our study provided new insights into the toxicology of Cd exposure.

Trematocine, a Novel Antimicrobial Peptide from the Antarctic Fish Trematomus bernacchii: Identification and Biological Activity

Antimicrobial peptides (AMPs) are short peptides active against a wide range of pathogens and, therefore, they are considered a useful alternative to conventional antibiotics. We have identified a new AMP in a transcriptome derived from the Antarctic fish Trematomus bernacchii. This peptide, named Trematocine, has been investigated for its expression both at the basal level and after in vivo immunization with an endemic Antarctic bacterium (Psychrobacter sp. TAD1). Results agree with the expected behavior of a fish innate immune component, therefore we decided to synthesize the putative mature sequence of Trematocine to determine the structure, the interaction with biological membranes, and the biological activity. We showed that Trematocine folds into a α-helical structure in the presence of both zwitterionic and anionic charged vesicles. We demonstrated that Trematocine has a highly specific interaction with anionic charged vesicles and that it can kill Gram-negative bacteria, possibly via a carpet like mechanism. Moreover, Trematocine showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values against selected Gram-positive and Gram-negative bacteria similar to other AMPs isolated from Antarctic fishes. The peptide is a possible candidate for a new drug as it does not show any haemolytic or cytotoxic activity against mammalian cells at the concentration needed to kill the tested bacteria.

Molecular characterization of novel mitochondrial peroxiredoxins from the Antarctic emerald rockcod and their gene expression in response to environmental warming

In the present study we describe the molecular characterization of the two paralogous mitochondrial peroxiredoxins from Trematomus bernacchii, a teleost that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase activity of these enzymes. The temporal expression of Prdx3 and Prdx5 mRNAs in response to short-term thermal stress showed a general upregulation of prdx3, suggesting that this isoform is the most affected by temperature increase. These data, together with the peculiar differences between the molecular structures of the two mitochondrial Prdxs in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges.

Transcription profiles of skin and head kidney from goldfish suffering hemorrhagic septicemia with an emphasis on the TLR signaling pathway

Hemorrhagic septicemia is an acute, highly fatal disease that affects goldfish (Carassius auratus). To gain a better understanding of related immune genes, the transcriptomes of the skin and head kidney of goldfish suffering hemorrhagic septicemia were sequenced, assembled, and characterized. Based on functional annotation, an extensive and diverse catalog of expressed genes were identified in both the skin and head kidney. As two different organs, pair-wise comparison identified 122/77 unigenes up/down-regulated (two-fold change with P<0.05) in the skin and head kidney. Most genes of the immune pathways were expressed and isolated in both skin and head kidney, including interferon (IFN) transcription factors 1-10 and Toll-like receptors (TLRs). Interferon regulatory factor 3 (IRF3), a key IFN transcription factor, was up-regulated at the transcriptional level by polyriboinosinic: polyribocytidylic acid (poly I:C) challenge and regulated the IFN response by increasing the activity of IFN-β and IFN-stimulated response element (ISRE)-containing promoter. This study will benefit the identification and understanding of novel genes that play important roles in the immunological reactions of fish suffering from hemorrhagic septicemia.

Molecular and Structural Characterization of MHC Class II β Genes Reveals High Diversity in the Cold-Adapted Icefish Chionodraco hamatus

This study reports the presence of two distinct MHC class II β genes in the Antarctic icefish Chionodraco hamatus, belonging to the classical (ChhaDAB) and nonclassical (ChhaDBB) evolutionary lineages. By the application of targeted sequencing approach, a remarkable molecular diversity in the exon 2 sequence of the highly expressed gene ChhaDAB has been observed, resulting in an estimate of 92 different variants translated in 87 different peptides from 54 analysed icefish individuals. A highly conservative estimate, based on a 95% sequence identity threshold clustering, translate this variability in 41 different peptide clusters belonging to four different clades and showing the signature of different kinds of selection. In stark contrast, the poorly expressed ChhaDBB gene displayed a very low level of molecular diversity within exon 2, in agreement with expectations for a nonclassical MHC class II β gene.

Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?

The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whereas successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding, and degrading proteins at their ambient temperatures of -1.86 °C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant overrepresentation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. We hypothesize that these extra methionines have been preferentially assimilated into the genome to act as redox sensors in the highly oxygenated waters of the Southern Ocean. This redox hypothesis is supported by analyses of notothenioids showing enrichment of genes associated with responses to environmental stress, particularly reactive oxygen species. So overall, although notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0 °C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.

Fish Lymphocytes: An Evolutionary Equivalent of Mammalian Innate-Like Lymphocytes?

Lymphocytes are the responsible of adaptive responses, as they are classically described, but evidence shows that subpopulations of mammalian lymphocytes may behave as innate-like cells, engaging non-self rapidly and without antigen presentation. The innate-like lymphocytes of mammals have been mainly identified as γδT cells and B1-B cells, exert their activities principally in mucosal tissues, may be involved in human pathologies and their functions and tissue(s) of origin are not fully understood. Due to similarities in the morphology and immunobiology of immune system between fish and mammals, and to the uniqueness of having free-living larval stages where the development can be precisely monitored and engineered, teleost fish are proposed as an experimental model to investigate human immunity. However, the homology between fish lymphocytes and mammalian innate-like lymphocytes is an issue poorly considered in comparative immunology. Increasing experimental evidence suggests that fish lymphocytes could have developmental, morphological, and functional features in common with innate-like lymphocytes of mammals. Despite such similarities, information on possible links between conventional fish lymphocytes and mammalian innate-like lymphocytes is missing. The aim of this review is to summarize and describe available findings about the similarities between fish lymphocytes and mammalian innate-like lymphocytes, supporting the hypothesis that mammalian γδT cells and B1-B cells could be evolutionarily related to fish lymphocytes.

Omics and cytokine discovery in fish: Presenting the Yellowtail kingfish (Seriola lalandi) as a case study

A continued programme of research is essential to overcome production bottlenecks in any aquacultured fish species. Since the introduction of genetic and molecular techniques, the quality of immune research undertaken in fish has greatly improved. Thousands of species specific cytokine genes have been discovered, which can be used to conduct more sensitive studies to understand how fish physiology is affected by aquaculture environments or disease. Newly available transcriptomic technologies, make it increasingly easier to study the immunogenetics of farmed species for which little data exists. This paper reviews how the application of transcriptomic procedures such as RNA Sequencing (RNA-Seq) can advance fish research. As a case study, we present some preliminary findings using RNA-Seq to identify cytokine related genes in Seriola lalandi. These will allow in-depth investigations to understand the immune responses of these fish in response to environmental change or disease and help in the development of therapeutic approaches.

Immune response of the Antarctic teleost Trematomus bernacchii to immunization with Psychrobacter sp. (TAD1)

Adult Trematomus bernacchii have been immunized intraperitoneally with heat-killed cells of the Antarctic marine bacterium Psychrobacter sp. (TAD1) up to 60 days. After immunizations and sampling at various times, fish sera were tested for specific IgM by ELISA, and different tissues (head kidney and spleen) were investigated for transcription of master genes of the acquired immune response (IgM, IgT, TRβ, TRγ). Results from ELISA assays showed a time-dependent induction of specific serum anti-TAD1 IgM, and western blot analysis of TAD1 lysates probed with fish sera revealed enhanced immunoreactivity in immunized animals compared to controls. Quantitative PCR analysis of transcripts coding for IgM, IgT, TRβ, TRγ was performed in T. bernacchii tissues to assess basal expression, and then on cDNAs of cells from head kidney and spleen of fish injected for 8, 24, and 72 h with inactivated TAD1. The results showed a differential basal expression of transcripts in the examined tissues, and a time-dependent strong up-regulation of IgT, TRβ, TRγ genes upon in vivo stimulation with TAD1. These results represent a first in vivo study on the mounting of a specific immune response in an Antarctic teleost species.

Integrated studies of organismal plasticity through physiological and transcriptomic approaches: examples from marine polar regions

Transcriptomic methods are now widely used in functional genomic research. The vast amount of information received from these studies comes along with the challenge of developing a precise picture of the functional consequences and the characteristic regulatory mechanisms. Here we assess recent studies in marine species and their adaptation to polar (and seasonal) cold and explore how they have been able to draw reliable conclusions from transcriptomic patterns on functional consequences in the organisms. Our analysis indicates that the interpretation of transcriptomic data suffers from insufficient understanding of the consequences for whole organism performance and fitness and comes with the risk of supporting only preliminary and superficial statements.We propose that the functional understanding of transcriptomic data may be improved by their tighter integration into overarching physiological concepts that support the more specific interpretation of the 'omics' data and, at the same time, can be developed further through embedding the transcriptomic phenomena observed. Such possibilities have not been fully exploited.In the context of thermal adaptation and limitation, we explore preliminary evidence that the concept of oxygen and capacity limited thermal tolerance (OCLTT) may provide sufficient complexity to guide the integration of such data and the development of associated functional hypotheses. At the same time, we identify a lack of methodological approaches linking genes and function to higher levels of integration, in terms of organism and ecosystem functioning, at temporal and geographical scales, to support more reliable conclusions and be predictive with respect to the effects of global changes.

Non-Antarctic notothenioids: Past phylogenetic history and contemporary phylogeographic implications in the face of environmental changes

The non-Antarctic Notothenioidei families, Bovichtidae, Pseudaphritidae and Eleginopsidae, diverged early from the main notothenioid lineage. They are important in clarifying the early evolutionary processes that triggered notothenioid evolution in the Antarctic. The early-diverged group represents 8% of all notothenioid species and never established themselves on the Antarctic shelf. Most attention has been paid to the Antarctic notothenioids and their limited physiological tolerance to climate change and increased temperatures. In this review, we discuss key life history traits that are characteristic of the non-Antarctic early-diverged notothenioid taxa as well as the genetic resources and population differentiation information available for this group. We emphasise the population fitness and dynamics of these species and indicate how resource management and conservation of the group can be strengthened through an integrative approach. Both Antarctic waters and the non-Antarctic regions face rapid temperature rises combined with strong anthropogenic exploitation. While it is expected that early-diverged notothenioid species may have physiological advantages over high Antarctic species, it is difficult to predict how climate changes might alter the geographic range, behaviour, phenology and ultimately genetic variability of these species. It is possible, however, that their high degree of endemism and dependence on local environmental specificities to complete their life cycles might enhance their vulnerability.

An Enriched European Eel Transcriptome Sheds Light upon Host-Pathogen Interactions with Vibrio vulnificus

Infectious diseases are one of the principal bottlenecks for the European eel recovery. The aim of this study was to develop a new molecular tool to be used in host-pathogen interaction experiments in the eel. To this end, we first stimulated adult eels with different pathogen-associated molecular patterns (PAMPs), extracted RNA from the immune-related tissues and sequenced the transcriptome. We obtained more than 2x10⁶ reads that were assembled and annotated into 45,067 new descriptions with a notable representation of novel transcripts related with pathogen recognition, signal transduction and the immune response. Then, we designed a DNA-microarray that was used to analyze the early immune response against Vibrio vulnificus, a septicemic pathogen that uses the gills as the portal of entry into the blood, as well as the role of the main toxin of this species (RtxA1₃) on this early interaction. The gill transcriptomic profiles obtained after bath infecting eels with the wild type strain or with a mutant deficient in rtxA1₃ were analyzed and compared. Results demonstrate that eels react rapidly and locally against the pathogen and that this immune-response is rtxA1₃-dependent as transcripts related with cell destruction were highly up-regulated only in the gills from eels infected with the wild-type strain. Furthermore, significant differences in the immune response against the wild type and the mutant strain also suggest that host survival after V. vulnificus infection could depend on an efficient local phagocytic activity. Finally, we also found evidence of the presence of an interbranchial lymphoid tissue in European eel gills although further experiments will be necessary to identify such tissue.