Molecular characterization and expression of CD2 in Nile tilapia (Oreochromis niloticus) in response to Streptococcus agalactiae stimulus

Unique duplication of IFNh genes in Nile tilapia (Oreochromis niloticus) reveals lineage-specific evolution of IFNh in perciform fishes

Fish appear to harbour a complex type I IFN repertoire containing subgroups a, b, c, d, e, f, and h, and IFNh is only reported in perciform fishes. However, no multiple copies of IFNh gene has been identified in fish to date. In this study, two IFNh genes named On-IFNh1 and On-IFNh2 were cloned from Nile tilapia, Oreochromis niloticus. The predicted proteins of On-IFNh1 and On-IFNh2 contain several structural features known in type I IFNs, and estimation of divergence time revealed that these two genes may have arisen from a much recent local duplication event. On-IFNh genes were constitutively expressed in all tissues examined, with the highest expression level observed in gill, and were rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). In addition, both recombinant On-IFNh1 and On-IFNh2 trigger a relative delayed but sustained induction of interferon-stimulated genes (ISGs), whereas recombinant On-IFNc elicits a rapid and transient expression of ISGs in vivo. The present study thus contributes to a better understanding of the functional properties of tilapia interferons, and also provides a new insight into the evolution of IFNh in fish.

Identification and characterization of tilapia CRFB1, CRFB2 and CRFB5 reveals preferential receptor usage of three IFN subtypes in perciform fishes

Type I interferons are a subset of cytokines playing central roles in host antiviral defense, and their effects depend on the interaction with the heterodimeric receptor complex. Surprisingly, two pairs of the receptor subunits, CRFB1 and CRFB5, and CRFB2 and CRFB5, have been identified in fish, but the studies about preferential receptor usage of different fish IFN subtypes are rather limited. In this study, the three receptor chains of type I IFNs named as On-CRFB1, On-CRFB2 and On-CRFB5 were identified in Nile tilapia, Oreochromis niloticus. These three genes were constitutively expressed in all tissues examined, with the highest expression level observed in muscle and liver, and were rapidly induced in liver following the stimulation of poly(I:C). Interestingly, it is possible that all three subtypes of tilapia IFNs are able to signal through two pairs of the receptor subunits, On-CRFB1 and On-CRFB5, and On-CRFB2 and On-CRFB5. More importantly, tilapia group I IFNs (On-IFNd and On-IFNh) preferentially signal through a receptor complex composed of On-CRFB1 and On-CRFB5, and group II IFNs (On-IFNc) preferentially signal through a receptor complex comprised of On-CRFB2 and On-CRFB5. The present study thus provides new insights into the receptor usage of group I and group II IFNs in fish.

Functional characterization of a group II interferon, IFNc in the perciform fish, Nile tilapia (Oreochromis niloticus)

Interferons are a family of class II α-helical cytokines playing vital roles in antiviral immune response, and little information is available to date regarding the interferon system of tilapia. In this study, a type I IFN gene, named On-IFNc, was identified in Nile tilapia, Oreochromis niloticus. The predicted protein of On-IFNc contains several structural features known in type I IFNs, and On-IFNc was clustered together with the known IFNc in fish into a separated clade in the phylogenetic tree. On-IFNc gene was constitutively expressed in all tissues examined, with the highest expression level observed in liver, and was rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). In addition, recombinant On-IFNc has been proven to markedly induce the expression of the antiviral effectors, Mx and viperin, the signalling components, STAT1, STAT2, and IRF9, and the transcription factors, IRF3 and IRF7, as well as the tyrosine phosphorylation of STAT1 and STAT2 in fish cells. Furthermore, recombinant On-IFNc has been proven to possess antiviral activity against ISKNV. The present study thus contributes to a better understanding of the functional properties of the type I IFN system in tilapia.

Single molecule real-time sequencing and RNA-seq unravel the role of long non-coding and circular RNA in the regulatory network during Nile tilapia (Oreochromis niloticus) infection with Streptococcus agalactiae

BACKGROUND

The tilapia aquaculture industry is facing heavy economic losses due to Streptococcus agalactiae (S. agalactiae) infections. While progress has been made in past years, the lack of a high-quality tilapia genome and transcript annotations makes systematic and comprehensive exploration for a non-coding RNA regulatory network associated with the infection process unfeasible, and it stunts further research focused on disease defense and treatment. Herein, single molecular real time sequencing (SMRT-Seq) and RNA-seq data were utilized to generate a high-quality transcript annotation. In addition, Changes in mRNA and non-coding RNA expression were also analyzed during a S. agalactiae infection in tilapia.

FINDINGS

In total, 16.79 Gb of clean data were obtained by sequencing on six SMRT cells, with 712,294 inserts (326,645 full-length non-chimeric reads and 354,188 non-full-length reads). A total of 197,952 consensus transcripts were obtained. Additionally, 55,857 transcript sequences were acquired, with 12,297 previously annotated and 43,560 newly identified transcripts. To further examine the immune response in Oreochromis niloticus following a S. agalactiae infection, a total of 470.62 Gb of clean data was generated by sequencing a library containing 18 S. agalactiae infected tilapia samples. Of the identified genes, 9911 were newly exploited, of which 7102 were functional annotated. Furthermore, 7874 mRNAs, 1281 long non-coding RNAs (out of 21,860 long non-coding RNAs), and 61 circular RNAs (out of 1026 circular RNAs) were found to be differentially expressed during infection, with the 1026 circRNAs not previously identified in tilapia. Moreover, k-means clustering and WGCNA analyses revealed that the immune response of tilapia to a S. agalactiae infection can be divided into three stages: cytokines driven rapid immune response, energy metabolism promotion, and the production of lysosomes and phagosomes. During this response, the head kidney and spleen have synergistic effects, while maintaining independent characteristics. Finally, lncRNA-mRNA (trans and cis), lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA regulatory networks were constructed and revealed that non-coding RNA is involved in the regulation of immune-related genes.

CONCLUSIONS

This study generated a greatly-improved transcript annotation for tilapia using long-read PacBio sequencing technology, and revealed the presence of a regulatory network comprised of non-coding RNAs in Nile tilapia infected with S. agalactiae.

Molecular cloning, characterization and expression profiles of CD2AP in Nile tilapia (Oreochromis niloticus) responding to Streptococcus agalactiae infection and interaction with CD2 cytoplasmic segment

The interaction between CD2-associated protein (CD2AP) and CD2 plays a vital role in lymphocyte adhesion and T cells activation in mammals. In this study, a CD2AP gene (GenBank accession number: MK579862; designated as On-CD2AP) was identified from tilapia (Oreochromis niloticus). Sequence analysis showed that On-CD2AP protein shares high similarity with mammals, including three Src homology 3 (SH3) domains, a section of poly proline motif and a coiled coil region. Transcription levels of On-CD2AP were detected in nine tissues of healthy Nile tilapia, and the highest expression levels were detected in the spleen and gill. On-CD2AP were significantly up-regulated in thymus, head kidney and brain after infected by Streptococcus agalactiae, as well as in head kidney leukocytes (HKLs) with LPS and LTA stimulation. Moreover, a section conserved pro-rich motif that are responsible for binding of CD2 to CD2AP were found in the CD2 cytoplasmic sequence of Nile tilapia (On-CD2C). A weak interaction between On-CD2AP and On-CD2C was proved by yeast two-hybrid assay. In addition, the recombinant proteins of CD2AP-His (rOn-CD2AP-His) and GST-CD2C (GST-rOn-CD2C) were obtained through prokaryotic expression system. His pull-down assay showed that rOn-CD2AP-His and GST-rOn-CD2C could bind to each other. These findings indicate that CD2AP is crucial in immune response during S.agalactiae infection, and the mechanism of interaction between CD2AP and CD2 is conservative in Nile tilapia.

Molecular and functional characterization of tilapia DDX41 in IFN regulation

DEAD-box helicase 41 (DDX41) is a key cytosolic DNA sensor playing critical roles in the regulation of type I IFN responses, and their functions have been well-characterized in mammals. However, little information is available regarding the function of fish DDX41. In this study, a DDX41 gene, named On-DDX41, was identified in Nile tilapia, Oreochromis niloticus. The predicted protein of On-DDX41 contains several structural features known in DDX41, including conserved DEADc and HELICc domains, and a conserved sequence "Asp-Glu-Ala-Asp (D-E-A-D)". On-DDX41 gene was constitutively expressed in all tissues examined, with the highest expression level observed in liver and muscle, and was inducible after poly(I:C) stimulation. Moreover, the overexpression of On-DDX41 can elicit a strong activation of both zebrafish IFN1 and IFN3 promoter in fish cells treated with poly(dA:dT). The present study thus contributes to a better understanding of the functional properties of DDX41 in fish.

Molecular characterization and expression of CD48 in Nile tilapia (Oreochromis niloticus) in response to different stimulus

CD48 is a glycosylphosphatidylinositol-anchored protein involved in lymphocyte adhesion, activation, and costimulation. In this study, the CD48 gene of tilapia (Oreochromis niloticus, named On-CD48), was cloned from the head kidney of tilapia. The coding sequences is 654 bp and encoding 217 amino acids. The deduced amino acid sequence of On-CD48 with an estimated molecular weight of 24.4 kDa and a theoretical pI of 5.03. Amino acid alignment indicated that it had two immunoglobulin-like domain conserved region. In healthy tilapia, the On-CD48 could be detected in all the examined tissues and the highest expression level in the spleen. The expression of On-CD48 in the spleen and head kidney was decreased after immunized by formalin-inactivated Streptococcus agalactiae, and the peak was observed in the spleen at 24 h and appeared again at 96 h, and in the head kidney gradual decline before 48 h then gradually increased to the original level. qPCR analysis of inactivated S. agalactiae, LPS and Poly I:C stimulated at the whole lymphocyte level showed that the stimulation of the Poly I:C was more sensitive. Prokaryotic expression results showed that efficient expression of On-CD48 protein could be realized after induced with 0.5 mmol L^-1 IPTG in E. coli BL21 (DE3) for 10 h at 18 °C. The result of subcellular localization showed that On-CD48 were evenly distributed in the whole cell of HEK-293T. Western Blot confirmed that the molecular weight of the recombinant On-CD48 was about 21 kDa, consistent with the predicted result. The results of this study will lay a strong foundation for the further study of On-CD48 molecular function in tilapia.

Multiomics analyses reveal that NOD-like signaling pathway plays an important role against Streptococcus agalactiae in the spleen of tilapia

Streptococcus aglactiae(GBS) infection in tilapia is a serious global disease that causes significant production loss. Here, we studied the role of GBS in the spleen and the spleen's response against the pathogen through dual RNA-seq and proteome technology. Animals were divided into three groups: control, virulent treated (HN016), and attenuated treated (YM001). Spleen samples were collected and analysis when a disease outbreak. Dual RNA-seq result showed the virulence factor genes of GBS, included CAMP factor, PGK, OCT, enolase, scpB, Sip, bca, were upregulation. downregulation of GapA, cylE, OCT, scpB, C5AP, rlmB, hly, FBP, in HN016 and YM001. But for proteomic, OCT and bca were downregulation, the others were upregulation. For host transcriptome KEGG analysis showed, the NOD-like receptor signaling pathway (NLRs) and TOLL-like receptor signaling pathway (TLRs) were upreguoation in HN016 infected fish than the control fish; But for proteome KEGG, only the NLRS was up, the TLRS was not change. Compared with YM001 infected fishes, for transcriptome, NLRs and TLRs in infected HN016 fishes were significance rise (p < 0.01); for proteome, the NLRs was up (p < 0.05), but TLRs was no change.Analysis of pathogen-host interaction showed that the peptidoglycan (PNG), CD2, LCK, and host's Zap70 were involved in the regulation of NLRs; PNG, LCK, and ZAP70 were involved in the regulation of TRLs. Conclusion: the virulent strain HN016 and attenuated strainYM001 differed in the quantity of virulence factors. In tilapia's innate immune system, NLRs was the main defense factors, but bacteria avoided the host defense through TLRs.

Molecular cloning, expression analysis, and the immune-related role of a thymosin β in the goldfish, Carassius auratus

β-Thymosins play critical roles in the regulation of many important physiological processes, but their function in teleost fishes remains poorly understood. In this study, the full-length cDNA coding for a thymosin β (Tβ) was cloned and identified in goldfish, Carassius auratus (gfTβ). The gfTβ cDNA consisted of 653 bp with an open reading frame of 135 bp that encodes a 44 amino acid polypeptide. Sequence analysis revealed one thymosin domain and a highly conserved actin-binding motif (¹⁸LKKTET²³). Expression of gfTβ transcript was detected ubiquitously in all tissues examined, with relatively higher levels in the brain, intestine, spleen, gill, skin, kidney, and testis. Cadmium and H₂O₂ exposure induced increases in gfTβ transcript levels in the liver and spleen. Moreover, gfTβ transcription was upregulated in response to LPS challenge in the spleen while Poly I:C treatment did not affect gfTβ expression. In vivo injection of recombinant gfTβ generated from an Escherichia coli system induced expression of T lymphocyte-related genes (RAG1 and CD8α). These results suggest that gfTβ may be involved in the immune response of teleost fishes via modulation of T lymphocyte development.

Costimulatory Function of Cd58/Cd2 Interaction in Adaptive Humoral Immunity in a Zebrafish Model

CD58 and CD2 have long been known as a pair of reciprocal adhesion molecules involved in the immune modulations of CD8⁺ T and NK-mediated cellular immunity in humans and several other mammals. However, the functional roles of CD58 and CD2 in CD4⁺ T-mediated adaptive humoral immunity remain poorly defined. Moreover, the current functional observations of CD58 and CD2 were mainly acquired from in vitro assays, and in vivo investigation is greatly limited due to the absence of a Cd58 homology in murine models. In this study, we identified cd58 and cd2 homologs from the model species zebrafish (Danio rerio). These two molecules share conserved structural features to their mammalian counterparts. Functionally, cd58 and cd2 were significantly upregulated on antigen-presenting cells and Cd4⁺ T cells upon antigen stimulation. Blockade or knockdown of Cd58 and Cd2 dramatically impaired the activation of antigen-specific Cd4⁺ T and mIgM⁺ B cells, followed by the inhibition of antibody production and host defense against bacterial infections. These results indicate that CD58/CD2 interaction was required for the full activation of CD4⁺ T-mediated adaptive humoral immunity. The interaction of Cd58 with Cd2 was confirmed by co-immunoprecipitation and functional competitive assays by introducing a soluble Cd2 protein. This study highlights a new costimulatory mechanism underlying the regulatory network of adaptive immunity and makes zebrafish an attractive model organism for the investigation of CD58/CD2-mediated immunology and disorders. It also provides a cross-species understanding of the evolutionary history of costimulatory signals from fish to mammals as a whole.

Conservation of structural and interactional features of CD28 and CD80/86 molecules from Nile tilapia (Oreochromis niloticus)

Interaction of CD28 with CD80 or CD86 molecules provides a costimulatory signals required in T cell activation. In this study, we cloned and analyzed a CD28 gene (On-CD28) and a CD80/86 gene (On-CD80/86) from Nile tilapia (Oreochromis niloticus). Sequence analysis revealed the typical characteristics of On-CD28 protein; for instance, the proline-based motif (¹¹⁷TYPPPL¹²²) is essential in binding of CD28 to CD80/86 ligands. Moreover, an extracellular Ig domain was found in On-CD80/86; this domain is responsible in binding of CD28 to CD80/86 receptors. Subcellular localization analysis showed that both On-CD28 and On-CD80/86 were distributed predominantly in the cytomembrane. Yeast two-hybrid assay showed that On-CD28 directly interacted with On-CD80/86. On-CD28 and On-CD80/86 transcripts were detected in all the examined tissues of healthy Nile tilapia, and the highest expression levels of On-CD28 and On-CD80/86 were detected in the brain and heart, respectively. Following a bacterial challenge using Streptococcus agalactiae in vivo, On-CD28 and On-CD80/86 were upregulated in head kidney, spleen, intestines, and brain. However, they showed different expression profiles in response to stimulation with inactivated S. agalactiae in vitro. These findings indicated that the interaction of On-CD28 with On-CD80/86 provides a costimulatory signals that possibly play an important role in T cell activation during S. agalactiae infection.

Molecular and functional characterization of peptidoglycan-recognition protein SC2 (PGRP-SC2) from Nile tilapia (Oreochromis niloticus) involved in the immune response to Streptococcus agalactiae

PGRP-SC2, the member of PGRP family, plays an important role in regulation of innate immune response. In this paper, a PGRP-SC2 gene of Nile tilapia, Oreochromis niloticus (designated as On-PGRP-SC2) was cloned and its expression pattern under the infection of Streptococcus agalactiae was investigated. Sequence analysis showed main structural features required for amidase activity were detected in the deduced amino acid sequence of On-PGRP-SC2. In healthy tilapia, the On-PGRP-SC2 transcripts could be detected in all the examined tissues, with the most abundant expression in the muscle. When infected with S. agalactiae, there was a clear time-dependent expression pattern of On-PGRP-SC2 in the spleen, head kidney and brain. The assays for the amidase activity suggested that recombinant On-PGRP-SC2 protein had a Zn(2+)-dependent PGN-degrading activity. Moreover, our works showed that recombinant On-PGRP-SC2 protein could significantly reduce bacterial load in target organs attacked by S. agalactiae. These findings indicated that On-PGRP-SC2 may play important roles in the immune response to S. agalactiae in Nile tilapia.