A genome‐wide survey of NOD‐like receptors in Chinese tongue sole (Cynoglossus semilaevis): Identification, characterization and expression analysis in response to bacterial infection

Abstract

As intracellular pathogen recognition receptors (PRRs), nucleotide-binding domain, leucine-rich repeat containing receptors (NLRs, NOD-like receptors) are involved in innate immune responses in vertebrates. However, there is no systemic study on NLRs in Chinese tongue sole (Cynoglossus semilaevis), a popular maricultured fish in China. In the present study, a genome-wide survey of NLRs was performed in C. semilaevis, with the identification of 29 NLRs, including five genes from the NLR-A subfamily (referred to as CsNOD1-5), two genes from the NLR-B subfamily, 18 genes from the NLR-C subfamily (referred to as CsNLR-C1 to 18) and four other NLR genes. Phylogenetic analysis implied that CsNOD1-5 contained conserved functional domains and had orthologous relationships with human NOD1-5. Moreover, CsNLR-C genes all possessed the FISHNA domain, which is a fish-specific NACHT subdomain. Expression analysis showed that CsNOD1-5 and CsNLR-C1/2 were ubiquitously expressed in various normal tissues. Bacterial infection with Vibro harveyi revealed distinct expression patterns of all the tested CsNLRs in gill, intestine, trunk kidney, liver and spleen. In particular, CsNOD1-4 and CsNLR-C2 were significantly upregulated in gills at 48 h post bacterial infection. In addition, CsNOD3 and CsNOD4 were significantly elevated in infectious intestine, trunk kidney, liver and spleen, revealing that their expressions were more sensitive to bacterial infection than other CsNLRs. Together with the computational protein-protein interaction network of CsNLRs, it was suggested that individual NLR genes had different roles in the innate immune cascades of C. semilaevi against bacterial infection. This study provides valuable information for further studies on CsNLR immune function.

Exosomal miRNAs in the plasma of Cynoglossus semilaevis infected with Vibrio harveyi: Pleiotropic regulators and potential biomarkers involved in inflammatory and immune responses

“…Moreover, nucleotide binding oligomerization domain–like receptors (NLRs) were another type of PRRs that were reported to be reactive to peptidoglycan (PGN)-derived molecules, bacterial RNA, endogenous danger signals, LPS, and so on in the cytoplasm, activating proinflammatory cytokines via the transcription factor nuclear factor–κB (NF-κB) signaling pathway and apoptosis via caspase1 ( 71 – 73 ). In Chinese tongue sole, a recent investigation showed that NLRs encoded by 29 genes were expressed ubiquitously in various tissues and some of them were sensitive to V. harveyi infection, especially those in the intestine, kidney, liver, and spleen ( 74 ). Therefore, the above-mentioned processes involved a series of signal transduction pathways and the regulation of transcription, which were also the major enriched functions by most target genes in the present study.…”

Copy number variation and population-specific immune genes in the model vertebrate zebrafish

“…Studies relying on short read-based sequencing typically report fish NLRomes in the range of 20-50 genes, similar to what is known from mammals [18][19][20]. However, short reads can underestimate copy numbers when the copied sequence itself is much longer.…”

Transcriptome Revealed the Macrophages Inflammatory Response Mechanism and NOD-like Receptor Characterization in Siberian Sturgeon (Acipenser baerii)

“…In recent years, based on the genome and transcriptome database, NLRs of teleost have been reported in zebrafish (Danio rerio) [11], channel catfish (Ictalurus punctatus) [12], miiuy croaker (Miichthys miiuy) [13], grass carp (Ctenopharyngodon Idella) [14], black rockfish (Sebastes schlegeli) [15], Chinese tongue sole (Cynoglossus semilaevis) [16], and turbot (Scophthalmus maximus L.) [17]. Piscine NLRs were classified into four subfamilies, NLR-A, NLR-B, NLR-C, and other NLRs.…”

“…The NLRs with the B30.2 domain in grass carp were named NLR-B30.2, and NLRX was classified as an NLR-A subfamily [14]. All NLRs of the Chinese tongue sole containing the FISNA domain were named NLR-C, and NOD3/NLRC3 and NOD5/NLRX1 belong to the NLR-A subfamily [16]. Unlike the Teleostei, the Acipenseriformes are independent at the early stage of differentiation of the Scleroichthys.…”