The polymorphisms of a MIF gene and their association with Vibrio resistance in the clam Meretrix meretrix

Comprehensive Multi-omics Approaches Provide Insights to Summer Mortality in the Clam Meretrix petechialis

Bivalve mass mortalities have been reported worldwide, which not only can be explained as a result of pathogen infection, but may reflect changes in environments. Although these episodes were often reported, there was limited information concerning the molecular responses to various stressors leading to summer mortality. In the present work, RNA sequencing (RNA-seq), tandem mass tagging (TMT)-based quantitative proteomics, and 16S rRNA sequencing were used to explore the natural outbreak of summer mortality in the clam Meretrix petechialis. We identified a total of 172 differentially expressed genes (DEGs) and 222 differentially expressed proteins (DEPs) in the diseased group compared to the normal group. The inconsistent expression profiles of immune DEGs/DEPs may be due to the immune dysregulation of the diseased clams. Notably, 11 solute carrier family genes were found among the top 20 down-regulated genes in the diseased group, indicating that weakened transmembrane transport ability might occur in the diseased clams. Integration analysis of transcriptomic and proteomic results showed that many metabolic processes such as "arginine and proline metabolism" and "tyrosine metabolism" were inhibited in the diseased group, suggesting metabolic inhibition. Moreover, 16S rRNA sequencing revealed that the microbial composition of clam hepatopancreas was disordered in the diseased group. The comparison of DEGs expression between the natural summer mortality event and an artificial challenge experiment involving both Vibrio infection and heat stress revealed 9/15 genes showing similar expression trends between the two conditions, suggesting that the summer mortality might be caused by a combination of high temperature and Vibrio infection. These results would deepen our understanding of summer mortality and provide candidate resistance markers for clam resistance breeding.

Characterization of the lipidomic profile of clam Meretrix petechialis in response to Vibrio parahaemolyticus infection

Vibrio parahaemolyticus is a devastating pathogen of clam Meretrix petechialis, which brings about huge economic losses in aquaculture breeding industry. In our previous study, we have found that Vibrio infection is closely associated with lipid metabolism of clams. In this study, an untargeted lipidomics approach was used to explore the lipid profiling changes upon Vibrio infection. The results demonstrated that the hepatopancreas of clams was composed of five lipid categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. And the content of lipid classes altered during Vibrio infection, implying that Vibrio infection altered intracellular lipid homeostasis in clams. Meanwhile, a total of 200 lipid species including 82 up-regulated and 118 down-regulated significantly were identified in response to Vibrio infection, of which ceramide (Cer), phosphatidylcholine (PC) and triglyceride (TG) accounted for the largest proportion. Notably, all Cers showed a significantly decreased trend while nearly all TG species were increased significantly during Vibrio infection, which suggested that Cer and TG could be determined as effective biomarkers. Furthermore, these differentially expressed lipid species were enriched in 20 metabolic pathways and sphingolipid metabolism was one of the most enriched pathways. These results evidenced how the lipid metabolism altered in the process of Vibrio infection and opened a new perspective on the response of marine bivalves to pathogen infection.

Function and association analysis of Cyclophilin A gene with resistance to Edwardsiella ictaluri in yellow catfish

Edwardsiella ictaluri (E. ictaluri) is one of the main bacterial pathogens in catfish which has caused serious economic loss to yellow catfish (Pelteobagrus fulvidraco) in China. In our previous work, we demonstrated that CypA was up-regulated at the early stage of E. ictaluri infection in yellow catfish and displayed strong chemotactic activity for leukocytes in vitro. However, the effect of CypA on E. ictaluri is unknown in vivo. Therefore, two homozygous transgenic zebrafish lines expressing yellow catfish CypA (TG-CypA-1 and TG-CypA-2) were generated. After challenged with E. ictaluri at a dose of 1.0 × 10⁴ CFU per adult fish, both two transgenic lines exhibited a higher resistance to bacterial infection than the wildtype zebrafish. Herein, CypA gene in E. ictaluri-challenged yellow catfish was screened for presence of polymorphisms by sequencing and six single nucleotide polymorphisms (SNPs) were identified. SNP association analysis revealed that 528T/C SNP in the first intron was significantly different in disease-susceptible and -resistant groups, which was confirmed in two independent populations of yellow catfish. Moreover, the relative expression of CypA in the resistant group (CC genotype in 528T/C SNP) was significantly higher than that in the susceptible group (TT genotype in 528T/C SNP) in different immune organs of yellow catfish including spleen, head kidney, body kidney and liver. Our results reveal the potential function of CypA in host defense to bacterial infection and suggest the SNP marker in CypA gene associated with the resistance to E. ictaluri may facilitate the selective breeding of disease-resistant yellow catfish in the future.

Expansion and loss events characterized the occurrence of MIF-like genes in bivalves

Macrophage migration inhibitory factor (MIF) dynamically connects innate and adaptive immune systems in vertebrate animals, allowing highly orchestrated systemic responses to various insults. The occurrence of MIF-like genes in non-vertebrate organisms suggests its origin from an ancestral metazoan gene, whose function is still a matter of debate. In the present work, by analyzing available genomic and transcriptomic data from bivalve mollusks, we identified 137 MIF-like sequences, which were classified into three types, based on phylogeny and conservation of key residues: MIF, D-DT, and the lineage-specific type MDL. Comparative genomics revealed syntenic conservation of homologous genes at the family level, the loss of D-DT in the Ostreidae family as well as the expansion of MIF-like genes in the Mytilidae family, possibly underpinning the neofunctionalization of duplicated gene copies. In M. galloprovincialis, MIF and one D-DT were mostly expressed in haemocytes and mantle rim of untreated animals, while D-DT paralogs often showed very limited expression, suggesting an accessory role or their persistence as relict genes.

Functional differentiation of three phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) in response to Vibrio anguillarum infection in turbot (Scophthalmus maximus)

PIK3CA has been extensively investigated from its molecular mechanism perspective and association with its mutations in different types of cancers. However, little has been reported regarding the pathological significance of PIK3CA expression in teleost. Here, in our present study, three PIK3CA genes termed SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were firstly identified in the genome of turbot S. maximus. Although these three genes located in different chromosomes, all of them share the same five domains. Phylogenetic and synteny analysis indicated that SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were three paralogs that may originate from duplication of the same ancestral PIK3CA gene. Subcellular localization analysis confirmed the cytoplasm distribution of these three paralogs. All three SmPIK3CA were ubiquitously expressed in examined tissues in turbot, with the higher expression levels in immune-related tissues such as blood, spleen, kidney, gills and intestines. Upon Vibrio anguillarum challenge, SmPIK3CAa and SmPIK3CA-like transcripts were significantly induced in spleen, intestine and blood despite of differential expression levels and responsive time points. Additionally, individuals in resistant group showed significantly higher expression level of both two genes than in the susceptible group. Moreover, four SNPs (102, 2530, 3027 and 3060) and one haplotype (Hap2) located in exon region of SmPIK3CA-like were identified and confirmed to be associated with V. anguillarum resistance in turbot by association analysis in different populations. Taken together, these results suggested that functional differentiation occurred in three SmPIK3CA paralogs with Vibrio anguillarum resistance and SmPIK3CAa and SmPIK3CA-like probable play potential roles in innate immune response to pathogenic invasions in turbot.

Two macrophage migration inhibitory factors (MIFs) from the clam Ruditapes philippinarum: Molecular characterization, localization and enzymatic activities

Macrophage migration inhibitory factor (MIF) is an evolutionarily ancient cytokine-like factor and plays a critical role in both innate and adaptive immunity. In the present study, two MIFs (designed as RpMIF-1 and RpMIF-2, respectively) were identified and characterized from the clam Ruditapes philippinarum by rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of RpMIF-1 and RpMFI-2 consisted of 531 and 722 nucleotides, encoding a polypeptide of 113 and 114 amino acid residues, respectively. Multiple alignments and phylogenetic analysis revealed that both RpMIF-1 and RpMIF-2 belonged to the MIF family. The conserved catalytic-site Pro² for tautomerase activity was identified in the deduced amino acid sequences of RpMIFs. Both RpMIF-1 and RpMIF-2 transcripts were constitutively expressed in examined tissues of R. philippinarum with dominant expression in hepatopancreas, gills and hemocytes. Immunolocalization analysis showed that RpMIF-1 and RpMIF-2 proteins were expressed in examined tissues with the exception of adductor muscle and foot. After Vibrio anguillarum and Micrococcus luteus challenge, the mRNA expression of RpMIFs was significantly modulated in hemocytes, gills and hepatopancreas. Recombinant RpMIF-1 and RpMIF-2 proteins possessed significant tautomerase activity and oxidoreductase activity, indicating that these two proteins was perhaps involved in inflammatory responses. In summary, our results suggested that RpMIF-1 and RpMIF-2 played an important role in the innate immunity of R. philippinarum.

Identification of an MITF gene and its polymorphisms associated with the Vibrio resistance trait in the clam Meretrix petechialis

Microphthalmia-associated transcription factor (MITF) regulates the transcription of its target genes by binding to their promoters. In this study, an MITF gene, MpMITF was identified in the clam Meretrix petechialis. The full-length cDNA of MpMITF is 3564 bp with an ORF of 1365 bp. The deduced amino acid sequence consists of a conserved functional structure of bHLH-LZ, which could bind with E-box. The mRNA and protein expression levels of MpMITF were significantly up-regulated 6 h post-Vibrio injection. The mRNA expression of MpMITF increased on day 2 and peaked on day 10 post-Vibrio immersion. Furthermore, MpMITF expression was significantly up-regulated in most resistant families of clams (P < 0.05) but did not change significantly in most susceptive families of clams after the Vibrio immersion challenge. These results suggest that, in clams, MpMITF participates in the immune response against a Vibrio infection. Genotyping in two clam groups with different resistant levels to Vibrio parahaemolyticus (i.e., 11-R and 11-S), thirteen SNPs and five haplotypes were detected in the DNA sequence of MpMITF, of which five SNPs and two haplotypes were associated with Vibrio resistance. Four SNPs (SNP2, 5, 6 and 13) and one haplotype (Hap1) were further confirmed to be associated with Vibrio resistance in M. petechialis by association analysis in different clam families. This study deepens the understanding of MITF in marine bivalves and provides potential candidate markers for resistance selection in the clam M. petechialis.