A C1q domain-containing protein in Pinctada fucata contributes to the innate immune response and elimination of the pathogen

A C1q domain-containing protein from Scapharca subcrenata may participate in the immune defense against pathogen infection

The C1q domain-containing proteins (C1qDCs) have been shown to play crucial roles in immune responses among invertebrates, but few studies have focused on immune regulatory pathways in bivalves. In this study, we identified a C1qDC gene with a typical C1q domain (designated as SsC1qDC1) from Scapharca subcrenata and characterized its potential immune response against pathogen infection. The full-length cDNA sequence of SsC1qDC1 was 870 bp, encoding a peptide of 259 amino acids with an N-terminal signal peptide. Sequence analysis indicated that SsC1qDC1 was not conserved compared with C1qDCs from other bivalves. SsC1qDC1 was detected in all examined tissues, with higher expression levels in hepatopancreas, mantle, and gill. Concurrently, the expressions of SsC1qDC1 increased significantly from eggs to the gastrula stage and increased remarkably following Vibrio parahaemolyticus challenge. RNA interference-mediated knockdown of SsC1qDC1 significantly repressed the expressions of maternally derived immune-related genes (Vg, Lysozyme, Dscam, TEP, complement C3, and C1qDC3), while remarkably augmenting the expression of phenoloxidase activation factor PAF3. Furthermore, compared to the controls, the phagocytosis rate and total number of hemocytes were markedly reduced in the SsC1qDC1-silenced ark shells post V. parahaemolyticus infection, and thus, a significant increase in mortality rate and hemocyte apoptotic levels. Collectively, these findings implied that SsC1qDC1 may play crucial roles in immune defense against pathogen infection in ark shells.

A novel complement C1q A chain from marbled flounder, Pseudopleuronectes yokohamae: genome characterization, expression and potential role in antibacterial immunity

This study systematically analyzed the molecular characteristics, tissue expression, and function of the marbled flounder (Pseudopleuronectes yokohamae) C1qA protein (PyC1qA) in fish immunity. PyC1qA contains a signal peptide, collagen-like region, and globular head. Its amino acid sequence and globular structure are highly conserved among multiple species, especially at key sites for pathogen recognition. Phylogenetic analysis showed that PyC1qA has a close evolutionary relationship with other marine fish (such as marbled flounder and European flounder) but is different from freshwater fish. Tissue expression analysis showed that PyC1qA is highly expressed in the skin, and pathogen stimulation experiments showed that its expression changes dynamically in multiple immune-related tissues, indicating that it plays an important role in humoral immunity. Functional studies have shown that recombinant PyC1qA (rPyC1qA) can bind to a variety of fish pathogens and significantly enhance the hemolytic and bactericidal abilities of fish serum. Co-immunoprecipitation experiments verified the specific interaction between PyC1qA and IgM, further supporting its role in regulating humoral immunity through the classical complement pathway. In addition, in vivo experiments showed that rPyC1qA inhibited the proliferation of pathogens in immune-related tissues, demonstrating its potential anti-infection ability. This study revealed for the first time the molecular and functional characteristics of marbled flounder C1qA protein, expanded our understanding of the fish complement system in immune defense, and provided an important theoretical basis for the prevention and control of aquaculture diseases.

Identification of the C1qDC gene family in grass carp (Ctenopharyngodon idellus) and the response of C1qA, C1qB, and C1qC to GCRV infection in vivo and in vitro

Proteins from the C1q domain-containing (C1qDC) family recognize self-, non-self-, and altered-self ligands and serves as an initiator molecule for the classical complement pathway as well as recognizing immune complexes. In this study, C1qDC gene family members were identified and analyzed in grass carp (Ctenopharyngodon idellus). Members of the C1q subfamily were cloned, and their response to infection with the grass carp virus was investigated. In the grass carp genome, 54 C1qDC genes and 67 isoforms have been identified. Most were located on chromosome 3, with 52 shared zebrafish homologies. Seven substantially differentially expressed C1qDC family genes were identified in the transcriptomes of cytokine-induced killer (CIK) cells infected with grass carp reovirus (GCRV), all of which exhibited sustained upregulation. The opening reading frames of grass carp C1qA, C1qB, and C1qC, belonging to the C1q subfamily, were determined to be 738, 732, and 735 base pairs, encoding 245, 243, and 244 amino acids with molecular weights of 25.81 kDa, 25.63 kDa and 26.16 kDa, respectively. Three genes were detected in the nine collected tissues, and their expression patterns were similar, with the highest expression levels observed in the spleen. In vivo after GCRV infection showed expression trends of C1qA, C1qB, and C1qC in the liver, spleen, and kidney. An N-type pattern in the liver and kidney was characterized by an initial increase followed by a decrease, with the highest expression occurring during the recovering period, and a V-type pattern in the spleen with the lowest expression levels during the death period. In vitro, after GCRV infection showed expression trends of C1qA, C1qB, and C1qC, and this gradually increased within the first 24 h, with a notable increase observed at the 24 h time point. After CIK cells incubation with purified recombinant proteins, rC1qA, rC1qB, and rC1qC for 3 h, followed by GCRV inoculation, the GCRV replication indicated that rC1qC exerted a substantial inhibitory effect on viral replication in CIK cells after 24 h of GCRV inoculation. These findings offer valuable insights into the structure, evolution, and function of the C1qDC family genes and provide a foundational understanding of the immune function of C1q in grass carp.

Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum

BACKGROUND

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum.

METHODS

The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.

RESULTS

A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.

CONCLUSIONS

Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

Invertebrate C1q Domain-Containing Proteins: Molecular Structure, Functional Properties and Biomedical Potential

C1q domain-containing proteins (C1qDC proteins) unexpectedly turned out to be widespread molecules among a variety of invertebrates, despite their lack of an integral complement system. Despite the wide distribution in the genomes of various invertebrates, data on the structure and properties of the isolated and characterized C1qDC proteins, which belong to the C1q/TNF superfamily, are sporadic, although they hold great practical potential for the creation of new biotechnologies. This review not only summarizes the current data on the properties of already-isolated or bioengineered C1qDC proteins but also projects further strategies for their study and biomedical application. It has been shown that further broad study of the carbohydrate specificity of the proteins can provide great opportunities, since for many of them only interactions with pathogen-associated molecular patterns (PAMPs) was evaluated and their antimicrobial, antiviral, and fungicidal activities were studied. However, data on the properties of C1qDC proteins, which researchers originally discovered as lectins and therefore studied their fine carbohydrate specificity and antitumor activity, intriguingly show the great potential of this family of proteins for the creation of targeted drug delivery systems, vaccines, and clinical assays for the differential diagnosis of cancer. The ability of invertebrate C1qDC proteins to recognize patterns of aberrant glycosylation of human cell surfaces and interact with mammalian immunoglobulins indicates the great biomedical potential of these molecules.

Full-length transcriptome analysis provides new insights into the diversity of immune-related genes in the threatened freshwater shellfish Solenaia oleivora

Solenaia oleivora, a valuable and rare bivalve endemic to China, is becoming a threatened freshwater sepcies. However, the lack of research on its genome and immune system will hinder advances in its conservation and artificial breeding. In this study, we obtained the full-length transcriptome of S. oleivora using PacBio sequencing. A total of 21,415 transcripts with an average length of 1,726 bp were generated. Among these transcripts, 12,084 had coding sequences (CDS), of which 8,639 were annotated in 6 databases. The structure analysis identified 625 transcript factors (TFs), 8,005 long non-coding RNAs (lncRNAs), and 5,288 simple sequences repeat (SSRs). Meanwhile, massive immune genes were identified from the transcriptome of S. oleivora. In terms of non-self-identification, 97 transcripts of pattern recognition receptors (PRRs) were discovered, including peptidoglycan recognition proteins (PGRPs), gram-negative bacteria binding proteins (GNBPs), toll-like receptors (TLRs), scavenger receptors (SRs), galectins (GALs), C-type lectins (CLTs), and fibrinogen-related protein (FREPs). For pathogen elimination, 7 transcripts related to antimicrobial peptides, lysozymes, and lysosomal enzymes were identified. Moreover, 33 complement-associated transcripts were found. This study enriched the genome resources of S. oleivora and provided new insights for the study of the immune system of S. oleivora.