New insights into the Manila clam and PAMPs interaction based on RNA-seq analysis of clam through in vitro challenges with LPS, PGN, and poly(I:C)

Abstract

Background: Manila clam (Ruditapes philippinarum) is a worldwide commercially important marine bivalve species. In recent years, however, microbial diseases caused high economic losses and have received increasing attention. To understand the molecular basis of the immune response to pathogen-associated molecular patterns (PAMPs) in R. philippinarum, transcriptome libraries of clam hepatopancreas were constructed at 24 h post-injection with Lipopolysaccharide (LPS), peptidoglycan (PGN), and polyinosinic-polycytidylic acid (poly(I:C)) and phosphatebuffered saline (PBS) control by using RNA sequencing technology (RNA-seq). Results: A total of 832, 839, and 188 differentially expressed genes (DEGs) were found in LPS, PGN, and poly(I:C) challenge group compared with PBS control, respectively. Several immune-related genes and pathways were activated in response to the different PAMPs, suggesting these genes and pathways might specifically participate in the immune response to pathogens. Besides, the analyses provided useful complementary data to compare different PAMPs challenges in vivo. Functional enrichment analysis of DEGs demonstrated that PAMPs responsive signal pathways were related to apoptosis, signal transduction, immune system, and signaling molecules and interaction. Several shared or specific DEGs response to different PAMPs were revealed in R. philippinarum, including pattern recognition receptors (PRRs), antimicrobial peptides (AMPs), interferon-induced proteins (IFI), and some other immune-related genes were found in the present work. Conclusions: This is the first study employing high throughput transcriptomic sequencing to provide valuable genomic resources and investigate Manila clam response to different PAMPs through in vivo challenges with LPS, PGN, and poly(I:C). The results obtained here provide new insights to understanding the immune characteristics of R. philippinarum response to different PAMPs. This information is critical to elucidate the molecular basis of R. philippinarum response to different pathogens invasion, which potentially can be used to develop effective control strategies for different pathogens.

Stimulation of Mytilus galloprovincialis Hemocytes With Different Immune Challenges Induces Differential Transcriptomic, miRNomic, and Functional Responses

“…This PAMP efficiently triggered the expression of many non-self-recognition and immune-response genes, such as TLRs, PGRPs, LBP and lectins (mantle gene, galaxin, and perlucin), among others. PGRP and different lectins were also induced by LPS in the hepatopancreas of R. philippinarum, although the TLR signalling pathway seemed to be unaffected (65). Interestingly, a high number of complement-related genes was induced in that case (65).…”

“…Two transcripts annotated as tubulin, namely, tubulin beta-5 chain and tubulin alpha chain, were overexpressed by 65.44-and 28.35-fold, respectively, after LPS stimulation. Overexpression of transcripts annotated as tubulin alpha-3 chain and dynein heavy chain were also observed in Manila clams stimulated with LPS or PGN (65). Tubulin chains constitute the cell microtubules, which are essential for phagocytosis, a pivotal mechanism both for the clearance of pathogens and the removal of apoptotic cells and debris to maintain homeostatic conditions (72).…”

“…This observation could be an indication that the antiviral response in mussel hemocytes would be biased towards miRNA transcription. Indeed, when Manila clams (Ruditapes philippinarum) were inoculated with the bacterial PAMPs LPS and peptidoglycan (PGN) and the viral stimulus poly I:C, lower gene modulation in the hepatopancreas was also observed in response to poly I:C (65). In contrast, the LPS miRNomic response is discrete when compared to the transcriptomic response, that it is by far the highest response elicited by the three PAMPs.…”

“…PGRP and different lectins were also induced by LPS in the hepatopancreas of R. philippinarum, although the TLR signalling pathway seemed to be unaffected (65). Interestingly, a high number of complement-related genes was induced in that case (65). The pathways of PAMP recognition have been proposed as driving mechanisms of innate immune memory (66,67).…”

Comparative Proteomics of Ostreid Herpesvirus 1 and Pacific Oyster Interactions With Two Families Exhibiting Contrasted Susceptibility to Viral Infection

“…In vertebrates, the IFN system is a major antiviral response, leading to the transcription of many interferon-stimulated genes (ISGs) that work together to inhibit the replication and spread of viruses ( 86 ). Several studies assumed that bivalves, including C. gigas , have an IFN-like system equivalent to the vertebrate type I IFN pathway ( 47 , 87 , 88 ). The modulation of IFN-genes, such as IFI44, in C. gigas infected with OsHV-1 was first observed by Renault et al.…”