Integrated RNA-seq and RNAi Analysis of the Roles of the Hsp70 and SP Genes in Red-Shell Meretrix meretrix Tolerance to the Pathogen Vibrio parahaemolyticus

Abstract

The “Wanlihong” Meretrix meretrix (WLH-M) clam is a new variety of this species that has a red shell and stronger Vibrio tolerance than ordinary M. meretrix (ORI-M). To investigate the molecular mechanisms responsible for the WLH-M strain’s tolerance to Vibrio , we challenged clams with Vibrio parahaemolyticus and then assessed physiological indexes and conducted transcriptome analysis and RNA interference experiments. The mortality, tissue bacterial load, and hemocyte reactive oxygen species level of ORI-M were significantly higher than those of WLH-M, whereas the content and activity of lysozyme were significantly lower. Gene Ontology functional annotation analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that immune and metabolic pathways were enriched in Vibrio -challenged clams. The expressions of the heat shock protein 70 ( Hsp70 ) and serine protease ( SP ) genes, which are involved in antibacterial immunity, were significantly upregulated in WLH-M but not in ORI-M, while the expression of the kynurenine 3-monooxygenase gene, a proinflammatory factor, was significantly downregulated in WLH-M. RNA interference experiments confirmed that Hsp70 and SP downregulation could result in increased mortality of WLH-M. Therefore, we speculate that Hsp70 and SP may be involved in the antibacterial immunity of WLH-M in vivo. Our data provided a valuable resource for further studies of the antibacterial mechanism of WLH-M and provided a foundation for the breeding of pathogen-resistant strains. Supplementary Information The online version contains supplementary material available at 10.1007/s10126-022-10156-6.

Strategies to increase the robustness of microbial cell factories

“…This approach has several advantages, such as fast and efficient processing capability, wide coverage, and high accuracy, and has been utilized in a variety of bacterial species to provide comprehensive information on gene functions. Integration of RNA-sequencing and RNA interference (RNAi) is also proved to be an efficient method to investigate the molecular mechanisms responsible for microbial tolerance (Zheng et al 2022). Clustered regularly interspaced short palindromic repeats (CRISPR) screens, which utilize the efficiency and flexibility of CRISPR-Cas (CRISPR-associated protein) genome editing, have become another popular and productive tool for uncovering previously unknown molecular mechanisms (Doench 2018;Bock et al 2022).…”