Integrative analysis of the miRNA-mRNA regulation network in hemocytes of Penaeus vannamei following Vibrio alginolyticus infection

Autophagy enhances the antibacterial response in Macrobrachium rosenbergii by modulating cellular metabolism and immune pathways

Autophagy plays a crucial role in innate and adaptive immunity against invading microorganisms. However, the mechanism underlying autophagy in Macrobrachium rosenbergii remains largely unknown. Here, we demonstrate that Aeromonas hydrophila activates autophagy in M. rosenbergii, according to Western blot, qRT-PCR, and transmission electron microscopy observations. Rapamycin treatment to activate autophagy in M. rosenbergii followed by stimulation with A. hydrophila significantly decreased the A. hydrophila OmpA copy number in the gills of M. rosenbergii. Furthermore, high-throughput RNA-seq analysis of M. rosenbergii gills treated with rapamycin revealed 1684 upregulated and 1500 downregulated differentially expressed genes (DEGs), most of which regulate metabolic pathways. A comprehensive joint analysis of the two transcriptomic databases for A. hydrophila infection and rapamycin treatment identified 15 upregulated and 25 downregulated DEGs, respectively. These genes enhance the immune defense of M. rosenbergii by negatively regulating metabolic pathways and promoting immune pathways. Our results provide a theoretical basis for further exploration of the antibacterial mechanism of M. rosenbergii.

A novel role of PvUCP4 in Penaeus vannamei in response to Vibrio alginolyticus challenge

Mitochondria are the energy production and metabolic centers of cells. About 90 % of reactive oxygen species come from mitochondria. Uncoupling proteins (UCPs) have a protective effect against oxidative stress in mitochondria. But this regulatory mechanism remains poorly understood in crustaceans. Here, we investigated the mechanism of PvUCP4 under vibrio alginolyticus challenge. Transcriptome analysis revealed that energy metabolism is a key pathway in the shrimp's immune response. Interestingly, PvUCP4, a mitochondrial uncoupling protein, was found to be inhibited, indicating its potential involvement in the shrimp's resistance to V. alginolyticus. Silencing PvUCP4 upregulates antioxidant enzyme gene expression, including SOD, CAT, and GPX. However, pretreatment with the ROS scavenger N-acetylcysteine revealed that silencing PvUCP4 had no effect on the expression of antioxidant genes. Pretreatment with LPS, a bacterial cell wall component, can rescue partial inhibition of DJ-1/NF-κB signaling pathway related genes caused by overexpression of PvUCP4. In addition, inhibiting PvUCP4 increased the expression of apoptosis-related genes and induced apoptosis. Ultimately, silencing PvUCP4 reduced the survival rate of shrimp under V. alginolyticus stress. Collectively, these findings suggest that PvUCP4 is neither dependent on the antioxidant enzyme system for its antioxidant effects nor on the negative feedback regulation of the DJ-1 pathway.

Transcriptomic insights into the resistance mechanism of Penaeus vannamei against highly lethal Vibrio parahaemolyticus

Highly lethal Vibrio disease (HLVD) caused by a virulent strain of Vibrio parahaemolyticus (VpHLVD), which poses a significant threat to Penaeus vannamei post-larvae, leads to substantial mortality and economic losses. To address this challenge, researchers have recently isolated a highly disease-resistant strain of P. vannamei shrimp. However, the underlying mechanisms that could improve disease resistance require further investigation. Our study found that disease-resistant shrimp exhibited a remarkable ability to prevent VpHLVD invasion effectively. To unravel the genetic basis of this resistance, we conducted a transcriptomic analysis with susceptible and disease-resistant shrimp at various time points (0, 6, and 12 h) post-infection with VpHLVD. Differential gene expression (DEGs) analysis of uninfected shrimp revealed that disease-resistant individuals displayed higher expression of immune-related genes and pathways compared to their susceptible counterparts. Simultaneously, they exhibited lower expression of Vibrio toxin-binding genes and Vibrio colonization gene, indicating enhanced defense mechanisms in the resistant shrimp. Upon VpHLVD infection, DEGs analysis also showed that susceptible shrimp attempt to mount a similar immune response as the disease-resistant shrimp during the early stages of infection. However, as the infection progresses, the defense strategies diverge between the two groups, with the peak of gene response occurring later in the disease-resistant shrimp. Our findings indicated that disease-resistant shrimp did not experience significant stress during the early stages of infection and are capable of effectively enhancing their immune response in the middle and late stages of the infection. In summary, our study enhanced the understanding of the mechanisms employed by disease-resistant shrimp to combat Vibrio, and would help to develop effective strategies for disease prevention and control, ultimately reducing the impact of HLVD on shrimp aquaculture.

Effects of Dietary 5-Aminolevulinic Acid on Growth, Nutrient Composition, and Intestinal Microflora in Juvenile Shrimp, Litopenaeus vannamei

5-Aminolevulinic acid (5-ALA) is an endogenous non-protein amino acid and has been used as a new type of growth promoter in aquaculture feed. This study explored the effects of 5-ALA on growth and intestinal health in juvenile shrimp, Litopenaeus vannamei. Shrimps were fed diets containing five different 5-ALA levels (0, 15, 30, 45, and 60 g/t) for 90 days. A concentration of 45 g/t 5-ALA significantly improved growth metrics, including the specific growth rate, protein efficiency, and feed conversion (P < 0.05). The optimal concentration of 5-ALA was 38.3 g/t, as indicated by broken-line regression. Dietary supplementation with 5-ALA increased the crude protein content of whole shrimp, but had no significant effect on the moisture, ash, or crude lipid content (P > 0.05). Suitable supplementation of 5-ALA (45 g/t, 60 g/t) improved the activities of the digestive enzymes alpha-amylase, pepsin, trypsin, and lipase, thus promoting digestion and absorption. Shrimp fed with 45 g/t 5-ALA had increased levels of essential amino acids in the muscles and a higher proportion of polyunsaturated fatty acids in the hepatopancreas. Supplementation with 45 or 60 g/t 5-ALA upregulated the expression of genes related to growth and molting, including chitinase, ecdysone receptor, retinoic X receptor, calcium/calmodulin-dependent protein kinase I, heat shock protein 60, and heat shock protein 70. Moreover, dietary supplementation with 5-ALA affected the abundance of intestinal flora, increased the number of beneficial bacteria, and improved intestinal health. These results indicated that 5-ALA may significantly benefit shrimp health and aquaculture productivity, providing a novel theoretical basis for further research into 5-ALA as a dietary supplement.

Differential expression of microRNAs in giant freshwater prawn (Macrobrachium rosenbergii) during the infection of Vibrio parahaemolyticus

MicroRNAs (miRNAs) are a category of small non-coding RNAs regarded as vital regulatory factors in various biological processes, especially immune regulation. The differently expressed miRNAs in Macrobrachium rosenbergii after the challenge of Vibrio parahaemolyticus were identified using high-throughput sequencing. A total of 18 known as well as 12 novel miRNAs were markedly differently expressed during the bacterial infection. The results of the target gene prediction and enrichment analysis indicated that a total of 230 target genes involved in a large variety of signaling pathways and biological processes were mediated by the miRNAs identified in the current research. Additionally, the effects of novel-miR-56, a representative differentially expressed miRNA identified in the previous infection experiment, on the immune-related gene expression in M. rosenbergii were explored. The expression of the immune-related genes including Spätzle1(Spz1), Spz4, Toll-like receptor 1 (TLR1), TLR2, TLR3, immune deficiency (IMD), myeloid differentiation factor 88 (MyD88), anti-lipopolysaccharide factor 1 (ALF1), crustin1, as well as prophenoloxidase (proPO) was significantly repressed in the novel-miR-56-overexpressed prawns. The expression of these genes tested in the novel-miR-56-overexpressed M. rosenbergii was still signally lower than the control in the subsequent V. parahaemolyticus challenge, despite the gene expression in each treatment increased significantly after the infection. Additionally, the cumulative mortality of the agomiR-56-treated prawns was significantly higher than the other treatments post the bacterial challenge. These results suggested that novel-miR-56 might function as a negative regulator of the immune-related gene expression of M. rosenbergii in the innate immune defense against V. parahaemolyticus.

Integration analysis of miRNA-mRNA uncovers the molecular immune mechanism of macrophage response to Aeromonas veronii infection

Macrophages are innate immunity cells which play pivotal roles in infectious immunity. Aeromonas veronii is a zoonotic agent capable of causing sepsis and poses a serious threat to public health. However, few studies have focused on miRNA-mRNA integration analysis to address the immune mechanisms of macrophage response to A. veronii infection. Herein, we characterized the immunophysiological, biochemical, and transcriptome changes of macrophage under A. veronii infection. We found that macrophages infected with A. veronii released large amounts of cytokines and triggered NLRP3-dependent pyroptosis. Subsequently, 603 differentially expressed miRNAs (DEMIs) and 3693 differentially expressed mRNAs (DEMs) were identified by RNA-seq analysis under A. veronii infection. Moreover, integrated analysis of miRNA-mRNA yielded 66 miRNA-target gene pairs composed of 41 DEMIs and 27 DEMs. We next identified the Toll-like receptor, NOD-like receptor, TNF and NF-κB pathways as necessary for macrophage to respond to A. veronii infection. miR-847 and miR-627 were involved in macrophage response to A. veronii infection by negatively regulating Pannexin-1 and thioredoxin interacting protein (TXNIP). Our findings elucidate the molecular mechanism of macrophage response to A. veronii infection at the miRNA level, providing many candidate miRNAs and mRNAs therapeutic targets for the prevention and treatment of A. veornii infectious diseases.

MicroRNA sequencing analysis reveals immune responses in hepatopancreas of Fenneropenaeus penicillatus under white spot syndrome virus infection

White Spot Disease is one of the most harmful diseases of the red tail shrimp, which can cause devastating economic losses due to the highest mortality up to 100% within a few days. MicroRNAs (miRNAs) are large class of small noncoding RNAs with the ability to post-transcriptionally repress the translation of target mRNAs. MiRNAs are considered to have a significant role in the innate immune response of crustaceans, particularly in relation to antiviral defense mechanisms. Numerous crustacean miRNAs have been verified to be required in host immune defense against viral infection, however, till present, the miRNAs functions of F. penicillatus defense WSSV infection have not been studied yet. Here in this study, for the first time, miRNAs involved in the F. penicillatus immune defense against WSSV infection were identified using high-throughput sequencing platform. A total of 432 miRNAs were obtained including 402 conserved miRNAs and 30 novel predicted miRNAs. Comparative analysis between the WSSV-challenged group and the control group revealed differential expression of 159 microRNAs in response to WSSV infection. Among these, 48 were up-regulated and 111 were down-regulated. Ten candidate MicroRNAs associated with immune activities were randomly selected for qRT-PCR analysis, which confirming the expression profiling observed in the MicroRNA sequencing data. As a result, most differentially expressed miRNAs were down-regulated lead to increase the expression of various target genes that mediated immune reaction defense WSSV infection, including genes related to signal transduction, Complement and coagulation cascade, Phagocytosis, and Apoptosis. Furthermore, the genes expression of the key members in Toll and Imd signaling pathways and apoptotic signaling were mediated by microRNAs to activate host immune responses including apoptosis against WSSV infection. These results will help to understand molecular defense mechanism against WSSV infection in F. penicillatus and to develop an effective WSSV defensive strategy in shrimp farming.

Integrated analysis of a miRNA-mRNA network related to immunity and autophagy in Macrobrachium rosenbergii infected with Aeromonas hydrophila

MicroRNAs (miRNAs) are a group of RNAs that regulate gene expression in the post-transcriptionally. miRNAs can regulate numerous processes, such as the immune response, due to their dynamic expression patterns. The giant freshwater prawn Macrobrachium rosenbergii is a major freshwater aquaculture prawn that is attacked by various bacteria, including Aeromonas hydrophila. For this study, we performed an analysis of the miRNA and mRNA transcriptome analysis of M. rosenbergii which was infected with A. hydrophila. We identified 56 differentially expressed miRNAs (DEMs) and 1542 differentially expressed mRNAs. Furthermore, an integrated analysis of miRNA-mRNA expression led to the identification of 729 differentially predicted target genes (DETGs) of the DEMs. Multiple functional categories related to immunity, apoptosis, and autophagy were found to be enriched in the DETGs. During the infection of M. rosenbergii by A. hydrophila, an elaborate regulatory network involving Toll and immune deficiency (IMD) signaling, mitogen-activated protein kinase (MAPK) signaling, lysosome, and cell apoptosis was formed by a complex interplay of 40 crucial DEMs and 22 DETGs, all associated with the immune and autophagy pathway. The findings suggest that infection with A. hydrophila triggers intricate responses in both miRNA and mRNA, significantly impacting immune and autophagy processes in M. rosenbergii.

Andrographis paniculata improves growth and non-specific immunity of shrimp Litopenaeus vannamei, and protects it from Vibrio alginolyticus by reducing oxidative stress and apoptosis

Andrographis paniculata (AP) is a traditional medicinal plant with many pharmacological activities, including anti-inflammatory, antimicrobial, immunity stimulation and so on. Several studies have reported that AP plays a strong role in promoting the immune system of aquatic animals to resist several pathogens. In the present study, we investigate the effects of a diet containing AP on the immune responses, growth, and the resistance to Vibrio alginolyticus (V. alginolyticus) in Litopenaeus vannamei (L. vannamei). Four diets were formulated by adding AP at the dosage of 0% (Control), 0.25%, 0.5%, and 1% in the basal diet, respectively. Each diet was randomly fed to one group with three replicates of shrimps in a 28-day feeding trial. The results showed that dietary AP improved the growth performance and non-specific immune function of shrimps. To investigate the effect of AP on disease resistance of L. vannamei, shrimps fed with diet containing AP were challenged with V. alginolyticus. Compared with the control group, the shrimps fed diet containing AP showed significantly higher survival. Furthermore, the hepatopancreas injury in the shrimp fed with AP was less than control group at 6 h after V. alginolyticus infection. However, no difference was observed in the degree of hepatopancreas injury between AP groups and control group at 12 h and 24 h after V. alginolyticus infection. Based on this result, the samples at 6 h after V. alginolyticus infection was selected for subsequent detection. Reactive oxygen species (ROS) accumulation in hemocytes and O₂^- production in hepatopancreas caused by V. alginolyticus infection was significantly reduced after feeding a diet containing 0.25% and 0.5% AP (p < 0.05). In addition, we found that feeding AP significantly up-regulated the expression of pro-apoptotic genes (Bax, Caspase 3, p53) and down-regulated the expression of anti-apoptotic genes (Bcl-2) in hepatopancreas after V. alginolyticus infection. In conclusion, AP promote the growth and immunity of L. vannamei, and protects shrimps against V. alginolyticus by regulating the oxidative damage and apoptosis. These results provide useful information regarding the effects of AP extracts as a shrimp feed additive for sustainable shrimp culture.

Holistic analysis of lysine acetylation in aquaculture pathogenic bacteria Vibrio alginolyticus under bile salt stress

Lysine acetylation modification is a dynamic and reversible post-translational modification, which plays an important role in the metabolism and pathogenicity of pathogenic bacteria. Vibrio alginolyticus is a common pathogenic bacterium in aquaculture, and bile salt can trigger the expression of bacterial virulence. However, little is known about the function of lysine acetylation in V. alginolyticus under bile salt stress. In this study, 1,315 acetylated peptides on 689 proteins were identified in V. alginolyticus under bile salt stress by acetyl-lysine antibody enrichment and high-resolution mass spectrometry. Bioinformatics analysis found that the peptides motif ^****A^*Kac^**** and ^*******Kac^****A^* were highly conserved, and protein lysine acetylation was involved in regulating various cellular biological processes and maintaining the normal life activities of bacteria, such as ribosome, aminoacyl-tRNA biosynthesis, fatty acid metabolism, two-component system, and bacterial secretion system. Further, 22 acetylated proteins were also found to be related to the virulence of V. alginolyticus under bile salt stress through secretion system, chemotaxis and motility, and adherence. Finally, comparing un-treated and treated with bile salt stress lysine acetylated proteins, it was found that there were 240 overlapping proteins, and found amino sugar and nucleotide sugar metabolism, beta-Lactam resistance, fatty acid degradation, carbon metabolism, and microbial metabolism in diverse environments pathways were significantly enriched in bile salt stress alone. In conclusion, this study is a holistic analysis of lysine acetylation in V. alginolyticus under bile salt stress, especially many virulence factors have also acetylated.

Andrographolide promote the growth and immunity of Litopenaeus vannamei, and protects shrimps against Vibrio alginolyticus by regulating inflammation and apoptosis via a ROS-JNK dependent pathway

Vibrio alginolyticus (V. alginolyticus) is one of the major pathogens causing mass mortality of shrimps worldwide, affecting energy metabolism, immune response and development of shrimps. In the context of the prohibition of antibiotics, it is necessary to develop a drug that can protect shrimp from V. alginolyticus. Andrographolide (hereinafter called Andr), a traditional drug used in Chinese medicine, which possesses diverse biological effects including anti-bacteria, antioxidant, immune regulation. In this study, we investigated the effect of Andr on growth, immunity, and resistance to V. alginolyticus infection of Litopenaeus vannamei (L. vannamei) and elucidate the underlying molecular mechanisms. Four diets were formulated by adding Andr at the dosage of 0 g/kg (Control), 0.5 g/kg, 1 g/kg, and 2 g/kg in the basal diet, respectively. Each diet was randomly fed to one group with three replicates of shrimps in a 4-week feeding trial. The results showed that dietary Andr improved the growth performance and non-specific immune function of shrimps. L. vannamei fed with Andr diets showed lower mortality after being challenged by V. alginolyticus. After 6 h of V. alginolyticus infection, reactive oxygen species (ROS) production, tissue injury, apoptosis, expression of inflammatory factors (IL-1 β and TNFα) and apoptosis-related genes (Bax, caspase3 and p53) were increased in hemocytes and hepatopancreas, while feeding diet with 0.5 g/kg Andr could inhibit the increase. Considering that JNK are important mediators of apoptosis, we examined the influence of Andr on JNK activity during V. alginolyticus infection. We found that Andr inhibited JNK activation induced by V. alginolyticus infection on L. vannamei. The ROS scavenger N-acetyl-l-cysteine (NAC) suppressed V. alginolyticus-induced inflammation and apoptosis, suggesting that ROS play an important role in V. alginolyticus-induced inflammation and apoptosis. Treated cells with JNK specific activator anisomycin, the inflammation and apoptosis inhibited by Andr were counteracted. Collectively, Andr promote the growth and immunity of L. vannamei, and protects shrimps against V. alginolyticus by regulating inflammation and apoptosis via a ROS-JNK dependent pathway. These results improve the understanding of the pathogenesis of V. alginolyticus infection and provide clues to the development of effective drugs against V. alginolyticus.