Integrative microRNA and mRNA analysis reveals regulation of ER stress in the Pacific white shrimp Litopenaeus vannamei under acute cold stress

Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis

The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.

Expression Regulation Mechanisms of Sea Urchin (Strongylocentrotus intermedius) Under the High Temperature: New Evidence for the miRNA-mRNA Interaction Involvement

In the context of global warming and continuous high temperatures in the northern part of China during summer, the mortality rate of our main breeding species, Strongylocentrotus intermedius, reached 80% in 2020. How sea urchins respond to high temperatures is of great concern to academia and industry. In this study, we examined the antioxidant enzyme activities of different color tube-footed sea urchins under heat stress and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. The results showed that the antioxidant enzyme activities of sea urchins were altered by thermal stress, and the changes in peroxidase activities of red tube-footed sea urchins were particularly significant. Investigations revealed that 1,079 differentially expressed genes (DEGs), 11 DE miRNAs, and 104 “DE miRNA-DEG” pairs in total were detected in sea urchins under high temperature stress. Several mRNA and miRNAs were significantly changed (e.g. HSP70, DnaJ11, HYAL, CALR, miR-184-p5, miR-92a, miR-92c, and miR-124-p5), suggesting these genes and miRNAs exerted important functions in response to high temperature. At the transcriptional level, red tube-footed sea urchins were found to be more sensitive to high temperature and could respond to high temperature rapidly. DE miRNA-mRNA network showed that miR-92b-3p and PC-5p-7420 were the most corresponding miRNAs. Five mRNAs (DnaJ11, SAR1B, CALR, HYOU1, TUBA) may be potential markers of sea urchin response to high temperature. Possible interaction between miRNA-mRNA could be linked to protein folding in the endoplasmic reticulum, Phagosomes, and calcium transport. This study provides a theoretical basis for the molecular mechanism of sea urchin heat tolerance and information that will aid in the selection and breeding of sea urchins with high temperature tolerance.

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

Penaeus vannamei is an important cultured shrimp that has high commercial value in the worldwide. However, the industry suffers heavy economic losses each year due to disease outbreaks caused by pathogenic bacteria. In the present study, after Vibrio alginolyticus infection, DNA damage in the hemocytes of the shrimp markedly increased, and autophagy and apoptosis increased significantly. Subsequently, hemocytes were sampled from the control and infected shrimp and sequenced for mRNA and microRNA (miRNA) 24 h after V. alginolyticus infection to better understand the response mechanism to bacterial infection in P. vannamei. We identified 1,874 and 263 differentially expressed mRNAs (DEGs) and miRNAs (DEMs) respectively, and predicted that 997 DEGs were targeted by DEMs. These DEGs were involved in the regulation of multiple signalling pathways, such as Toll and IMD signalling, TGF-beta signalling, MAPK signalling, and cell apoptosis, during Vibrio alginolyticus infection of the shrimp. We identified numerous mRNA-miRNA interactions, which provide insight into the defense mechanism that occur during the antimicrobial process of P. vannamei.

A unique miR775-GALT9 module regulates leaf senescence in Arabidopsis during post-submergence recovery by modulating ethylene and the abscisic acid pathway

The submergence-induced hypoxic condition negatively affects the plant growth and development, and causes early onset of senescence. Hypoxia alters the expression of a number of microRNAs (miRNAs). However, the molecular function of submergence stress-induced miRNAs in physiological or developmental changes and recovery remains poorly understood. Here, we show that miR775 is an Arabidopsis thaliana-specific young and unique miRNA that possibly evolved non-canonically. miR775 post-transcriptionally regulates GALACTOSYLTRANSFERASE 9 (GALT9) and their expression is inversely affected at 24 h of complete submergence stress. The overexpression of miR775 (miR775-Oe) confers enhanced recovery from submergence stress and reduced accumulation of RBOHD and ROS, in contrast to wild-type and MIM775 Arabidopsis shoot. A similar recovery phenotype in the galt9 mutant indicates the role of the miR775-GALT9 module in post-submergence recovery. We predicted that Golgi-localized GALT9 is potentially involved in protein glycosylation. The altered expression of senescence-associated genes (SAG12, SAG29 and ORE1), ethylene signalling (EIN2 and EIN3) and abscisic acid (ABA) biosynthesis (NCED3) pathway genes occurs in miR775-Oe, galt9 and MIM775 plants. Thus, our results indicate the role for the miR775-GALT9 module in post-submergence recovery through a crosstalk between the ethylene signalling and ABA biosynthesis pathways.

Whole Transcriptome Analysis Revealed a Stress Response to Deep Underground Environment Conditions in Chinese Hamster V79 Lung Fibroblast Cells

Background: Prior studies have shown that the proliferation of V79 lung fibroblast cells could be inhibited by low background radiation (LBR) in deep underground laboratory (DUGL). In the current study, we revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL.

Methods: Whole transcriptome analysis including lncRNA, mRNAs, circ RNA and miRNA was performed in V79 cells cultured for two days in DUGL and above ground laboratory (AGL), respectively. The differentially expressed (DE) lncRNA, mRNA, circRNA, and miRNA in V79 cells were identified by the comparison between DUGL and AGL groups. Quantitative real-time polymerase chain reaction(qRT-PCR)was conducted to verify the selected RNA sequencings. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed for the DE mRNAs which enabled to predict target genes of lncRNA and host genes of circRNA.

Results: With |log₂(Fold-change)| ≥ 1.0 and p < 0.05, a total of 1257 mRNAs (353 mRNAs up-regulated, 904 mRNAs down-regulated), 866 lncRNAs (145 lncRNAs up-regulated, 721 lncRNAs down-regulated), and 474 circRNAs (247 circRNAs up-regulated, 227 circRNAs down-regulated) were significantly altered between the two groups. There was no significant difference in miRNA between the two groups. The altered RNA profiles were mainly discovered in lncRNAs, mRNAs and circRNAs. DE RNAs were involved in many pathways including ECM-RI, PI3K-Akt signaling, RNA transport and the cell cycle under the LBR stress of the deep underground environment.

Conclusion: Taken together, these results suggest that the LBR in the DUGL could induce transcriptional repression, thus reducing metabolic process and reprogramming the overall gene expression profile in V79 cells.

Impacts of microplastics on three different juvenile shrimps: Investigating the organism response distinction

The effects of microplastics (MPs) on aquaculture animals have raised increasing concern, but studies on MPs contamination in cultured shrimp are still limited. Therefore, the responses of three widely farmed shrimp species to MPs, including Penaeus monodon (P. monodon), Marsupenaeus japonicas (M. japonicus) and Litopenaeus vannamei (L. vannamei), were investigated in this study. The results showed that the mortality of P. monodon, M. japonicus and L. vannamei were 47%, 53% and 20% respectively after 48 h of 300 mg/L MPs exposure. After 48 h of 100 mg/L MPs exposure, for P. monodon, the MPs content in water and excreta were significantly different from that in M. japonicus and L. vannamei. For genes expressions, the expression of catalase (Cat) was significantly increased and the expression of apoptosis protein (IAP) was inhibited in these three shrimps, but only the expression of Lysozyme (Lys) was increased in L. vannamei after MPs exposure. After 48 h of depuration, the Cat and IAP expression of P. monodon and M. japonicus was significant decreased while the IAP and Lys expression of L. vannamei still maintained at a high level. The results suggested that the metabolic rate of MPs in P. monodon was significantly higher than that in M. japonicus and L. vannamei. The tolerance of L. vannamei to MPs was higher than that of P. monodon and M. japonicas and their different responses in anti-microbial gene might be one of the reasons for the difference of their mortality. This study provides the first report comparing the organism response distinction in cultured shrimp and enriching to the understanding of the impact of MPs on ecosystem.

Insight into the immune and microbial response of the white-leg shrimp Litopenaeus vannamei to microplastics

Microplastics (MPs) are a new type of environmental pollutant. To investigate the response of shrimp and their microflora to MPs, Litopenaeus vannamei (L. vannamei) was exposed to different concentrations of MPs (0, 50, 500, and 5000 μg/L, i.e., C, L, M and H groups) for 48 h. The survival rate, intake of MPs, immune-related gene expression and microbial response under MP exposure were detected. The results showed that the survival rate in the H group was significantly lower than those in the C, L and M groups, while the relative expression levels of proPO, TLR and ALF in the M and H groups were significantly higher than those in the C and L groups. For the microbial response, microbial community richness in the L group was significantly decreased, while community richness and diversity in the H group were significantly increased compared with those in the C group. The relative abundances of 3, 4 and 11 taxa were significantly changed after MP treatment at the phylum, class and genus levels, respectively. The results suggested that short-term exposure to low concentrations of MPs did not cause immune defense responses or death but affected the balance of bacterial composition in shrimp. Exposure to high concentrations of MPs can induce immune responses and microbial changes and can even cause death in shrimp. These findings increase our understanding of MP impacts on aquatic organisms.

New insights into the immune regulation and tissue repair of Litopenaeus vannamei during temperature fluctuation using TMT-based proteomics

To investigate shrimp immunoregulation and tissue self-repair mechanism during temperature fluctuation stage, Litopenaeus vannamei (L. vannamei) was treated under conditions of gradual cooling from an acclimation temperature (28 °C, C group) to 13 °C (T group) in 2 days with a cooling rate of 7.5 °C/d and then rewarmed to 28 °C (R group) with the same rate. Tandem mass tags (TMT) -based proteomics technology was used to investigate the protein abundance changes of intestine in L. vannamei during temperature fluctuation. The results showed that a total of 5796 proteins with function annotation were identified. Of which, the abundances of 1978 proteins (34%) decreased after cooling and then increased after rewarming, 1498 proteins (26%) increased during the whole stage, 1263 proteins (22%) increased after cooling and then decreased after rewarming and 1057 proteins (18%) decreased during the whole stage. Differentially expressed proteins such as C-lectin, NFκBIA and Caspase may contributed to the regulation of immunity and tissue repair of shrimp intestine during the temperature fluctuation stage. These findings contribute to the better understanding of shrimp' regulatory mechanism against adverse environment.

Proteomic Characterization of Proliferation Inhibition of Well-Differentiated Laryngeal Squamous Cell Carcinoma Cells Under Below-Background Radiation in a Deep Underground Environment

Background: There has been a considerable concern about cancer induction in response to radiation exposure. However, only a limited number of studies have focused on the biological effects of below-background radiation (BBR) in deep underground environments. To improve our understanding of the effects of BBR on cancer, we studied its biological impact on well-differentiated laryngeal squamous cell carcinoma cells (FD-LSC-1) in a deep underground laboratory (DUGL). Methods: The growth curve, morphological, and quantitative proteomic experiments were performed on FD-LSC-1 cells cultured in the DUGL and above-ground laboratory (AGL). Results: The proliferation of FD-LSC-1 cells from the DUGL group was delayed compared to that of cells from the AGL group. Transmission electron microscopy scans of the cells from the DUGL group indicated the presence of hypertrophic endoplasmic reticulum (ER) and a higher number of ER. At a cutoff of absolute fold change ≥ 1.2 and p < 0.05, 807 differentially abundant proteins (DAPs; 536 upregulated proteins and 271 downregulated proteins in the cells cultured in the DUGL) were detected. KEGG pathway analysis of these DAPs revealed that seven pathways were enriched. These included ribosome (p < 0.0001), spliceosome (p = 0.0001), oxidative phosphorylation (p = 0.0001), protein export (p = 0.0001), thermogenesis (p = 0.0003), protein processing in the endoplasmic reticulum (p = 0.0108), and non-alcoholic fatty liver disease (p = 0.0421). Conclusion: The BBR environment inhibited the proliferation of FD-LSC-1 cells. Additionally, it induced changes in protein expression associated with the ribosome, gene spliceosome, RNA transport, and energy metabolism among others. The changes in protein expression might form the molecular basis for proliferation inhibition and enhanced survivability of cells adapting to BBR exposure in a deep underground environment. RPL26, RPS27, ZMAT2, PRPF40A, SNRPD2, SLU7, SRSF5, SRSF3, SNRPF, WFS1, STT3B, CANX, ERP29, HSPA5, COX6B1, UQCRH, and ATP6V1G1 were the core proteins associated with the BBR stress response in cells.

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment affecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the effect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and differentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable difference between the two laboratories, whereby γ ray dose rate was significantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g. ribosome, RNA transport and oxidative phosphorylation) were significantly enriched. These data suggest that proliferation of V79 cells was inhibited in the DUGL, likely because cells were exposed to reduced background radiation. The apparent changes in the proteome profile may have induced cellular changes that delayed proliferation but enhanced survival, rendering V79 cells adaptable to the changing environment.

The immune defense response of Pacific white shrimp (Litopenaeus vannamei) to temperature fluctuation

Temperature is a significant environmental factor contributing to the success of aquaculture. To investigate the immune defense response during temperature fluctuation, Litopenaeus vannamei (L. vannamei) was treated under conditions of gradual cooling from an acclimation temperature of 28 °C (C group) to 13 °C (T group) in 2 days with a cooling rate of 7.5 °C/d and then rewarmed to 28 °C (R group) using the same rate. Relative expression of immune defense system-related genes and intestinal microbial composition in L. vannamei were investigated. The results showed that with a decrease in temperature, the expression of TLR, IMD, proPO and Casp3 in intestine was significantly decreased, while the expression of Muc-3A, Muc-5AC, Muc-17, IAP, p53, HSP70, MT and Fer was significantly increased after cooling. After temperature recovery, gene expression generally showed a trend of recovering to the normal level (C). Intestinal microbial analysis showed that, compared with the C group, the Chao and Ace indexes, the relative abundance of microflora from the Phylum Bacteroidetes, Class Alphaproteobacteria, and Class Bacteroidia, significantly decreased in the R group. The results revealed that cold-stress may decrease microbial community richness, alter the bacterial community in general and reduce shrimp immunity to pathogens and antibacterial activity. As a result, during temperature fluctuation shrimp may mobilize the immune defense system through upregulating the expression of Muc genes, anti-apoptosis related genes, and antioxidant related genes in order to maintain organism homeostasis as well as to repair damaged intestinal tissue.