Identification of ATP synthase α subunit as a new maternal factor capable of protecting zebrafish embryos from bacterial infection

Zebrafish ANGPT4, member of fibrinogen-related proteins, is an LTA-, LPS- and PGN-binding protein with a bacteriolytic activity

Fibrinogen-related proteins (FREPs) are a family of glycoproteins that contain a fibrinogen-like (FBG) domain. Many members of FREPs have been shown to play an important role in innate immune response in both vertebrates and invertebrates. Here we reported the immune functional characterization of ANGPT4, member of FREPs, in zebrafish Danio rerio. Quantitative real time PCR showed that the expression of zebrafish ANGPT4 gene is up-regulated by the challenge with lipoteichoic acid (LTA) or lipopolysaccharides (LPS), hinting its involvement in innate immune response. The recombinant ANGPT4 (rANGPT4) could bind to both gram-positive bacteria Staphylococcus aureus and Bacillus subtilis and the gram-negative bacteria Escherichia coli and Aeromonas hydrophila as well as the pathogen-associated molecular patterns (PAMPs) on the bacterial surfaces including LTA, LPS and peptidoglycan (PGN), suggesting it capable of identifying pathogens via LTA, LPS and PGN. In addition, rANGPT4 also displayed strong bacteriolytic activities against both gram-positive and -negative bacteria tested via inducing membrane depolarization and intracellular ROS production. Moreover, the bacterial clearance assay in vivo showed that the rANGPT4 could also accelerate the clearance of bacteria in zebrafish embryos/larvae. Finally, we showed that the eukaryotically expressed recombinant ANGPT4 maintained antibacterial activity and binding activity to bacteria and LTA, LPS and PGN. All these suggested that ANGPT4 could not only capable of recognizing pathogens via LTA, LPS and PGN, but also capable of killing the Gram-positive and Gram-negative bacteria, in innate immune response. This work also provides further information to understand the biological roles of FREPs and the innate immunity in vertebrates.

Proteomics analysis of resistance mechanism of Trichoderma harzianum under U(VI) stress

Trichoderma harzianum has a certain resistance to Hexavalent Uranium (U(VI)), but its resistance mechanism is unknown. Based on proteomics sequencing using DIA mode, differentially expressed proteins (DEPs) of Trichoderma harzianum under U(VI) stress were identified. GO enrichment, KEGG annotation analysis and DEPs annotation were performed. The results showed that 8 DEPs, 8 DEPs and 15 DEPs were obtained in the low-dose, medium-dose and high-dose groups, respectively. The functional classification of GO demonstrated that DEPs were associated with 17 molecular functions, 5 biological processes, and 5 cellular components. Furthermore, DEPs were enriched in transport and catabolism, energy metabolism, translation, and signal transduction. These findings showed that Trichoderma harzianum was significantly changed in protein expression and signaling pathway after U(VI) exposure. Therefore, these results have provided Trichoderma harzianum with a theoretical background that can be applied to environmental cleanup.

Systematic Proteomics Study on the Embryonic Development of Danio rerio

The early development of zebrafish (Danio rerio) is a complex and dynamic physiological process involving cell division, differentiation, and movement. Currently, the genome and transcriptome techniques have been widely used to study the embryonic development of zebrafish. However, the research of proteomics based on proteins that directly execute functions is relatively vacant. In this work, we apply label-free quantitative proteomics to explore protein profiling during zebrafish's embryogenesis, and a total of 5961 proteins were identified at 10 stages of zebrafish's early development. The identified proteins were divided into 11 modules according to weighted gene coexpression network analysis (WGCNA), and the characteristics between modules were significantly different. For example, mitochondria-related functions enriched the early development of zebrafish. Primordial germ cell-related proteins were identified at the 4-cell stage, while the eye development event is dominated at 5 days post fertilization (dpf). By combining with published transcriptomics data, we discovered some proteins that may be involved in activating zygotic genes. Meanwhile, 137 novel proteins were identified. This study comprehensively analyzed the dynamic processes in the embryonic development of zebrafish from the perspective of proteomics. It provided solid data support for further understanding of the molecular mechanism of its development.

Rapid microbial viability assay using scanning electron microscopy: a proof-of-concept using Phosphotungstic acid staining

Multiple stains have been historically utilized in electron microscopy to provide proper contrast and superior image quality enabling the discovery of ultrastructures. However, the use of these stains in microbiological viability assessment has been limited. Phosphotungstic acid (PTA) staining is a common negative stain used in scanning electron microscopy (SEM). Here, we investigate the feasibility of a new SEM-PTA assay, aiming to determine both viable and dead microbes. The optimal sample preparation was established by staining bacteria with different PTA concentrations and incubation times. Once the assay conditions were set, we applied the protocol to various samples, evaluating bacterial viability under different conditions, and comparing SEM-PTA results to culture. The five minutes 10% PTA staining exhibited a strong distinction between viable micro-organisms perceived as hypo-dense, and dead micro-organisms displaying intense internal staining which was confirmed by high Tungsten (W) peak on the EDX spectra. SEM-PTA viability count after freezing, freeze-drying, or oxygen exposure, were concordant with culture. To our knowledge, this study is the first contribution towards PTA staining of live and dead bacteria. The SEM-PTA strategy demonstrated the feasibility of a rapid, cost-effective and efficient viability assay, presenting an open-view of the sample, and providing a potentially valuable tool for applications in microbiome investigations and antimicrobial susceptibility testing.

Protein-protein networks analysis of differentially expressed genes unveils the key phenomenon of biological process with respect to reproduction in endangered catfish, C. Magur

Clarias magur (magur) is an important freshwater catfish with high potential in the aquaculture sector in its geographical ranges of distribution. One of the impediments to realise its full aquaculture potential is the lack of understanding key genes involved in its reproduction pathways. Nonetheless, very limited information is available on brain and gonads, with respect to reproduction related issues of magur at molecular level. The present study was aimed at understanding the interaction of the brain-gonad system by analysing differentially expressed genes (DEG) in brains and gonads of male and female magur using a protein-protein network interaction study. In brief, 641, 541, 225 and 245 DEGs, respectively, in ovary, testis and female brain and male-brain of magur were used as input in String database 11.0 and Cytoscape v 3.8.0 plug-in Network Analyzer for PPI network construction followed by network superimposition, network merging and analysis. A total of 13 key genes in female brain & ovary and 12 key genes in male brain & testis were obtained based on the network topological parameter betweenness centrality and nodes degree. Among them, cyp19a1b and amh genes in male brain-testis and Tp53 and exo1 genes in female brain-ovary were identified as hub genes having a high level of interaction and expression with other key genes in the network. Further, functional annotation study of these genes revealed their active involvement in important pathways related to reproduction. This is the first report exploring the interaction of brain and gonads in the regulation of magur reproduction through a protein-protein interaction network. The 25 key genes identified in the combined network are involved in various pathways, like neuropeptide signalling pathway, oxytocin receptor-mediated signalling pathway, corticotrophin-releasing factor receptor signalling pathway and reproduction process, which could lead to a better understanding of the magur reproductive system.

Identification and functional characterization of zebrafish ELAVL1b as a new member of antimicrobial protein

Previous studies have shown that ELAVL1 play multiple roles and may be associated with immune response. However, it remains largely unknown about the direct roles of ELAVL1 during a bacterial infection. After reporting the zebrafish ELAVL1a is a maternal immune factor that can protect zebrafish embryos from bacterial infection, here we studied the immune function of zebrafish ELAVL1b. In this study, we showed that zebrafish elavl1b was markedly up-regulated by LTA and LPS treatment, suggesting it may be involved in anti-infectious responses. We also showed that zebrafish recombinant ELAVL1b (rELAVL1b) could bind to both the Gram-positive and negative bacteria M. luteus and S. aureus, E. coli and A. hydrophila as well as their signature molecules LTA and LPS, hinting it may act as a pattern recognition receptor, capable of identifying pathogens. In addition, rELAVL1b could directly kill the Gram-positive and negative bacteria tested via inducing membrane depolarization and intracellular ROS production. Collectively, our results indicate that zebrafish ELAVL1b plays an immune-relevant role as a newly-characterized antimicrobial protein. This work also provides further information to understand the biological roles of ELAVL family and the innate immunity in vertebrates.

Bacterial-agglutinating and opsonic activities of RIPK1 in zebrafish

Many studies have demonstrated that receptor interacting protein kinase-1 acts as a crucial mediator in the regulation of immune response, but evidence remains lacking for its direct interaction with bacteria. In this study, we found that challenge with lipopolysaccharide and lipoteichoic acid resulted in a significantly increased transcriptional expression of receptor interacting protein kinase-1 in zebrafish, suggesting the receptor interacting protein kinase-1 is implicated in anti-infectious responses. In accordance, we found that recombinant receptor interacting protein kinase-1 was not only able to bind to Gram-negative and -positive bacteria via interaction with lipopolysaccharide and lipoteichoic acid, but also agglutinate both Gram-negative and -positive bacteria in a Ca²⁺-dependent manner.

Identification of zebrafish PLEKHF2 presents in egg/embryos as an antibacterial protein

PLEKHF2 proteins are widespread in animals, but their functions and mechanisms remain poorly defined. Here we clearly demonstrate that PLEKHF2 is a newly identified present abundantly in the eggs/embryos of zebrafish. We also show that recombinant PLEKHF2 acts as a pattern recognition receptor capable of identifying the bacterial signature molecule PGN, LPS, and LTA, binding the bacteria, and functions as an antibacterial effector directly killing the bacteria. In brief, these results indicate that PLEKHF2 is an antibacterial protein, a novel role assigned to PLEKHF2 proteins.

Fungicidal Activity of AP10W, a Short Peptide Derived from AP-2 Complex Subunit mu-A, In Vitro and In Vivo

With the increase in the incidence of fungal infections, and the restrictions of existing antifungal drugs, the development of novel antifungal agents is urgent. Here we prove that AP10W, a short peptide derived from AP-2 complex subunit mu-A, displays conspicuous antifungal activities against the main fungal pathogens of human infections Candida albicans and Aspergillus fumigatus. We also show that AP10W suppresses the fungal biofilm formation, and reduces the pre-established fungal biofilms. AP10W appears to exert its fungicidal activity through a mode of combined actions, including interaction with the fungal cell walls via laminarin, mannan and chitin, enhancement of cell wall permeabilization, induction of membrane depolarization, and increase in intracellular ROS generation. Importantly, we demonstrate that AP10W exhibits little toxicity towards mammalian fibroblasts, and effectively promotes the healing of wounded skins infected by C. albicans. These together indicate that AP10W is a new member of fungicidal agents. It also suggests that AP10W has a considerable potential for future development as a novel antifungal drug.

Identification and functional characterization of Cofilin-1 as a new member of antimicrobial protein

Cofilin-1 (Cfl1), a member of the ADF/cofilin family, has been identified as one of differentially expressed proteins in human dendritic cells challenged with lipopolysaccharide (LPS), suggesting that it may be involved in immune response. Here we showed that zebrafish cfl1 was markedly up-regulated by LPS and LTA treatment. We also showed that zebrafish recombinant Cfl1 (rCfl1) not only bound to the Gram-negative and positive bacteria A. hydrophila and S. aureus as well as their signature molecules LPS and LTA but also inhibited the growth of the bacteria. Moreover, we found that the heparin-binding motif-containing regions of Cfl1, i.e., Cfl1_9-25, Cfl1_34-51 and Cfl1_108-125, like rCfl1, were also able to bind to LPS and LTA and to inhibit the bacterial growth. rCfl1, Cfl1_9-25, Cfl1_34-51, and Cfl1_108-125 were all able to cause bacterial cell destruction, to induce membrane depolarization, and to stimulate intracellular ROS production. Finally, we showed that zebrafish Cfl1 could protect developing embryos/larvae against attack by the potential pathogen A. hydrophila. These data together indicate that zebrafish Cfl1 plays an immune-relevant role as a newly-characterized antimicrobial protein.

40S ribosomal protein S18 is a novel maternal peptidoglycan-binding protein that protects embryos of zebrafish from bacterial infections

Previous studies have shown that ribosomal proteins play important roles in ribosome assembly and protein translation, but other biological functions remain ill-defined. Here it is clearly demonstrated that RPS18 is a newly identified PGN-binding protein which is present abundantly in the eggs/embryos of zebrafish. Recombinant RPS18 not only identifies the bacterial signature molecule PGN, LPS, and LTA, and binds the bacteria as a pattern recognition receptor, but also kills the Gram-positive and Gram-negative bacteria as an antibacterial effector molecule. What is important is that, we reveal that microinjection of rRPS18 into early embryos significantly improved the resistance of the embryos against pathogenic Aeromonas hydrophila challenge, and co-injection of anti-RPS18 antibody could markedly reduced this improved bacterial resistance. In summary, these results indicate that RPS18 is a maternal immune factor that can protect the early embryos of zebrafish against pathogenic attacks. This work also provides another angle for understanding the biological functions of ribosomal proteins.

Identification and functional characterization of AP-2 complex subunit mu-A as a new member of antimicrobial protein

AP-2 complex subunit mu-A (AP2M1A) is a component of the adaptor complexes that link clathrin to receptors in coated vesicles. It has recently been shown to be involved in the resistance to oxidative damage, challenging the conventional role of AP2M1A. Here we demonstrated that AP2M1A was a heparin-binding protein abundantly stored in eggs and embryos of zebrafish, and its gene expression was markedly up-regulated by LPS and LTA treatment. We also showed that recombinant AP2M1A (rAP2M1A) was not only able to interact with Gram-negative and Gram-positive bacteria as well as their signature molecules LPS and LTA, but also able to inhibit the growth of the bacteria. Additionally, we found that AP2M1A354-382 that contained 2 closely positioned heparin-binding motifs could also bind to LPS and LTA, and inhibit the bacterial growth. Both rAP2M1A and AP2M1A354-382 were shown to execute antibacterial activity by a combined action of destabilization/destruction of bacterial cell wall through interaction with LPS and LTA, disturbance of the usually polarized membrane through depolarization, and apoptosis/necrosis through intracellular ROS production. Finally, we showed that AP2M1A could protect zebrafish developing embryos/larvae against attack by the potential pathogen Aeromonas hydrophila. All these demonstrate for the first time that AP2M1A is a maternal antimicrobial protein previously uncharacterized. It also establishes a correlation between antibacterial activity and heparin-binding motifs.

Fos Facilitates Gallid Alpha-Herpesvirus 1 Infection by Transcriptional Control of Host Metabolic Genes and Viral Immediate Early Gene

Gallid alpha-herpesvirus 1, also known as avian infectious laryngotracheitis virus (ILTV), continues to cause huge economic losses to the poultry industry worldwide. Similar to that of other herpesvirus-encoded proteins, the expression of viral genes encoded by ILTV is regulated by a cascade, and the underlying regulatory mechanism remains largely unclear. The viral immediate-early (IE) gene ICP4 plays a prominent role in the initiation of the transcription of early and late genes during ILTV replication. In this study, we identified AP-1 as the key regulator of the transcription of ILTV genes by bioinformatics analysis of genome-wide transcriptome data. Subsequent functional studies of the key members of the AP-1 family revealed that Fos, but not Jun, regulates ILTV infection through AP-1 since knockdown of Fos, but not Jun, by gene silencing significantly reduced ICP4 transcription and subsequent viral genome replication and virion production. Using several approaches, we identified ICP4 as a bona fide target gene of Fos that regulated Fos and has Fos response elements within its promoter. Neither the physical binding of Jun to the promoter of ICP4 nor the transcriptional activity of Jun was observed. In addition, knockdown of Fos reduced the transcription of MDH1 and ATP5A1, genes encoding two host rate-limiting enzymes essential for the production of the TCA intermediates OAA and ATP. The biological significance of the transcriptional regulation of MDH1 and ATP5A1 by Fos in ILTV infection was supported by the fact that anaplerosis of OAA and ATP rescued both ICP4 transcription and virion production in infected cells under when Fos was silenced. Our study identified the transcription factor Fos as a key regulator of ILTV infection through its transcription factor function on both the virus and host sides, improving the current understanding of both avian herpesvirus–host interactions and the roles of AP-1 in viral infection.

Interaction between extracellular ATP5A1 and LPS alleviates LPS-induced neuroinflammation in mice

Neuroinflammation is one of the main causes of Alzheimer's disease (AD). The presence of Lipopolysaccharide (LPS) in senile plaques (SP) of AD suggests that it plays a role in AD pathogenesis. ATP5A1 (F1F0-ATP synthase F1 α subunit) is abundant in SP. Further, the protein has recently been found to have an anti-infection role in zebrafish embryos. In the present study, we observed that LPS levels were higher in the brains of APP/PS1 mice than in control mice, and LPS co-localised with ATP5A1 in amyloid plaques. The interaction of recombinant ATP5A1(rATP5A1) and LPS was evidenced by cellular thermal shift assay and enzyme-linked immunosorbent assay-based binding assay in vitro. Neuroinflammation in the brain of a mouse model was induced by intracerebroventricular injection of LPS. The addition of rATP5A1 relieved LPS-induced reduction of spontaneous locomotor ability, depressive-like behaviour, and working memory impairment. Furthermore, rATP5A1 suppressed the activation of astrocytes and microglia, IL-1β accumulation, and tau phosphorylation induced by LPS. Taken together, findings suggest that ATP5A1 is involved in the regulation of LPS-mediated neuroinflammation in AD.

ELAVL1a is an immunocompetent protein that protects zebrafish embryos from bacterial infection

Previous studies have shown that ELAVL1 plays multiple roles, but its overall biological function remains ill-defined. Here we clearly demonstrated that zebrafish ELAVL1a was a lipoteichoic acid (LTA)- and LPS-binding protein abundantly stored in the eggs/embryos of zebrafish. ELAVL1a acted not only as a pattern recognition receptor, capable of identifying LTA and LPS, as well as bacteria, but also as an effector molecule, capable of inhibiting the growth of Gram-positive and -negative bacteria. Furthermore, we reveal that the C-terminal 62 residues of ELAVL1a positioned at 181–242 were indispensable for ELAVL1a antibacterial activity. Additionally, site-directed mutagenesis revealed that the hydrophobic residues Val192/Ile193, as well as the positively charged residues Arg203/Arg204, were the functional determinants contributing to the antimicrobial activity of rELAVL1a. Importantly, microinjection of rELAVL1a into embryos markedly promoted their resistance against pathogenic Aeromonas hydrophila challenge, and this pathogen-resistant activity was considerably reduced by co-injection of anti-ELAVL1a antibody or by knockdown with morpholino for elavl1a. Collectively, our results indicate that ELAVL1a is a maternal immune factor that can protect zebrafish embryos from bacterial infection. This work also provides another angle for understanding the biological roles of ELAVL1a.

Ni et al. show that RNA-binding protein ELAVL1a is abundantly stored in the eggs and embryos of zebrafish, serving as a first-line innate immune player. They find that ELAVL1a recognizes molecular patterns of bacteria to inhibit bacterial growth. This study suggests that ELAVL1a is a maternal immune factor protecting zebrafish embryos from bacterial infection.

Identification of the 14-3-3 β/α-A protein as a novel maternal peptidoglycan-binding protein that protects embryos of zebrafish against bacterial infections

14-3-3 proteins are widespread in animals, but their functions and mechanisms remain poorly defined. Here we clearly demonstrate that 14-3-3 β/α-A is a newly identified PGN-binding protein present abundantly in the eggs/embryos of zebrafish. We also show that recombinant 14-3-3 β/α-A acts as a pattern recognition receptor capable of identifying the bacterial signature molecule PGN, binding the bacteria, and functions as an antibacterial effector molecule directly killing the bacteria. Importantly, microinjection of r14-3-3 β/α-A into early embryos significantly enhanced the resistance of the embryos against pathogenic A. hydrophila challenge, and this enhanced bacterial resistance was markedly reduced by co-injection of anti-14-3-3 β/α-A antibody. Collectively, these results indicate that 14-3-3 β/α-A is a maternal PGN-binding protein that can protect the early embryos of zebrafish against pathogenic attacks, a novel role assigned to 14-3-3 β/α-A proteins. This work also provides new insights into 14-3-3 proteins that are widely distributed in various animals.

Identification of β tubulin IVb as a pattern recognition receptor with opsonic activity

Previous studies have shown that tubulins play important role in immune responses of both plants and animals, but no experiments have been performed to study the mode of action of tubulins in immune defense. In addition, there is little convincing experimental evidence of functional commitment for specific tubulin isotypes in animals. In the present, we showed that expression of β-tubulin IVb gene was affected by both LPS and LTA, hinting its involvement in anti-infectious response. We also showed that recombinant zebrafish β-tubulin IVb not only interacted with LPS and LTA as well as Gram-negative and -positive bacteria but also agglutinated both Gram-negative and -positive bacteria in a Ca²⁺-dependent fashion. Interestingly, recombinant β-tubulin IVb could enhance the phagocytosis of bacteria by macrophages. Moreover, we demonstrated that β-tubulin IVb was present extracellularly in the serum of zebrafish and mouse. Collectively, these suggest that β-tubulin IVb may be physiologically involved in the systematic immunity of host via acting as a pattern recognition receptor and an opsonin. This also provides a new angle to understand the roles of β-tubulin IVb.