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

Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a significant global public health issue with high mortality rates and challenges posed by drug-resistant strains, emphasizing the continued need for new therapeutic targets and effective treatment strategies. Transcriptomics is a highly effective tool for the development of novel anti-tuberculosis drugs. However, most studies focus only on changes in gene expression levels at specific time points. This study screened for genes with altered expression patterns from available transcriptomic data and analysed their association with the TB progression. Initially, a total of 1228 genes with altered expression patterns were identified through two-way analysis of variance (ANOVA). We define genes with a P-value less than 0.05 for the combined effect of infection and time on gene expression as those with altered expression patterns. Gene Ontology (GO) enrichment analysis revealed that the biological functions of these genes mainly involve DNA translation, RNA processing, and transcriptional regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that these genes are primarily associated with fatty acid degradation, pyruvate metabolism, arginine and proline metabolism, as well as cholesterol metabolism signaling pathways. Subsequent Protein-protein interaction (PPI) analysis and Receiver Operating Characteristic (ROC) curve analysis identified four core genes closely associated with TB progression, namely Rac Family Small GTPase 1 (RAC1), Ring-Box 1 (RBX1), Mitochondrial Ribosomal Protein L33 (MRPL33), and ELAV Like RNA Binding Protein 1 (ELAVL1). Q-PCR experiments confirmed that Mtb infection led to changes in the gene expression patterns of RAC1, RBX1, MRPL33, and ELAVL1 in THP-1 cells. These four genes may serve as core biomarkers for TB progression and can be utilized in the development of more effective anti-tuberculosis drugs and host therapy.

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.