Gene duplication, conservation, and divergence of activating transcription factor 5 gene in zebrafish.

Activating transcription factor 5 (Atf5) is a member of the ATF/CREB family of transcription factors and involved in diverse cellular functions and diseases in mammals. However, the function of atf5 remains largely unknown in fish. Here, we report the expression pattern and function of duplicated atf5 genes in zebrafish. The results showed that the gene structures of zebrafish atf5a and atf5b were similar to their mammalian orthologs. Zebrafish Atf5a and Atf5b shared an amino acid sequence identity of 40.7%. Zebrafish atf5a and atf5b had maternal origin with dynamic expression during embryonic development. Zebrafish atf5a mRNA is mainly enriched in olfactory epithelium, midbrain, and hindbrain, while zebrafish atf5b mRNA is mainly detected in midbrain, hindbrain, and liver during embryogenesis. The results of acute hypoxia experiment showed that atf5a mRNA was significantly upregulated in the brain, liver, and muscle, while atf5b mRNA was just increased significantly in the brain. Functional analysis showed that knockdown of atf5a affects the development of the ciliated neurons in zebrafish embryos. The effect was enhanced when atf5a MO was co-injected with atf5b MO. The development of ciliated neurons in zebrafish embryos was not affected by injection of atf5b MO alone. atf5a knockdown also affects the development of early-born olfactory neurons. The effects caused by atf5a knockdown could be rescued by atf5b mRNA. These results suggest that the duplicated atf5 genes may have evolved divergently and play redundant biological roles in the development of olfactory sensory neurons in zebrafish.

Effect of Gut Microbiota-Derived Metabolites on Immune Checkpoint Inhibitor Therapy: Enemy or Friend?

The human gut is inhabited by hundreds of billions of commensal microbiota that collectively produce thousands of small molecules and metabolites with local and systemic effects on the physiology of the host. Much evidence from preclinical to clinical studies has gradually confirmed that the gut microbiota can regulate anti-tumor immunity and affect the efficacy of cancer immune checkpoint inhibitors (ICIs) therapy. In particular, one of the main modes of gut microbiota regulating anti-tumor immunity is through metabolites, which are small molecules that can be transported in the body and act on local and systemic anti-tumor immune responses to promote ICIs immunotherapy efficacy. We discuss the functions of microbial metabolites in humans, focusing on the effects and mechanisms of microbial metabolites on immunotherapy, and analyze their potential applications as immune adjuvants and therapeutic targets to regulate immunity and enhance ICIs. In summary, this review provides the basis for the rational design of microbiota and microbial metabolite-based strategies of enhancing ICIs.

Alternative splicing of medaka bcl6aa and its repression by Prdm1a and Prdm1b.

Bcl6 and Prdm1 (Blimp1) are a pair of transcriptional factors that repressing each other in mammals. Prdm1 represses the expression of bcl6 by binding a cis-element of the bcl6 gene in mammals. The homologs of Bcl6 and Prdm1 have been identified in teleost fish. However, whether these two factors regulate each other in the same way in fish like that in mammals is not clear. In this study, the regulation of bcl6aa by Prdm1 was investigated in medaka. The mRNA of bcl6aa has three variants (bcl6aaX1-X3) at the 5'-end by alternative splicing detected by RT-PCR. The three variants can be detected in adult tissues and developing embryos of medaka. Prdm1a and prdm1b are expressed in the tissues and embryos where and when bcl6aa is expressed. The expression of prdm1a was high while the expression of bcl6aa was low, and vice versa, detected in the spleen after stimulation with LPS or polyI:C. In vitro reporter assay indicated that bcl6aa could be directly repressed by both Prdm1a and Prdm1b in a dosage-dependent manner. After mutation of the key base, G, of all predicted binding sites in the core promoter region of bcl6aa, the repression by Prdm1a and/or Prdm1b disappeared. The binding site of Prdm1 in the bcl6aa gene is GAAAA(T/G). These results indicate that both Prdm1a and Prdm1b directly repress the expression of bcl6aa by binding their binding sites where the 5'-G is critical in medaka fish.

Identification, expression and functional analysis of prmt7 in medaka Oryzias latipes.

Arginine methylation is an important posttranslational modification and catalyzed by a family of protein arginine methyltransferases (PRMTs). PRMT7 is the type III PRMT and produces solely monomethylarginine products. PRMT7 has been found to play important roles in multiple biological processes in mammals. However, the expression pattern and function of Prmt7 remain largely unknown in fish. In this study, we characterized the medaka prmt7 gene and determined its expression pattern and function during embryogenesis and germ cell development. The results showed that the chromosomal location and gene structure of medaka prmt7 were similar to its mammalian orthologs. Comparisons of deduced amino acid sequences indicated that medaka Prmt7 was a homolog of human PRMT7 with two methyltransferase domains. Reverse transcription-polymerase chain reaction (RT-PCR) and real time RT-PCR revealed that medaka prmt7 had maternal origin with continuous and dynamical expression during embryonic development. Whole-mount in situ hybridization analysis observed that the transcripts of prmt7 were ubiquitous at morula and gastrula stage, and were later riched in the brain and otic vesicles during embryogenesis. In the adult stage, prmt7 messenger RNA was detected in all examined tissues with the high levels in the ovary and testis. The expression of prmt7 in the gonads was restricted to oocytes of the ovary and spermatids/sperm of the testis. Functional analysis showed that knockdown of medaka prmt7 did not reduce the total number of primordial germ cells (PGCs) in vivo but significantly affected PGCs distribution during embryonic development. These results indicate that prmt7 may be involved in germ cell development in medaka.

Identification, expression pattern, and immune response of Tim-1 and Tim-4 in embryos and adult medaka (Oryzias latipes).

T-cell immunoglobulin (Ig) and mucin domain-containing 1 (Tim-1) and Tim-4 are two members of the Tim family. In mammals, Tim-1 and Tim-4 are proteins mainly expressed in immune cells and are associated with immune response. In the present study, medaka Oryzias latipes' Tim-1 (OlTim-1) and OlTim-4 were identified and characterized using bioinformatics analyses. With the use of reverse-transcription polymerase chain reaction, the expression profiles of OlTim-1 and OlTim-4 were examined in embryos and adult fish and in immune tissues following the intraperitoneal injection of stimulants. The results revealed that OlTim-1 possesses a cytoplasmic region, a transmembrane region, a mucin domain, and an Ig-like domain, while OlTim-4 is composed of two Ig-like domains and a mucin domain, but without the transmembrane region and cytoplasmic region. OlTim-1 and OlTim-4 expressions are detectable from the gastrula stage on, indicating that they are zygotic genes. Furthermore, OlTim-1 and OlTim-4 are expressed ubiquitously in the adult. Administration of immune stimulants, namely lipopolysaccharides and polyinosinic:polycytidylic acid, significantly increased the expression levels of OlTim-1 and OlTim-4 in the liver and intestine within 1 day and in the head, kidney, and spleen within 3 to 4 days postinjection. These results suggest that OlTim-1 and OlTim-4 are possibly involved in both innate and adaptive immunities.

Iturin A-like lipopeptides from Bacillus subtilis trigger apoptosis, paraptosis, and autophagy in Caco-2 cells.

This study revealed that iturin A-like lipopeptides produced by Bacillus subtillis induced both paraptosis and apoptosis in heterogeneous human epithelial colorectal adenocarcinoma (Caco-2) cells. Autophagy was simultaneously induced in Caco-2 cells treated with iturin A-like lipopeptides at the early stage and inhibited at the later stage. A western blot analysis showed that the lipopeptides induced apoptosis in Caco-2 cells via a mitochondrial-dependent pathway, as indicated by upregulated expression of the apoptotic genes bax and bad and downregulated expression of the antiapoptotic gene bcl-2. The induction of paraptosis in Caco-2 cells was indicated by the occurrence of many cytoplasmic vacuoles accompanied by endoplasmic reticulum (ER) dilatation and mitochondrial swelling and dysfunction. ER stress also occurred with significant increases in reactive oxygen species and Ca2+ levels in cells. Autophagy was detected by a transmission electron microscopy analysis and by upregulated expression of LC3-II and downregulated expression of LC3-I. The inhibition of autophagy at the later stage was shown by upregulated expression of p62. This study revealed the capability of iturin A-like B. subtilis lipopeptides to simultaneously execute antitumor potential via multiple pathways.

Bcl6aa and bcl6ab are ubiquitously expressed and are inducible by lipopolysaccharide and polyI:C in adult tissues of medaka Oryzias latipes.

B-cell lymphoma-6 (Bcl6) is a transcriptional repressor that plays important roles in various physiological activities such as innate and adaptive immune response, lymphocyte differentiation, and cell cycle regulation in mammals. Two homologs of Bcl6a, namely Bcl6aa and Bcl6ab, are identified in teleost fish including medaka Oryzias latipes. The expression profiles of bcl6aa and bcl6ab in medaka were studied using reverse-transcription polymerase chain reaction and in situ hybridization. The transcripts of bcl6aa and bcl6ab were detected from very early embryos such as the four-cell stage until hatching. Bcl6aa and bcl6ab were clearly detected in the embryonic body from 5 days postfertilization onward by in situ hybridization. Bcl6aa was specifically expressed in the retina, whereas bcl6ab was expressed in entire embryonic body. The results referred to that both bcl6aa and bcl6ab originate maternally in the zygotes and may play major roles in embryogenesis of medaka. The transcripts of bcl6aa and bcl6ab were detected in all examined adult tissues, including immune organs such as the gill, spleen, kidney, liver, and intestine. The expression of bcl6aa and bcl6ab in the liver, spleen, head-kidney, and intestine could be upregulated or downregulated by lipopolysaccharide and polyriboinosinic-polyribocytidylic acid. These results indicate that both bcl6aa and bcl6ab may be involved in immune response in medaka.

Development of a paper-based method to detect Hg2+ in waste water using iturin from Bacillus subtilis.

Colorimetric, fluorescence, and paper-based method were developed to measure the Hg2+ level in water using iturin A, a lipopeptide produced by Bacillus subtilis. Firstly, iturin was used to synthesize highly stable and uniformly sized silver nanoparticles (AgNPs). Secondly, the iturin-AgNPs were found to be highly selective and sensitive to Hg2+. The absorbance of the reaction system showed a good linear correlation with the Hg2+ concentration from 0.5 to 5 mg/L at 450 nm in the UV-Vis spectroscopy detection with the limit of detection (LOD) of 0.5 mg/L. When the reaction system was detected by fluorescence measurement, a good linear relationship was found between the fluorescence intensity and Hg2+ concentration from 0.05 to 0.5 mg/ at 415 nm with the LOD of 0.05 mg/L. Lastly, a paper-based detection method was developed. The developed method was successfully used to detect Hg2+ in contaminated polluted waters and showed acceptable results in terms of sensitivity, selectivity and stability. The paper-based method could distinguish Hg2+ at levels higher than 0.05 mg/L, thereby meeting the guidelines of the effluent quality standard for industries (0.05 mg/L). In summary, this method can be used daily by various industries to monitor the Hg2+ level in effluent water.

Capability of iturin from Bacillus subtilis to inhibit Candida albicans in vitro and in vivo.

Candida albicans is a fungal pathogen that is difficult to cure clinically. The current clinic C. albicans-inhibiting drugs are very harmful to humans. This study revealed the potential of iturin fractions from Bacillus subtilis to inhibit C. albicans in free status (MIC = 32 µg/mL) and natural biofilm in vitro. The inhibition mechanism was identified as an apoptosis pathway via the decrease of mitochondrial membrane potential, the increase of the reactive oxygen species (ROS) accumulation, and the induction of nuclear condensation. For in vivo experiments, the C. albicans infection model was constructed via intraperitoneal injection of 1 × 108C. albicans cells into mice. One day after the infection, iturin was used to treat infected mice at different concentrations alone and in combination with amphotericin B (AmB) by intraperitoneal injection. The treatment with AmB alone could cause the death of infected mice, whereas treatment with 15 mg/kg iturin per day alone led to the survival of all infected mice throughout the study. After continuously treated for 6 days, all mice were sacrificed and analyzed. As results, the combination of 15 mg/kg iturin and AmB at a ratio of 2:1 had the most efficient effect to remove the fungal burden in the kidney and cure the infected mice by reversing the symptoms caused by C. albicans infection, such as the loss of body weight, change of immunology cells in blood and cytokines in serum, and damage of organ structure and functions. Overall, iturin had potential in the development of efficient and safe drugs to cure C. albicans infection.

Synthesis of silver nanoparticles and its contribution to the capability of Bacillus subtilis to deal with polluted waters.

Bacillus subtilis widely exists in environment and shows a capability to deal with heavy metals and dyes in polluted waters by adsorption or biological oxidation and reduction. Little is known about the roles of lipopeptides in this capability of B. subtilis. In this study, we found that the lipopeptides produced by B. subtilis could reduce silver ions to silver nanoparticles (AgNPs) and iturin was identified as the major effective fraction. Furthermore, the synthesized AgNPs was successfully used to catalyze the reduction of organic dyes and reduce Pb2+ contamination in water. The formation of AgNPs was confirmed by the features analyzed by UV-vis spectroscopy, dynamic light scattering, high-resolution transmission electron microscopy (HR-TEM), and selected area electron diffraction (SAED). The formed AgNPs showed crystalline, with small size (~ 20 nm) and spherical shape. The biosynthesis of AgNPs was significantly accelerated by UV irradiation. A pH of 10 resulted in the highest formation rate, while pH 9.2 provided the most stability of AgNPs. In mechanisms, tyrosine and the polypeptide were identified as the major groups in iturin-A to form AgNPs via Ar-OH groups. The study revealed that iturin played important roles for the capability of B. subtilis to treat polluted water via a possible way by synthesizing AgNPs and then catalyzing the reduction of organic dyes and reducing the contamination of Pb2+.

Identification, characterization, expression profiles of OlHavcr2 in medaka (Oryzias latipes).

Hepatitis A virus cellular receptor2 (Havcr2) also named T-cell immunoglobulin and mucin domain containing-3 (Tim-3) was initially described as a T helper 1-specific cell surface protein, a member of Tim family implicated in the regulating process of adaptive and innate immune responses. Here, medaka (Oryzias latipes) Havcr2 (OlHavcr2) was isolated and characterized. Unlike other Havcr2 proteins, OlHavcr2 possesses two Ig-like domains but lacks cytoplasmic and transmembrane domains. RT-PCR results revealed that OlHavcr2 mRNA was expressed strongly in the liver, moderately in the intestine, heart and ovary, and weakly in the muscle, gill, brain, eye, spleen, and testis. OlHavcr2 expression begun from gastrula stage and was maintained until hatching. The signal of OlHavcr2 was mainly identified in the blood system in the yolk sac by in situ hybridization. These results indicated that OlHavcr2 is expressed ubiquitously in adult tissues, and is a zygotic gene expressed from gastrula onwards in embryogenesis. OlHavcr2 may play a significant role in the blood system of medaka. In the immune organs, OlHavcr2 expression was affected by the immune stimulants, lipopolysaccharide and poly I:C, suggesting that OlHavcr2 was involved in innate immunity and adaptive immunity in medaka.

Origination, change, and modulation of geriatric disease-related gut microbiota during life.

The age-related changes in the diversity and composition of the gut microbiota are well described in recent studies. These changes have been suggested to be influenced by age-associated weakening of the immune system and low-grade chronic inflammation, resulting in numerous age-associated pathological conditions. Gut microbiota homeostasis is important throughout the life of the host by providing vital functions to regulate various immunological functions and homeostasis. Based on published results, we summarize the relationship between the gut microbiota and aging-related diseases, especially Parkinson's disease, immunosenescence, rheumatoid arthritis, bone loss, and metabolic syndrome. The change in composition of the gut microbiota and gut ecosystem during life and its influence on the host immunologic and metabolic phenotype are also analyzed to determine factors that affect aging-related diseases. Approaches to maintain host health and prevent or cure geriatric diseases are also discussed.

Production of bioproducts by endophytic fungi: chemical ecology, biotechnological applications, bottlenecks, and solutions.

Endophytes are microorganisms that colonize the interior of host plants without causing apparent disease. They have been widely studied for their ability to modulate relationships between plants and biotic/abiotic stresses, often producing valuable secondary metabolites that can affect host physiology. Owing to the advantages of microbial fermentation over plant/cell cultivation and chemical synthesis, endophytic fungi have received significant attention as a mean for secondary metabolite production. This article summarizes currently reported results on plant-endophyte interaction hypotheses and highlights the biotechnological applications of endophytic fungi and their metabolites in agriculture, environment, biomedicine, energy, and biocatalysts. Current bottlenecks in industrial development and commercial applications as well as possible solutions are also discussed.

Biological activity of lipopeptides from Bacillus.

The lipopeptides of Bacillus are small metabolites that contain a cyclic structure formed by 7-10 amino acids (including 2-4 D-amino acids) and a beta-hydroxy fatty acid with 13-19 C atoms. These lipopeptides exhibit a variety of biological activities, including interactions with biofilms, and anti-fungal, anti-inflammatory, anti-tumor, anti-virus, and anti-platelet properties. The multiple activities of lipopeptides have stimulated significant interest in the exploitation of these lipopeptides for use as antibiotics, feed additives, anti-tumor agents, urgent thrombolytic therapeutic agents, and drug delivery systems. Understanding the natural function of these structurally diverse lipopeptides in Bacillus provides insight into microbial regulatory programs and is required for efficient development of more effective products. Currently, there is still insufficient knowledge of the direct target of these lipopeptides, and continued efforts are needed to enhance their biosynthesis efficiency for industrial applications.

Expression of mep50 in adult and embryos of medaka fish (Oryzias latipes).

Protein arginine methylation is important for gene regulation and biological processes. Methylosome protein 50 (Mep50) is identified as a partner of protein arginine methyltransferase 5 (Prmt5), a major enzyme capable of symmetric dimethylation, in mammals and Xenopus. The isolation and characterization of medaka mep50 were reported in this paper. Medaka Mep50 is a homolog of human MEP50 with six WD40 domains. Medaka mep50 was ubiquitously expressed in the adult tissues and had maternal origin with continuous and dynamical expression during embryonic development detected by RT-PCR and in situ hybridization. A strong interaction of medaka Mep50 and Prmt5 was shown by yeast two hybridization. The expression pattern of mep50 is similar to that of prmt5 in medaka. The results suggested that medaka Mep50 could be a partner of Prmt5 and might play major roles in a variety of tissues in medaka.

Germ cell-specific expression of dead end (dnd) in rare minnow (Gobiocypris rarus).

Rare minnow (Gobiocypris rarus) is an emerging model fish in China, and the development of its gonads is still elusive. Germ cell-specific genes are conserved in animals. Dead end (Dnd) was first documented as a germ granule component in zebrafish. Here, we report the cloning and expression profile of dnd in rare minnow. RT-PCR results showed that dnd is expressed specifically in the gonads of both sexes, is maternal in origin and is expressed continuously during embryogenesis. Dnd mRNA could be detected exclusively in the germ cells of the testis and ovary. Temporal expression of dnd mRNA is similar to that of vasa and dnd in zebrafish during embryogenesis. Taken together, dnd mRNA is restricted to the germ cells of rare minnow.

Identification and expression profiles of prdm1 in medaka Oryzias latipes.

Mouse Prdm1, also known as Blimp1, plays important roles in maturation and survival of lymphoid cells, as well as in organogenesis of muscle, limb, sensor organs and primordial germ cells. The homologues of mouse prdm1 have been identified in a diverse of animals including zebrafish and fugu. Here, we report the identification and expression profiles of two homologues of prdm1, namely prdm1a and prdm1b in medaka, Oryzias latipes. The transcripts of prdm1a and prdm1b were detectable in all the tissues including immune organs such as gill, spleen, kidney, liver and intestine that we have checked on. The transcripts of prdm1a could be detected in the embryonic shield at mid-gastrula stage and later in the somite, eye, otic vesicle, branchial arches, fin, intestine and cloaca during embryogenesis using in situ hybridization. Moreover, the expression of prdm1a in the liver of both medaka and zebrafish could be up-regulated by the immune stimuli including lipopolysaccharide, polyI:C and the grass carp reovirus, similarly to the up-regulation of IL1B. These results indicate that Prdm1a may play important roles in embryogenesis and also in immune response in fish.

HIRA is essential for the development of gibel carp.

HIRA is one of the chaperones of histone H3.3. Mutation of Hira results in embryonic lethality in mice, suggesting a critical role in embryogenesis. However, Hira-mutated Drosophila may survive to adults, indicating that it is dispensable in Drosophila development. The role of Hira in fish development is unknown. In this study we first investigated the expression of Hira during embryogenesis of gibel carp (Carassius auratus gibelio) by whole-mount in situ hybridization. We found that Hira signal appeared ubiquitously in the early embryos. After gastrulation, it appeared mainly along the anterior-posterior axis, including the tail bud. In hatching period, the signal was detected in head, heart, and the endoderm region on the back of yolk. Then by microinjection with morpholino-HIRA at the beginning of development, we observed delayed gastrulation and abnormal somitogenesis in gibel carp embryos. The HIRA morphants exhibited short trunk, limited yolk extension, and twisted tail. Most of the mutants died during embryogenesis or shortly after hatching. The rest of the HIRA morphants could survive to larvae but with severe defects in organogenesis. These data suggest that HIRA may be essential for the development of gibel carp, and this function is conserved in vertebrates.

Maternal methylosome protein 50 is essential for embryonic development in medaka Oryzias latipes.

Methylosome protein 50 (Mep50) is a protein that is rich in WD40 domains, which mediate and regulate a variety of physiological processes in organisms. Previous studies indicated the necessity of Mep50 in embryogenesis in mice Mus musculus and fish. This study aimed to further understand the roles of maternal Mep50 in early embryogenesis using medaka Oryzias latipes as a model. Without maternal Mep50, medaka zygotes developed to the pre-early gastrula stage but died later. The transcriptome of the embryos at the pre-early gastrula stage was analyzed by RNA sequencing. The results indicated that 1572 genes were significantly upregulated and 741 genes were significantly downregulated in the embryos without maternal Mep50. In the differentially expressed genes (DEGs), the DNA-binding proteins, such as histones and members of the small chromosome maintenance complex, were enriched. The major interfered regulatory networks in the embryos losing maternal Mep50 included DNA replication and cell cycle regulation, AP-1 transcription factors such as Jun and Fos, the Wnt pathway, RNA processing, and the extracellular matrix. Quantitative RT-PCR verified 16 DEGs, including prmt5, H2A, cpsf, jun, mcm4, myc, p21, ccne2, cdk6, and col1, among others. It was speculated that the absence of maternal Mep50 could potentially lead to errors in DNA replication and cell cycle arrest, ultimately resulting in cell apoptosis. This eventually resulted in the failure of gastrulation and embryonic death. The results indicate the importance of maternal Mep50 in early embryonic development, particularly in medaka fish.

Methylosome protein 50 is necessary for oogenesis in medaka.

Methylosome protein 50 (Mep50) functions as a partner to protein arginine methyltransferase 5. MEP50 serves as a coactivator for both the androgen receptor and estrogen receptor in humans. Mep50 plays a crucial role in the development of germ cells in Drosophila. The precise role of Mep50 in oogenesis remains unclear in vertebrates. The objective of this study was to investigate the role of Mep50 in oogenesis in medaka fish. Disruption of Mep50 resulted in impaired oogenesis and the formation of multiple oocyte follicles in medaka. RNA-seq analysis revealed significant differential gene expression in the mutant ovary, with 4542 genes up-regulated and 1264 genes down-regulated. The regulated genes were found to be enriched in cellular matrices and ECM-receptor interaction, the Notch signaling pathway, the PI3K-Akt signaling pathway, the MAPK signaling pathway, the Hippo signaling pathway, and the Jak-Stat pathway, among others. In addition, the genes related to the hypothalamus-pituitary-gonad axis, steroid metabolism, and IGF system were impacted. Furthermore, the mutation of mep50 caused significant alterations in alternative splicing of pre-mRNA in ovarian cells. Quantitative RT-PCR results validated the findings from RNA-seq analysis in the specific genes, including akt2, map3k5, yap1, fshr, cyp17a, igf1, ythdc2, cdk6, and col1, among others. The findings of this study demonstrate that Mep50 plays a crucial role in oogenesis, participating in a diverse range of biological processes such as steroid metabolism, cell matrix regulation, and signal pathways. This may be achieved through the regulation of gene expression via mRNA splicing in medaka ovarian cells.