Analysis of the nicotinamide phosphoribosyltransferase family provides insight into vertebrate adaptation to different oxygen levels during the water-to-land transition

Zebrafish nampt-a mutants are viable despite perturbed primitive hematopoiesis

BACKGROUND

Nicotinamide phosphoribosyltransferase (Nampt) is required for recycling NAD+ in numerous cellular contexts. Morpholino-based knockdown of zebrafish nampt-a has been shown to cause abnormal development and defective hematopoiesis concomitant with decreased NAD+ levels. However, surprisingly, nampt-a mutant zebrafish were recently found to be viable, suggesting a discrepancy between the phenotypes in knockdown and knockout conditions. Here, we address this discrepancy by directly comparing loss-of-function approaches that result in identical defective transcripts in morphants and mutants.

RESULTS

Using CRISPR/Cas9-mediated mutagenesis, we generated nampt-a mutant lines that carry the same mis-spliced mRNA as nampt-a morphants. Despite reduced NAD+ levels and perturbed expression of specific blood markers, nampt-a mutants did not display obvious developmental defects and were found to be viable. In contrast, injection of nampt-a morpholinos into wild-type or mutant nampt-a embryos caused aberrant phenotypes. Moreover, nampt-a morpholinos caused additional reduction of blood-related markers in nampt-a mutants, suggesting that the defects observed in nampt-a morphants can be partially attributed to off-target effects of the morpholinos.

CONCLUSIONS

Our findings show that zebrafish nampt-a mutants are viable despite reduced NAD+ levels and a perturbed hematopoietic gene expression program, indicating strong robustness of primitive hematopoiesis during early embryogenesis.

The role of visfatin/ NAMPT in the regulation of feeding in goldfish (Carassius auratus)

The protein NAMPT (nicotinamide phosphoribosyltransferase, encoded by the NAPMT gene) is present in two forms. The intracellular form of NAMPT (iNAMPT) is the rate-limiting enzyme in a major nicotinamide adenine dinucleotide (NAD) biosynthetic pathway and regulates cellular metabolism. NAMPT is also secreted by cells in the extracellular milieu, and referred to as extracellular NAMPT (eNAMPT or visfatin). In mammals, visfatin has been linked to various metabolic disorders. However, the role of visfatin in regulating energy homeostasis in fish is not known. In this study, we assessed the effects of nutritional status on NAMPT mRNA expression and the effects of visfatin peripheral injections on food intake and the expression of appetite regulators in goldfish. Our results show that NAMPT is widely expressed in peripheral tissues and brain. Fasting induced increases in NAMPT expression in liver but had no effect on either brain or intestine NAMPT expression levels. Intraperitoneal injections of visfatin (400 ng/g) induced an increase in food intake and in expression levels of hepatic leptin and sirtuin1. Visfatin injections decreased intestine CCK and PYY, and telencephalon (but not hypothalamic) orexin and NPY expression levels. Visfatin did not affect plasma glucose levels, intestine ghrelin or brain CART, POMC and AgRP expressions. These data suggest that visfatin/NAMPT might be involved in the regulation of feeding and energy homeostasis in goldfish.

The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish

Mitochondria are fundamental for life and require balanced ion exchange to maintain proper functioning. The mitochondrial cation exchanger LETM1 sparks interest because of its pathophysiological role in seizures in the Wolf Hirschhorn Syndrome (WHS). Despite observation of sleep disorganization in epileptic WHS patients, and growing studies linking mitochondria and epilepsy to circadian rhythms, LETM1 has not been studied from the chronobiological perspective. Here we established a viable letm1 knock-out, using the diurnal vertebrate Danio rerio to study the metabolic and chronobiological consequences of letm1 deficiency. We report diurnal rhythms of Letm1 protein levels in wild-type fish. We show that mitochondrial nucleotide metabolism is deregulated in letm1-/- mutant fish, the rate-limiting enzyme of NAD+ production is up-regulated, while NAD+ and NADH pools are reduced. These changes were associated with increased expression amplitude of circadian core clock genes in letm1-/- compared with wild-type under light/dark conditions, suggesting decreased NAD(H) levels as a possible mechanism for circadian system perturbation in Letm1 deficiency. Replenishing NAD pool may ameliorate WHS-associated sleep and neurological disorders.

Nicotinamide phosphoribosyltransferase (Nampt) of hybrid crucian carp protects intestinal barrier and enhances host immune defense against bacterial infection

Nicotinamide phosphoribosyltransferase (Nampt) can act extracellularly as a mediator of inflammation or intracellularly as a rate-limiting enzyme, regulating nicotinamide adenine dinucleotide (NAD) biosynthesis in the NAD salvage pathway. Nampt exerts important immunological functions during infection in mammals. However, the in vivo function of fish Nampt in immune regulation and inflammation is essentially unknown. With an aim to elucidate the antimicrobial mechanism of Nampt in fish, we in this study examined the function of Nampt from hybrid crucian carp. Hybrid crucian carp Nampt (WR-Nampt) possesses the conserved nicotinamide phosphoribosyltransferase domain and shows high similarity to that of mammalian Nampt. WR-Nampt is expressed in multiple tissues and is upregulated by bacterial infection. Overexpression of WR-Nampt significantly increased the number of goblet cells of distal intestine. In addition, WR-Nampt induced significant inductions in the expression of the antimicrobial molecules (IL-22, Hepcidin-1, LEAP-2 and MUC2) and tight junctions (ZO-1 and Occludin). Consistent with this, fish administered with WR-Nampt significantly alleviated the intestinal permeability and apoptosis, thereby enhancing host's resistance against bacterial infection. Together these results revealed the potential effect of WR-Nampt in intestinal barrier and immune defense against bacterial infection.

Macrophages provide a transient muscle stem cell niche via NAMPT secretion

Skeletal muscle regenerates through the activation of resident stem cells. Termed satellite cells, these normally quiescent cells are induced to proliferate by wound-derived signals¹. Identifying the source and nature of these cues has been hampered by an inability to visualize the complex cell interactions that occur within the wound. Here we use muscle injury models in zebrafish to systematically capture the interactions between satellite cells and the innate immune system after injury, in real time, throughout the repair process. This analysis revealed that a specific subset of macrophages 'dwell' within the injury, establishing a transient but obligate niche for stem cell proliferation. Single-cell profiling identified proliferative signals that are secreted by dwelling macrophages, which include the cytokine nicotinamide phosphoribosyltransferase (Nampt, which is also known as visfatin or PBEF in humans). Nampt secretion from the macrophage niche is required for muscle regeneration, acting through the C-C motif chemokine receptor type 5 (Ccr5), which is expressed on muscle stem cells. This analysis shows that in addition to their ability to modulate the immune response, specific macrophage populations also provide a transient stem-cell-activating niche, directly supplying proliferation-inducing cues that govern the repair process that is mediated by muscle stem cells. This study demonstrates that macrophage-derived niche signals for muscle stem cells, such as NAMPT, can be applied as new therapeutic modalities for skeletal muscle injury and disease.

The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels

The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity. However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48-54 million years ago (Mya) and expanded into five duplicates (chiron1-5) in zebrafish 1-4 Mya. The chiron genes (chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD⁺ synthesis pathway, chirons could directly catalyze the NAD⁺ rate-limiting reaction and probably impact two energy metabolism genes (nmnat1 and naprt) to be under positive selection in Danioninae fishes. Together, these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD⁺ biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian.

Ancient duplications and functional divergence in the interferon regulatory factors of vertebrates provide insights into the evolution of vertebrate immune systems

Interferon regulatory factors (IRFs) were first discovered as transcription factors that regulate the transcription of human interferon (IFN)-β. Increasing evidence shows that they might be important players involved in Adaptive immune system (AIS) evolution. Although numbers of IRFs have been identified in chordates, the evolutionary history and functional diversity of this gene family during the early evolution of vertebrates have remained obscure. Using IRF HMM profile and HMMER searches, we identified 148 IRFs in 11 vertebrates and 4 protochordates. For them, we reconstructed the phylogenetic relationships, determined the synteny conservation, investigated the profile of natural selection, and analyzed the expression patterns in four "living fossil" vertebrates: lamprey, elephant shark, coelacanth and bichir. The results from phylogeny and synteny analysis imply that vertebrate IRFs evolved from three predecessors, instead of four as suggested in a previous study, as results from an ancient duplication followed by special expansions and lost during the vertebrate evolution. The profile of natural selection and expression reveals functional dynamics during the process. Together, they suggest that the 2nd whole-genome duplication (2WGD) provided raw materials for innovation in the IRF family, and that the birth of type-I IFN might be an important factor inducing the establishment of IRF-mediated immune networks. As a member involved in the AIS evolution, IRF provide insights into the process and mechanism involved in the complexity and novelties of vertebrate immune systems.