Evolution of TNF-induced apoptosis reveals 550 My of functional conservation

A Network Approach to White Band Disease Challenged Staghorn Coral Acropora cervicornismicroRNAs and Their Targets

Coral reefs are increasingly threatened by disease outbreaks, yet little is known about the genetic mechanisms underlying disease resistance. Since the 1970s, White Band Disease (WBD) has decimated the Caribbean staghorn coral Acropora cervicornis. However, 15% or more of individuals are highly disease-resistant, and the genes controlling the production of Argonaut proteins, involved in microRNA (miRNA) post-transcriptional gene silencing, are up-regulated in WBD-resistant corals. This suggests that miRNAs may be key regulators of coral immunity. In this study, we conducted an in situ disease transmission experiment with five healthy-exposed control tanks and five WBD-exposed tanks, each containing 50 A. cervicornis genotypes, sampled over 7 days and then sequenced miRNAs from 12 replicate genotypes, including 12 WBD-exposed and 12 healthy-exposed control fragments from two time points. We identified 67 bona fide miRNAs in A. cervicornis, 3 of which are differentially expressed in disease-resistant corals. We performed a phylogenetic comparison of miRNAs across cnidarians and found greater conservation of miRNAs in more closely related taxa, including all three differentially expressed miRNAs being conserved in more than one Acropora coral. One of the three miRNAs has putative genomic targets involved in the cnidarian innate immunity. In addition, community detection coupled with over-representation analysis of our miRNA-messenger RNA (mRNA) target network found two key unique A. cervicornis miRNAs regulating multiple important immune-related pathways such as Toll-like receptor pathway, endocytosis, and apoptosis. These findings highlight how multiple miRNAs may help the coral host maintain immune homeostasis in the presence of environmental stress including disease.

Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China

Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.

Quantification of cytosolic 'free' calcium in isolated coral cells with confocal microscopy

Despite its prominent role as an intracellular messenger in all organisms, cytosolic free calcium ([Ca2+]i) has never been quantified in corals or cnidarians in general. Ratiometric calcium dyes and cell imaging have been key methods in successful research on [Ca2+]i in model systems, and could be applied to corals. Here, we developed a procedure to quantify [Ca2+]i in isolated cells from the model coral species Stylophora pistillata using Indo-1 and confocal microscopy. We quantified [Ca2+]i in coral cells with and without intracellular dinoflagellate symbionts, and verified our procedure on cultured mammalian cells. We then used our procedure to measure changes in [Ca2+]i in coral cells exposed to a classic inhibitor of [Ca2+]i regulation, thapsigargin, and also used it to record elevations in [Ca2+]i in coral cells undergoing apoptosis. Our procedure paves the way for future studies into intracellular calcium in corals and other cnidarians.

Induction of apoptosis by double-stranded RNA was present in the last common ancestor of cnidarian and bilaterian animals

Apoptosis, a major form of programmed cell death, is an essential component of host defense against invading intracellular pathogens. Viruses encode inhibitors of apoptosis to evade host responses during infection, and to support their own replication and survival. Therefore, hosts and their viruses are entangled in a constant evolutionary arms race to control apoptosis. Until now, apoptosis in the context of the antiviral immune system has been almost exclusively studied in vertebrates. This limited phyletic sampling makes it impossible to determine whether a similar mechanism existed in the last common ancestor of animals. Here, we established assays to probe apoptosis in the sea anemone Nematostella vectensis, a model species of Cnidaria, a phylum that diverged approximately 600 million years ago from the rest of animals. We show that polyinosinic:polycytidylic acid (poly I:C), a synthetic long double-stranded RNA mimicking viral RNA and a primary ligand for the vertebrate RLR melanoma differentiation-associated protein 5 (MDA5), is sufficient to induce apoptosis in N. vectensis. Furthermore, at the transcriptomic level, apoptosis related genes are significantly enriched upon poly(I:C) exposure in N. vectensis as well as bilaterian invertebrates. Our phylogenetic analysis of caspase family genes in N. vectensis reveals conservation of all four caspase genes involved in apoptosis in mammals and revealed a cnidarian-specific caspase gene which was strongly upregulated. Altogether, our findings suggest that apoptosis in response to a viral challenge is a functionally conserved mechanism that can be traced back to the last common ancestor of Bilateria and Cnidaria.

Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms

The intracellular coral-dinoflagellate symbiosis is the engine that underpins the success of coral reefs, one of the most diverse ecosystems on the planet. However, the breakdown of the symbiosis and the loss of the microalgal symbiont (i.e. coral bleaching) due to environmental changes are resulting in the rapid degradation of coral reefs globally. There is an urgent need to understand the cellular physiology of coral bleaching at the mechanistic level to help develop solutions to mitigate the coral reef crisis. Here, at an unprecedented scope, we present novel models that integrate putative mechanisms of coral bleaching within a common framework according to the triggers (initiators of bleaching, e.g. heat, cold, light stress, hypoxia, hyposalinity), cascades (cellular pathways, e.g. photoinhibition, unfolded protein response, nitric oxide), and endpoints (mechanisms of symbiont loss, e.g. apoptosis, necrosis, exocytosis/vomocytosis). The models are supported by direct evidence from cnidarian systems, and indirectly through comparative evolutionary analyses from non-cnidarian systems. With this approach, new putative mechanisms have been established within and between cascades initiated by different bleaching triggers. In particular, the models provide new insights into the poorly understood connections between bleaching cascades and endpoints and highlight the role of a new mechanism of symbiont loss, i.e. 'symbiolysosomal digestion', which is different from symbiophagy. This review also increases the approachability of bleaching physiology for specialists and non-specialists by mapping the vast landscape of bleaching mechanisms in an atlas of comprehensible and detailed mechanistic models. We then discuss major knowledge gaps and how future research may improve the understanding of the connections between the diverse cascade of cellular pathways and the mechanisms of symbiont loss (endpoints).

Heat-tolerant intertidal rock pool coral Porites lutea can potentially adapt to future warming

The growing threat of global warming on coral reefs underscores the urgency of identifying heat-tolerant corals and discovering their adaptation mechanisms to high temperatures. Corals growing in intertidal rock pools that vary markedly in daily temperature may have improved heat tolerance. In this study, heat stress experiments were performed on scleractinian coral Porites lutea from subtidal habitat and intertidal rock pool of Weizhou Island in the northern South China Sea. Thermotolerance differences in corals from the two habitats and their mechanisms were explored through phenotype, physiological indicators, ITS2, 16S rRNA, and RNA sequencing. At the extremely high temperature of 34°C, rock pool P. lutea had a stronger heat tolerance than those in the subtidal habitat. The strong antioxidant capacity of the coral host and its microbial partners was important in the resistance of rock pool corals to high temperatures. The host of rock pool corals at 34°C had stronger immune and apoptotic regulation, downregulated host metabolism and disease-infection-related pathways compared to the subtidal habitat. P. lutea, in this habitat, upregulated Cladocopium C15 (Symbiodiniaceae) photosynthetic efficiency and photoprotection, and significantly increased bacterial diversity and coral probiotics, including ABY1, Ruegeria, and Alteromonas. These findings indicate that rock pool corals can tolerate high temperatures through the integrated response of coral holobionts. These corals may be 'touchstones' for future warming. Our research provides new insights into the complex mechanisms by which corals resist global warming and the theoretical basis for coral reef ecosystem restoration and selection of stress-resistant coral populations.

Immune activation of the p75 neurotrophin receptor: implications in neuroinflammation

Despite structural similarity with other tumor necrosis factor receptor superfamily (TNFRSF) members, the p75 neurotrophin receptor (p75NTR, TNFR16) mediates pleiotropic biological functions not shared with other TNFRs. The high level of p75NTR expression in the nervous system instead of immune cells, its utilization of co-receptors, and its interaction with soluble dimeric, rather than soluble or cell-tethered trimeric ligands are all characteristics which distinguish it from most other TNFRs. Here, we compare these attributes to other members of the TNFR superfamily. In addition, we describe the recent evolutionary adaptation in B7-1 (CD80), an immunoglobulin (Ig) superfamily member, which allows engagement to neuronally-expressed p75NTR. B7-1-mediated binding to p75NTR occurs in humans and other primates, but not lower mammals due to specific sequence changes that evolved recently in primate B7-1. This discovery highlights an additional mechanism by which p75NTR can respond to inflammatory cues and trigger synaptic elimination in the brain through engagement of B7-1, which was considered to be immune-restricted. These observations suggest p75NTR does share commonality with other immune co-modulatory TNFR family members, by responding to immunoregulatory cues. The evolution of primate B7-1 to bind and elicit p75NTR-mediated effects on neuronal morphology and function are discussed in relationship to immune-driven modulation of synaptic actions during injury or inflammation.

Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies

Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.

Understanding Crassostrea virginica tolerance of Perkinsus marinus through global gene expression analysis

Disease tolerance, a host's ability to limit damage from a given parasite burden, is quantified by the relationship between pathogen load and host survival or reproduction. Dermo disease, caused by the protozoan parasite P. marinus, negatively impacts survival in both wild and cultured eastern oyster (C. virginica) populations. Resistance to P. marinus has been the focus of previous studies, but tolerance also has important consequences for disease management in cultured and wild populations. In this study we measured dermo tolerance and evaluated global expression patterns of two sensitive and two tolerant eastern oyster families experimentally challenged with distinct doses of P. marinus (0, 106, 107, and 108 parasite spores per gram wet weight, n = 3-5 individuals per family per dose). Weighted Gene Correlation Network Analysis (WGCNA) identified several modules correlated with increasing parasite dose/infection intensity, as well as phenotype. Modules positively correlated with dose included transcripts and enriched GO terms related to hemocyte activation and cell cycle activity. Additionally, these modules included G-protein coupled receptor, toll-like receptor, and tumor necrosis factor pathways, which are important for immune effector molecule and apoptosis activation. Increased metabolic activity was also positively correlated with treatment. The module negatively correlated with infection intensity was enriched with GO terms associated with normal cellular activity and growth, indicating a trade-off with increased immune response. The module positively correlated with the tolerant phenotype was enriched for transcripts associated with "programmed cell death" and contained a large number of tripartite motif-containing proteins. Differential expression analysis was also performed on the 108 dosed group using the most sensitive family as the comparison reference. Results were consistent with the network analysis, but signals for "programmed cell death" and serine protease inhibitors were stronger in one tolerant family than the other, suggesting that there are multiple avenues for disease tolerance. These results provide new insight for defining dermo response traits and have important implications for applying selective breeding for disease management.

The Aging Human Liver: The Weal and Woe of Evolutionary Legacy

Aging is characterized by the progressive decline of biological integrity and its compensatory mechanisms as well as immunological dysregulation. This goes along with an increasing risk of frailty and disease. Against this background, we here specifically focus on the aging of the human liver. For the first time, we shed light on the intertwining evolutionary underpinnings of the liver's declining regenerative capacity, the phenomenon of inflammaging, and the biotransformation capacity in the process of aging. In addition, we discuss how aging influences the risk for developing nonalcoholic fatty liver disease, hepatocellular carcinoma, and/or autoimmune hepatitis, and we describe chronic diseases as accelerators of biological aging.

Sharks Provide Evidence for a Highly Complex TNFSF Repertoire in the Jawed Vertebrate Ancestor

Cytokines of the TNF superfamily (TNFSF) control many immunological processes and are implicated in the etiology of many immune disorders and diseases. Despite their obvious biological importance, the TNFSF repertoires of many species remain poorly characterized. In this study, we perform detailed bioinformatic, phylogenetic, and syntenic analyses of five cartilaginous fish genomes to identify their TNFSF repertoires. Strikingly, we find that shark genomes harbor ∼30 TNFSF genes, more than any other vertebrate examined to date and substantially more than humans. This is due to better retention of the ancestral jawed vertebrate TNFSF repertoire than any other jawed vertebrate lineage, combined with lineage-specific gene family expansions. All human TNFSFs appear in shark genomes, except for lymphotoxin-α (LTA; TNFSF1) and TNF (TNFSF2), and CD70 (TNFSF7) and 4-1BBL (TNFSF9), which diverged by tandem duplications early in tetrapod and mammalian evolution, respectively. Although lacking one-to-one LTA and TNF orthologs, sharks have evolved lineage-specific clusters of LTA/TNF co-orthologs. Other key findings include the presence of two BAFF (TNFSF13B) genes along with orthologs of APRIL (TNFSF13) and BALM (TNFSF13C) in sharks, and that all cartilaginous fish genomes harbor an ∼400-million-year-old cluster of multiple FASLG (TNFSF6) orthologs. Finally, sharks have retained seven ancestral jawed vertebrate TNFSF genes lost in humans. Taken together, our data indicate that the jawed vertebrate ancestor possessed a much larger and diverse TNFSF repertoire than previously hypothesized and oppose the idea that the cartilaginous fish immune system is “primitive” compared with that of mammals.

Lower cold tolerance of tropical Porites lutea is possibly detrimental to its migration to relatively high latitude refuges in the South China Sea

As high temperature stress due to climate change threatens tropical corals, cooler areas at relatively high latitudes may be potential refuges. Tolerance to low temperatures is critical in determining whether corals can successfully migrate to higher latitudes. However, the physiological and molecular adaptations that protect corals from low temperature stress are unclear. In this study, scleractinian Porites lutea samples from the tropical Xisha Islands (XS) and subtropical Daya Bay (DY) in the South China Sea were subjected to a reduction in ambient temperature from 26 to 12°C. Differences in physiological changes and gene expression were analysed. P. lutea from both XS and DY exhibited physiological bleaching under low temperature stress, and the Symbiodiniaceae density, Fv/Fm, and chlorophyll-α content were significantly reduced. Symbiosome antioxidative stress and metabolic enzyme activity first increased and then decreased. RNA-seq analysis showed that the host responded to low temperature stress by activating immune, apoptotic, and autophagic pathways and reducing metabolic levels. Nevertheless, Symbiodiniaceae lacked the physiological regulatory capacity to adapt to low temperatures. The lower cold tolerance of XS tropical P. lutea may attribute to lower oxidative stress resistance, lower photosynthetic capacity, worse energy supply, and higher susceptibility to bacterial and viral infections and diseases in XS corals. The difference in cold tolerance may result from genetic differences between the geographic populations and is possibly detrimental to the migration of tropical coral to relatively high latitude refuges. This study provides a theoretical basis for anthropogenically assisted coral migration as a response to global change.

Development of a portable toolkit to diagnose coral thermal stress

Coral bleaching, precipitated by the expulsion of the algal symbionts that provide colonies with fixed carbon is a global threat to reef survival. To protect corals from anthropogenic stress, portable tools are needed to detect and diagnose stress syndromes and assess population health prior to extensive bleaching. Here, medical grade Urinalysis strips, used to detect an array of disease markers in humans, were tested on the lab stressed Hawaiian coral species, Montipora capitata (stress resistant) and Pocillopora acuta (stress sensitive), as well as samples from nature that also included Porites compressa. Of the 10 diagnostic reagent tests on these strips, two appear most applicable to corals: ketone and leukocytes. The test strip results from M. capitata were explored using existing transcriptomic data from the same samples and provided evidence of the stress syndromes detected by the strips. We designed a 3D printed smartphone holder and image processing software for field analysis of test strips (TestStripDX) and devised a simple strategy to generate color scores for corals (reflecting extent of bleaching) using a smartphone camera (CoralDX). Our approaches provide field deployable methods, that can be improved in the future (e.g., coral-specific stress test strips) to assess reef health using inexpensive tools and freely available software.

Molecular Characterization, Evolution and Expression Analysis of TNFSF14 and Three TNFSF Receptors in Spotted Gar Lepisosteus oculatus

The tumor necrosis superfamily (TNFSF) and their receptors (TNFRs) play an essential role in inflammatory responses. In this study, tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 were identified in spotted gar. All the genes have conserved genomic organization and synteny with their respective homologs in zebrafish and humans. The putative TNFSF protein contains a typical TNF homology domain in the extracellular region. All three TNFRSFs possess characteristic cysteine-rich domains. TNFRSF1a has a death domain in the cytosolic region which is absent in the TNFRSF1b and TNFRSF14. Notably, TNFRSF14 lacks a transmembrane domain and is predicted to be secreted. Protein structure modeling revealed that the key residues involved in the interaction between TNFSF14 and TNFRSF14 are well conserved in spotted gar. All four genes were ubiquitously expressed in the spleen, liver, kidney, gills and intestine. Infection with Klebsiella pneumoniae resulted in remarkable downregulation of tnfsf14 and tnfrsf14 in tissues but upregulation of tnfrsf1a and tnfrsf1b. The results indicate that tnfsf14, tnfrsf1a, tnfrsf1b and tnfrsf14 are involved in the immune response to bacterial infection, and expand knowledge on the TNF system in the primitive ray-finned fish.

Chronic cerebral aspects of long COVID, post-stroke syndromes and similar states share their pathogenesis and perispinal etanercept treatment logic

The chronic neurological aspects of traumatic brain injury, post-stroke syndromes, long COVID-19, persistent Lyme disease, and influenza encephalopathy having close pathophysiological parallels that warrant being investigated in an integrated manner. A mechanism, common to all, for this persistence of the range of symptoms common to these conditions is described. While TNF maintains cerebral homeostasis, its excessive production through either pathogen-associated molecular patterns or damage-associated molecular patterns activity associates with the persistence of the symptoms common across both infectious and non-infectious conditions. The case is made that this shared chronicity arises from a positive feedback loop causing the persistence of the activation of microglia by the TNF that these cells generate. Lowering this excess TNF is the logical way to reducing this persistent, TNF-maintained, microglial activation. While too large to negotiate the blood-brain barrier effectively, the specific anti-TNF biological, etanercept, shows promise when administered by the perispinal route, which allows it to bypass this obstruction.

The evolution of regulated cell death pathways in animals and their evasion by pathogens

The coevolution of host-pathogen interactions underlies many human physiological traits associated with protection from or susceptibility to infections. Among the mechanisms that animals utilize to control infections are the regulated cell death pathways of pyroptosis, apoptosis, and necroptosis. Over the course of evolution these pathways have become intricate and complex, coevolving with microbes that infect animal hosts. Microbes, in turn, have evolved strategies to interfere with the pathways of regulated cell death to avoid eradication by the host. Here, we present an overview of the mechanisms of regulated cell death in Animalia and the strategies devised by pathogens to interfere with these processes. We review the molecular pathways of regulated cell death, their roles in infection, and how they are perturbed by viruses and bacteria, providing insights into the coevolution of host-pathogen interactions and cell death pathways.

Background to new treatments for COVID-19, including its chronicity, through altering elements of the cytokine storm

Anti-tumour necrosis factor (TNF) biologicals, Dexamethasone and rIL-7 are of considerable interest in treating COVID-19 patients who are in danger of, or have become, seriously ill. Yet reducing sepsis mortality by lowering circulating levels of TNF lost favour when positive endpoints in earlier simplistic models could not be reproduced in well-conducted human trials. Newer information with anti-TNF biologicals has encouraged reintroducing this concept for treating COVID-19. Viral models have had encouraging outcomes, as have the effects of anti-TNF biologicals on community-acquired COVID-19 during their long-term use to treat chronic inflammatory states. The positive outcome of a large scale trial of dexamethasone, and its higher potency late in the disease, harmonises well with its capacity to enhance levels of IL-7Rα, the receptor for IL-7, a cytokine that enhances lymphocyte development and is increased during the cytokine storm. Lymphoid germinal centres required for antibody-based immunity can be harmed by TNF, and restored by reducing TNF. Thus the IL-7- enhancing activity of dexamethasone may explain its higher potency when lymphocytes are depleted later in the infection, while employing anti-TNF, for several reasons, is much more logical earlier in the infection. This implies dexamethasone could prove to be synergistic with rIL-7, currently being trialed as a COVID-19 therapeutic. The principles behind these COVID-19 therapies are consistent with the observed chronic hypoxia through reduced mitochondrial function, and also the increased severity of this disease in ApoE4-positive individuals. Many of the debilitating persistent aspects of this disease are predictably susceptible to treatment with perispinal etanercept, since they have cerebral origins.

Metabolomic signatures of coral bleaching history

Coral bleaching has a profound impact on the health and function of reef ecosystems, but the metabolomic effects of coral bleaching are largely uncharacterized. Here, untargeted metabolomics was used to analyse pairs of adjacent Montipora capitata corals that had contrasting bleaching phenotypes during a severe bleaching event in 2015. When these same corals were sampled four years later while visually healthy, there was a strong metabolomic signature of bleaching history. This was primarily driven by betaine lipids from the symbiont, where corals that did not bleach were enriched in saturated lyso-betaine lipids. Immune modulator molecules were also altered by bleaching history in both the coral host and the algal symbiont, suggesting a shared role in partner choice and bleaching response. Metabolomics from a separate set of validation corals was able to predict the bleaching phenotype with 100% accuracy. Experimental temperature stress induced phenotype-specific responses, which magnified differences between historical bleaching phenotypes. These findings indicate that natural bleaching susceptibility is manifested in the biochemistry of both the coral animal and its algal symbiont. This metabolome difference is stable through time and results in different physiological responses to temperature stress. This work provides insight into the biochemical mechanisms of coral bleaching and presents a valuable new tool for resilience-based reef restoration.

Liver regeneration observed across the different classes of vertebrates from an evolutionary perspective

The liver is a key organ that performs diverse functions such as metabolic processing of nutrients or disposal of dangerous substances (xenobiotics). Accordingly, it seems to be protected by several mechanisms throughout the life of organisms, one of which is compensatory hyperplasia, also known as liver regeneration. This review is a recapitulation of the scientific reports describing the different ways in which the various classes of vertebrates deal with liver injuries, where since mammals have an improved molecular toolkit, exhibit optimized regeneration of the liver compared to lower vertebrates. The main molecules involved in the compensatory process, such as proinflammatory and inhibitory cytokines, are analyzed across vertebrates with an evolutionary perspective. In addition, the possible significance of this mechanism is discussed in the context of the long life span of vertebrates, especially in the case of mammals.

Ancestral role of TNF-R pathway in cell differentiation in the basal metazoan Hydra

Tumour necrosis factor receptors (TNF-Rs) and their ligands, tumour necrosis factors, are highly conserved proteins described in all metazoan phyla. They function as inducers of extrinsic apoptotic signalling and facilitate inflammation, differentiation and cell survival. TNF-Rs use distinct adaptor molecules to activate signalling cascades. Fas-associated protein with death domain (FADD) family adaptors often mediate apoptosis, and TNF-R-associated factor (TRAF) family adaptors mediate cell differentiation and inflammation. Most of these pathway components are conserved in cnidarians, and, here, we investigated the Hydra TNF-R. We report that it is related to the ectodysplasin receptor, which is involved in epithelial cell differentiation in mammals. In Hydra, it is localised in epithelial cells with incorporated nematocytes in tentacles and body column, indicating a similar function. Further experiments suggest that it interacts with the Hydra homologue of a TRAF adaptor, but not with FADD proteins. Hydra FADD proteins colocalised with Hydra caspases in death effector filaments and recruited caspases, suggesting that they are part of an apoptotic signalling pathway. Regulating epithelial cell differentiation via TRAF adaptors therefore seems to be an ancient function of TNF-Rs, whereas FADD-caspase interactions may be part of a separate apoptotic pathway.

Gene expression kinetics of Exaiptasia pallida innate immune response to Vibrio parahaemolyticus infection

BACKGROUND

Recent sequencing projects on early-diverging metazoans such as cnidarians, have unveiled a rich innate immunity gene repertoire; however, little is known about immunity gene regulation in the host's early response against marine bacterial pathogens over time. Here, we used RNA-seq on the sea anemone Exaiptasia pallida (Ep) strain CC7 as a model to depict the innate immune response during the onset of infection with the marine pathogenic bacteria Vibrio parahaemolyticus (Vp) clinical strain O3:K6, and lipopolysaccharides (LPS) exposure. Pairwise and time series analyses identified the genes responsive to infection as well as the kinetics of innate immune genes over time. Comparisons between the responses to live Vp and purified LPS was then performed.

RESULTS

Gene expression and functional analyses detected hundreds to thousands of genes responsive to the Vp infection after 1, 3, 6 and 12 h, including a few shared with the response to LPS. Our results bring to light the first indications that non-canonical cytoplasmic pattern recognition receptors (PRRs) such as NOD-like and RIG-I-like receptor homologs take part in the immune response of Ep. Over-expression of several members of the lectin-complement pathways in parallel with novel transmembrane and Ig containing ficolins (CniFLs) suggest an active defense against the pathogen. Although lacking typical Toll-like receptors (TLRs), Ep activates a TLR-like pathway including the up-regulation of MyD88, TRAF6, NF-κB and AP-1 genes, which are not induced under LPS treatment and therefore suggest an alternative ligand-to-PRR trigger. Two cytokine-dependent pathways involving Tumor necrosis factor receptors (TNFRs) and several other potential downstream signaling genes likely lead to inflammation and/or apoptosis. Finally, both the extrinsic and intrinsic apoptotic pathways were strongly supported by over-expression of effector and executioner genes.

CONCLUSIONS

To our knowledge, this pioneering study is first to follow the kinetics of the innate immune response in a cnidarian during the onset of infection with a bacterial pathogen. Overall, our findings reveal the involvement of both novel immune gene candidates such as NLRs, RLRs and CniFLs, and previously identified TLR-like and apoptotic pathways in anthozoan innate immunity with a large amount of transcript-level evidence.

Tumor Necrosis Factor Superfamily: Ancestral Functions and Remodeling in Early Vertebrate Evolution

The evolution of the tumor necrosis factor superfamily (TNFSF) in early vertebrates is inferred by comparing the TNFSF genes found in humans and nine fishes: three agnathans, two chondrichthyans, three actinopterygians, and the sarcopterygian Latimeria chalumnae. By combining phylogenetic and synteny analyses, the TNFSF sequences detected are classified into five clusters of genes and 24 orthology groups. A model for their evolution since the origin of vertebrates is proposed. Fifteen TNFSF genes emerged from just three progenitors due to the whole-genome duplications (WGDs) that occurred before the agnathan/gnathostome split. Later, gnathostomes not only kept most of the genes emerged in the WGDs but soon added several tandem duplicates. More recently, complex, lineage-specific patterns of duplications and losses occurred in different gnathostome lineages. In agnathan species only seven to eight TNFSF genes are detected, because this lineage soon lost six of the genes emerged in the ancestral WGDs and additional losses in both hagfishes and lampreys later occurred. The orthologs of many of these lost genes are, in mammals, ligands of death-domain-containing TNFSF receptors, indicating that the extrinsic apoptotic pathway became simplified in the agnathan lineage. From the patterns of emergence of these genes, it is deduced that both the regulation of apoptosis and the control of the NF-κB pathway that depends in modern mammals on TNFSF members emerged before the ancestral vertebrate WGDs.

Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont

A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease-associated bacteria increased at 32°C, which may affect immune responses in heat-stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non-selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.

Apoptosis in gonadal somatic cells of scleractinian corals: implications of structural adjustments for gamete production and release

Apoptosis is an evolutionarily conserved process of programmed cell death. Here, we show structural changes in the gonads caused by apoptosis during gametogenesis in the scleractinian coral, Euphyllia ancora. Anatomical and histological analyses revealed that from the non-spawning to the spawning season, testes and ovaries increased in size due to active proliferation, differentiation and development of germ cells. Additionally, the thickness and cell density of the gonadal somatic layer decreased significantly as the spawning season approached. Further analyses demonstrated that the changes in the gonadal somatic layer were caused by apoptosis in a subpopulation of gonadal somatic cells. The occurrence of apoptosis in the gonadal somatic layer was also confirmed in other scleractinian corals. Our findings suggest that decreases in thickness and cell density of the gonadal somatic layer are structural adjustments facilitating oocyte and spermary (male germ cell cluster) enlargement and subsequent gamete release from the gonads. In animal reproduction, apoptosis in germ cells is an important process that controls the number and quality of gametes. However, apoptosis in gonadal somatic cells has rarely been reported among metazoans. Thus, our data provide evidence for a unique use of apoptosis in animal reproduction.

A multiomic analysis of in situ coral-turf algal interactions

Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.

The Coming Decade of Cell Death Research: Five Riddles

Active cell death, in its many forms, is a fundamental biological process. Studies over the past several decades have explored the functions and consequences of cellular demise and elucidated several of the key cell death pathways. Here, I pose five questions, or riddles, that might provide a guide to the next decade of cell death research. Focusing mainly on four types of active cell death (apoptosis, necroptosis, pyroptosis, and ferroptosis) mainly in mammals, this Perspective explores the possible research directions that might answer these riddles, or at least prompt new ones.

Programmed Cell Death in the Evolutionary Race against Bacterial Virulence Factors

Innate immune sensors can recognize when host cells are irrevocably compromised by pathogens, and in response can trigger programmed cell death (pyroptosis, apoptosis, and necroptosis). Innate sensors can directly bind microbial ligands; for example, NAIP/NLRC4 detects flagellin/rod/needle, whereas caspase-11 detects lipopolysaccharide. Other sensors are guards that monitor normal function of cellular proteins; for instance, pyrin monitors Rho GTPases, whereas caspase-8 and receptor-interacting protein kinase (RIPK)3 guards RIPK1 transcriptional signaling. Some proteins that need to be guarded can be duplicated as decoy domains, as seen in the integrated decoy domains within NLRP1 that watch for microbial attack. Here, we discuss the evolutionary battle between pathogens and host innate immune sensors/guards, illustrated by the Red Queen hypothesis. We discuss in depth four pathogens, and how they either fail in this evolutionary race (Chromobacterium violaceum, Burkholderia thailandensis), or how the evolutionary race generates increasingly complex virulence factors and host innate immune signaling pathways (Yersinia species, and enteropathogenic Escherichia coli [EPEC]).

Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host

Theory suggests that the direct transmission of beneficial endosymbionts (mutualists) from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile's ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae) during the planktonic larval stage was advantageous, as is widely assumed, in the ecologically important and threatened Caribbean reef-building coral Orbicella faveolata. Following larval acquisition, similar changes occurred in host energetic lipid use and gene expression regardless of whether their symbionts were photosynthesizing, suggesting the symbionts did not provide the energetic benefit characteristic of the mutualism in adults. Larvae that acquired photosymbionts isolated from conspecific adults on their natal reef exhibited a reduction in swimming, which may interfere with their ability to find suitable settlement substrate, and also a decrease in survival. Larvae exposed to two cultured algal species did not exhibit differences in survival, but decreased their swimming activity in response to one species. We conclude that acquiring photosymbionts during the larval stage confers no advantages and can in fact be disadvantageous to this coral host. The timing of symbiont acquisition appears to be a critical component of a host's life history strategy and overall reproductive fitness, and this timing itself appears to be under selective pressure.

Transcriptomic analyses highlight the likely metabolic consequences of colonization of a cnidarian host by native or non-native Symbiodinium species

Reef-building corals and some other cnidarians form symbiotic relationships with members of the dinoflagellate family Symbiodinaceae. As Symbiodinaceae is a highly diverse taxon, the physiological interactions between its members and their hosts are assumed to differ between associations. The presence of different symbiont types is known to affect expression levels of specific host genes, but knowledge of the effects on the transcriptome more broadly remains limited. In the present study, transcriptome profiling was conducted on the tropical corallimorpharian, Ricordea yuma, following the establishment of symbiosis with either the ‘homologous’ symbiont Symbiodinium goreaui (also known as Cladocopium goreaui; ITS2 type C1) or ‘heterologous’ symbionts (predominantly S. trenchii, which is also known as Durusdinium trenchii; ITS2 type D1a) isolated from a different corallimorpharian host (Rhodactis indosinensis). Transcriptomic analyses showed that genes encoding host glycogen biosynthesis pathway components are more highly induced during colonization by the homologous symbiont than by the heterologous symbiont. Similar patterns were also observed for several other genes thought to facilitate symbiotic nutrient exchange, including those involved in lipid translocation/storage and metabolite transport. The gene expression results presented here imply that colonization by homologous or heterologous Symbiodinium types may have very different metabolic consequences for the Ricordea host, supporting the notion that even though some cnidarians may be able to form novel symbioses after bleaching, the metabolic performance of these may be compromised.

This article has an associated First Person interview with the first author of the paper.

Summary: Colonization by the homologous symbiont, Symbiodinium goreaui, resulted in greater glycogen synthesis and ammonium assimilation capacity in the host than when it was colonized by a heterologous symbiont (S. trenchii).

TNFα is responsible for the canonical offspring number-size trade-off

There is a canonical life-history trade-off between quantity and quality of offspring, but molecular determinants for this are unknown. Here, we show that knockout of tumor necrosis factor (TNF-KO) in mice switched a relation between the number and size of developing embryos from expectedly negative to unexpectedly positive. Depletion of TNFα imbalanced humoral and trophic maintenance of embryo growth during gestation with respect to the litter size. The levels of embryotrophic GM-CSF cytokine and placental efficiency attained positive correlations with the number and size of embryos in TNF-KO females. Thus, TNFα oversees mother’s resource allocations to balance embryo growth with the number of offspring. Consequently, this suggests an intricate link between the number-size trade-off and immunity given a pivotal role of TNFα in immune homeostasis.

Comparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution

Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral ‘core’ genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.

The Tumor Necrosis Factor Family: Family Conventions and Private Idiosyncrasies

The tumor necrosis factor (TNF) cytokine family and the TNF/nerve growth factor (NGF) family of their cognate receptors together control numerous immune functions, as well as tissue-homeostatic and embryonic-development processes. These diverse functions are dictated by both shared and distinct features of family members, and by interactions of some members with nonfamily ligands and coreceptors. The spectra of their activities are further expanded by the occurrence of the ligands and receptors in both membrane-anchored and soluble forms, by "re-anchoring" of soluble forms to extracellular matrix components, and by signaling initiation via intracellular domains (IDs) of both receptors and ligands. Much has been learned about shared features of the receptors as well as of the ligands; however, we still have only limited knowledge of the mechanistic basis for their functional heterogeneity and for the differences between their functions and those of similarly acting cytokines of other families.

Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism

Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions unique to corals (competing with neighbouring colonies over benthic space). Similar to observations in mammals, PAF production was higher in regions of active tissue growth and increased when corals were exposed to elevated levels of ultraviolet light. PAF production also increased when corals were attacked by the stinging cells of a neighbouring colony, though only the attacked coral exhibited an increase in PAF. This reaction was observed in adjacent areas of the colony, indicating that this response is coordinated across multiple polyps including those not directly subject to the stress. PAF and Lyso-PAF are involved in coral stress responses that are both shared with mammals and unique to the ecology of cnidarians.

Genetic and molecular basis of the immune system in the brachiopod Lingula anatina

The extension of comparative immunology to non-model systems, such as mollusks and annelids, has revealed an unexpected diversity in the complement of immune receptors and effectors among evolutionary lineages. However, several lophotrochozoan phyla remain unexplored mainly due to the lack of genomic resources. The increasing accessibility of high-throughput sequencing technologies offers unique opportunities for extending genome-wide studies to non-model systems. As a result, the genome-based study of the immune system in brachiopods allows a better understanding of the alternative survival strategies developed by these immunologically neglected phyla. Here we present a detailed overview of the molecular components of the immune system identified in the genome of the brachiopod Lingula anatina. Our findings reveal conserved intracellular signaling pathways as well as unique strategies for pathogen detection and killing in brachiopods.

Zoanthid mucus as new source of useful biologically active proteins

Palythoa caribaeorum is a very common colonial zoanthid in the coastal reefs of Brazil. It is known for its massive production of mucus, which is traditionally used in folk medicine by fishermen in northeastern Brazil. This study identified biologically active compounds in P. caribaerum mucus. Crude mucus was collected during low tides by the manual scraping of colonies; samples were maintained in an ice bath, homogenized, and centrifuged at 16,000 g for 1 h at 4 °C; the supernatant (mucus) was kept at -80 °C until use. The enzymatic (proteolytic and phospholipase A₂), inhibitory (metallo, cysteine and serine proteases), and hemagglutinating (human erythrocyte) activities were determined. The results showed high levels of cysteine and metallo proteases, intermediate levels of phosholipase A₂, low levels of trypsin, and no elastase and chymotrypsin like activities. The mucus showed potent inhibitory activity on snake venom metalloproteases and cysteine proteinase papain. In addition, it showed agglutinating activity towards O⁺, B⁺, and A⁺ erythrocyte types. The hemostatic results showed that the mucus prolongs the aPTT and PT, and strongly inhibited platelet aggregation induced by arachidonic acid, collagen, epinephrine, ADP, and thrombin. The antimicrobial activity was tested on 15 strains of bacteria and fungi through the radial diffusion assay in agar, and no activity was observed. Compounds in P. caribaeorum mucus were analyzed for the first time in this study, and our results show potential pharmacological activities in these compounds, which are relevant for use in physiopathological investigations. However, the demonstration of these activities indicates caution in the use of crude mucus in folk medicine. Furthermore, the present or absent activities identified in this mucus suggest that the studied P. caribaeorum colonies were in thermal stress conditions at the time of sample collection; these conditions may precede the bleaching process in zoanthids. Hence, the use of mucus as an indicator of this process should be evaluated in the future.

RNA-Seq Reveals Extensive Transcriptional Response to Heat Stress in the Stony Coral Galaxea fascicularis

Galaxea fascicularis, a stony coral belonging to family Oculinidae, is widely distributed in Red Sea, the Gulf of Aden and large areas of the Indo-Pacific oceans. So far there is a lack of gene expression knowledge concerning this massive coral. In the present study, G. fascicularis was subjected to heat stress at 32.0 ± 0.5°C in the lab, we found that the density of symbiotic zooxanthellae decreased significantly; meanwhile apparent bleaching and tissue lysing were observed at 10 h and 18 h after heat stress. The transcriptome responses were investigated in the stony coral G. fascicularis during heat bleaching using RNA-seq. A total of 42,028 coral genes were assembled from over 439 million reads. Gene expressions were compared at 10 and 18 h after heat stress. The significantly upregulated genes found in the Control_10h vs. Heat_10h comparison, presented mainly in GO terms related with DNA integration and unfolded protein response; and for the Control_18h vs. Heat_18h comparison, the GO terms include DNA integration. In addition, comparison between groups of Control_10h vs. Heat_10h and Control_18h vs. Heat_18h revealed that 125 genes were significantly upregulated in common between the two groups, whereas 21 genes were significantly downregulated in common, all these differentially expressed genes were found to be involved in stress response, DNA integration and unfolded protein response. Taken together, our results suggest that high temperature could activate the stress response at the early stage, and subsequently induce the bleaching and lysing through DNA integration and unfolded protein response, which are able to disrupt the balance of coral-zooxanthella symbiosis in the stony coral G. fascicularis.

Systemic response of the stony coral Pocillopora damicornis against acute cadmium stress

Heavy metals have become one of the main pollutants in the marine environment and a major threat to the growth and reproduction of stony corals. In the present study, the density of symbiotic zooxanthellae, levels of crucial physiological activities and the transcriptome were investigated in the stony coral Pocillopora damicornis after the acute exposure to elevated cadmium concentration. The density of symbiotic zooxanthellae decreased significantly during 12-24h period, and reached lowest at 24h after acute cadmium stress. No significant changes were observed in the activity of glutathione S-transferase during the entire stress exposure. The activities of superoxide dismutase and catalase, and the concentration of glutathione decreased significantly, but the activation level of caspase3 increased significantly after cadmium exposure. Furthermore, transcriptome sequencing and bioinformatics analysis revealed 3538 significantly upregulated genes and 8048 significantly downregulated genes at 12h after the treatment. There were 12 overrepresented GO terms for significantly upregulated genes, mostly related to unfolded protein response, endoplasmic reticulum stress and apoptosis. In addition, a total of 32 GO terms were overrepresented for significantly downregulated genes, and mainly correlated with macromolecular metabolic processes. These results collectively suggest that acute cadmium stress could induce apoptosis by repressing the production of the antioxidants, elevating oxidative stress and activating the unfolded protein response. This cascade of reactions would result to the collapse of the coral-zooxanthella symbiosis and the expulsion of symbiotic zooxanthellae in the stony coral P. damicornis, ultimately leading to coral bleaching.

Just So Stories about the Evolution of Apoptosis

Apoptosis is a form of active cell death engaged by developmental cues as well as many different cellular stresses in which the dying cell essentially 'packages' itself for removal. The process of apoptotic cell death, as defined at the molecular level, is unique to the Metazoa (animals). Yet active cell death exists in non-animal organisms, and in some cases molecules involved in such death show some sequence similarities to those involved in apoptosis, leading to extensive speculation regarding the evolution of apoptosis. Here, we examine such speculation from the perspective of the functional properties of molecules of the mitochondrial apoptotic cell death pathway. We suggest scenarios for the evolution of one pathway of apoptosis, the mitochondrial pathway, and consider how they might be tested. We conclude with a 'Just So Story' of how the mitochondrial pathway of apoptosis might have evolved during eukaryotic evolution.

Functionality of intrinsic disorder in tumor necrosis factor-α and its receptors

Tumor necrosis factor-α (TNF-α) is a pleiotropic inflammatory cytokine that exerts potent cytotoxic effects on solid tumor cells, while not affecting their normal counterparts. It is also known that TNF-α exerts many of its biological functions via interaction with specific receptors. To understand the potential roles of intrinsic disorder in the functioning of this important cytokine, we explored the peculiarities of intrinsic disorder distribution in human TNF-α and its homologs from various species, ranging from zebrafish to chimpanzee. We also studied the peculiarities of intrinsic disorder distribution in human TNF-α receptors, TNFR1 and TNFR2. Analysis revealed that cytoplasmic domains of TNF-α and its receptors are expected to be highly disordered. Furthermore, although the sequence identities of analyzed TNF-α homologs range from 99.57% (between human and chimpanzee proteins) to 22.33% (between frog and fish proteins), their intrinsic disorder profiles are characterized by a remarkable similarity. These observations indicate that the peculiarities of distribution of the intrinsic disorder propensity within the amino acid sequences are evolutionary conserved, and therefore could be of functional importance for this family of proteins. We also show that disordered and flexible regions of human TNF-α and its TNFR1 and TNFR2 receptors are crucial for some of their biological activities.

De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

Background

Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals (“healthy”), GA lesion tissue from diseased corals (“GA-affected”) and apparently healthy tissue from diseased corals (“GA-unaffected”). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease.

Results

The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system.

Conclusion

This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4090-y) contains supplementary material, which is available to authorized users.

Coral cell separation and isolation by fluorescence-activated cell sorting (FACS)

BACKGROUND

Generalized methods for understanding the cell biology of non-model species are quite rare, yet very much needed. In order to address this issue, we have modified a technique traditionally used in the biomedical field for ecological and evolutionary research. Fluorescent activated cell sorting (FACS) is often used for sorting and identifying cell populations. In this study, we developed a method to identify and isolate different cell populations in corals and other cnidarians.

METHODS

Using fluorescence-activated cell sorting (FACS), coral cell suspension were sorted into different cellular populations using fluorescent cell markers that are non-species specific. Over 30 different cell markers were tested. Additionally, cell suspension from Aiptasia pallida was also tested, and a phagocytosis test was done as a downstream functional assay.

RESULTS

We found that 24 of the screened markers positively labeled coral cells and 16 differentiated cell sub-populations. We identified 12 different cellular sub-populations using three markers, and found that each sub-population is primarily homogeneous. Lastly, we verified this technique in a sea anemone, Aiptasia pallida, and found that with minor modifications, a similar gating strategy can be successfully applied. Additionally, within A. pallida, we show elevated phagocytosis of sorted cells based on an immune associated marker.

CONCLUSIONS

In this study, we successfully adapted FACS for isolating coral cell populations and conclude that this technique is translatable for future use in other species. This technique has the potential to be used for different types of studies on the cellular stress response and other immunological studies.

The meteorology of cytokine storms, and the clinical usefulness of this knowledge

The term cytokine storm has become a popular descriptor of the dramatic harmful consequences of the rapid release of polypeptide mediators, or cytokines, that generate inflammatory responses. This occurs throughout the body in both non-infectious and infectious disease states, including the central nervous system. In infectious disease it has become a useful concept through which to appreciate that most infectious disease is not caused directly by a pathogen, but by an overexuberant innate immune response by the host to its presence. It is less widely known that in addition to these roles in disease pathogenesis these same cytokines are also the basis of innate immunity, and in lower concentrations have many essential physiological roles. Here we update this field, including what can be learned through the history of how these interlinking three aspects of biology and disease came to be appreciated. We argue that understanding cytokine storms in their various degrees of acuteness, severity and persistence is essential in order to grasp the pathophysiology of many diseases, and thus the basis of newer therapeutic approaches to treating them. This particularly applies to the neurodegenerative diseases.

Elevated ammonium reduces the negative effect of heat stress on the stony coral Pocillopora damicornis

Climate change and environmental pollution have been threatening the survival of corals. In the present study, whole transcriptomes of the coral Pocillopora damicornis were sequenced under high temperature and elevated ammonium. After reads mapping and abundance estimation, differentially expressed genes were obtained in the Control/Heat, Control/Heat_NH4 and Heat/Heat_NH4 comparisons. Five overrepresented GO terms centering the tumor necrosis factor signaling pathway were noted for significantly upregulated genes in the Control/Heat and Control/Heat_NH4 comparisons. In addition, five GO terms related to apoptosis and cell death were overrepresented for significantly upregulated genes in the Control/Heat comparison but not in the Control/Heat_NH4 comparison. The expression level of 112 genes in these GO terms increased significantly in the Heat group, but only 44 genes showed the increase trend in the Heat_NH4 group. These results collectively suggested that elevated ammonium could reduce the negative effect of heat stress on the coral P. damicornis.

The cell specificity of gene expression in the response to heat stress in corals

Previous transcriptional studies in heat-stressed corals have shown that many genes are responsive to generalized heat stress whereas the expression patterns of specific gene networks after heat stress show strong correlations with variation in bleaching outcomes. However, where these specific genes are expressed is unknown. In this study, we employed in situ hybridization to identify patterns of spatial gene expression of genes previously predicted to be involved in general stress response and bleaching. We found that tumor necrosis factor receptors (TNFRs), known to be strong responders to heat stress, were not expressed in gastrodermal symbiont-containing cells but were widely expressed in specific cells of the epidermal layer. The transcription factors AP-1 and FosB, implicated as early signals of heat stress, were widely expressed throughout the oral gastrodermis and epidermis. By contrast, a G protein-coupled receptor gene (GPCR) and a fructose bisphosphate aldolase C gene (aldolase), previously implicated in bleaching, were expressed in symbiont-containing gastrodermal cells and in the epidermal tissue. Finally, chordin-like/kielin (chordin-like), a gene highly correlated to bleaching, was expressed solely in the oral gastrodermis. From this study, we confirm that heat-responsive genes occur widely in coral tissues outside of symbiont-containing cells. Joint information about expression patterns in response to heat and cell specificity will allow greater dissection of the regulatory pathways and specific cell reactions that lead to coral bleaching.

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence

Holobionts are assemblages of microbial symbionts and their macrobial host. As extant representatives of some of the oldest macro-organisms, corals and algae are important for understanding how holobionts develop and interact with one another. Using untargeted metabolomics, we show that non-self interactions altered the coral metabolome more than self-interactions (i.e. different or same genus, respectively). Platelet activating factor (PAF) and Lyso-PAF, central inflammatory modulators in mammals, were major lipid components of the coral holobionts. When corals were damaged during competitive interactions with algae, PAF increased along with expression of the gene encoding Lyso-PAF acetyltransferase; the protein responsible for converting Lyso-PAF to PAF. This shows that self and non-self recognition among some of the oldest extant holobionts involve bioactive lipids identical to those in highly derived taxa like humans. This further strengthens the hypothesis that major players of the immune response evolved during the pre-Cambrian.

Effects of elevated ammonium on the transcriptome of the stony coral Pocillopora damicornis

The survival of corals worldwide has been seriously threatened by eutrophication events concomitant with the increase in ocean pollution. In the present study, whole transcriptomes of the stony coral Pocillopora damicornis exposed to elevated ammonium were sequenced. A total of 121,366,983 pair-end reads were obtained, and 209,337 genes were assembled, including 42,399 coral-derived and 54,874 zooxanthella-derived genes. Further, a comparison of the control versus stress group revealed 6572 differentially expressed genes. For 1015 significantly upregulated genes, 24 GO terms were overrepresented, among which 3 terms related to apoptosis and cell death induction included one caspase, five bcl-2-like proteins, and two tumor necrosis factor receptor superfamily member genes. For 5557 significantly downregulated genes, the top 10 overrepresented terms were related to metabolism and signal transduction. These results indicate that apoptosis and cell death could be induced under elevated ammonium, suggesting that metabolic regulation and signal transduction might be involved in the reconstruction of the coral-zooxanthellae symbiotic balance in the stony coral P. damicornis.

Viruses and the origin of microbiome selection and immunity

The last common metazoan ancestor (LCMA) emerged over half a billion years ago. These complex metazoans provided newly available niche space for viruses and microbes. Modern day contemporaries, such as cnidarians, suggest that the LCMA consisted of two cell layers: a basal endoderm and a mucus-secreting ectoderm, which formed a surface mucus layer (SML). Here we propose a model for the origin of metazoan immunity based on external and internal microbial selection mechanisms. In this model, the SML concentrated bacteria and their associated viruses (phage) through physical dynamics (that is, the slower flow fields near a diffusive boundary layer), which selected for mucin-binding capabilities. The concentration of phage within the SML provided the LCMA with an external microbial selective described by the bacteriophage adherence to mucus (BAM) model. In the BAM model, phage adhere to mucus protecting the metazoan host against invading, potentially pathogenic bacteria. The same fluid dynamics that concentrated phage and bacteria in the SML also concentrated eukaryotic viruses. As eukaryotic viruses competed for host intracellular niche space, those viruses that provided the LCMA with immune protection were maintained. If a resident virus became pathogenic or if a non-beneficial infection occurred, we propose that tumor necrosis factor (TNF)-mediated programmed cell death, as well as other apoptosis mechanisms, were utilized to remove virally infected cells. The ubiquity of the mucosal environment across metazoan phyla suggest that both BAM and TNF-induced apoptosis emerged during the Precambrian era and continue to drive the evolution of metazoan immunity.

The Evolution of Antiviral Defense Systems

Self-replicating genetic material presumably provided the architecture necessary for generating the last universal ancestor of all nucleic-acid-based life. As biological complexity increased in the billions of years that followed, the same genetic material also morphed into a wide spectrum of viruses and other parasitic genetic elements. The resulting struggle for existence drove the evolution of host defenses, giving rise to a perpetual arms race. This Perspective summarizes the antiviral mechanisms evident across the tree of life, discussing each in their evolutionary context to postulate how the coevolution of host and pathogen shaped the cellular antiviral defenses we know today.

Excess cerebral TNF causing glutamate excitotoxicity rationalizes treatment of neurodegenerative diseases and neurogenic pain by anti-TNF agents

The basic mechanism of the major neurodegenerative diseases, including neurogenic pain, needs to be agreed upon before rational treatments can be determined, but this knowledge is still in a state of flux. Most have agreed for decades that these disease states, both infectious and non-infectious, share arguments incriminating excitotoxicity induced by excessive extracellular cerebral glutamate. Excess cerebral levels of tumor necrosis factor (TNF) are also documented in the same group of disease states. However, no agreement exists on overarching mechanism for the harmful effects of excess TNF, nor, indeed how extracellular cerebral glutamate reaches toxic levels in these conditions. Here, we link the two, collecting and arguing the evidence that, across the range of neurodegenerative diseases, excessive TNF harms the central nervous system largely through causing extracellular glutamate to accumulate to levels high enough to inhibit synaptic activity or kill neurons and therefore their associated synapses as well. TNF can be predicted from the broader literature to cause this glutamate accumulation not only by increasing glutamate production by enhancing glutaminase, but in addition simultaneously reducing glutamate clearance by inhibiting re-uptake proteins. We also discuss the effects of a TNF receptor biological fusion protein (etanercept) and the indirect anti-TNF agents dithio-thalidomides, nilotinab, and cannabinoids on these neurological conditions. The therapeutic effects of 6-diazo-5-oxo-norleucine, ceptriaxone, and riluzole, agents unrelated to TNF but which either inhibit glutaminase or enhance re-uptake proteins, but do not do both, as would anti-TNF agents, are also discussed in this context. By pointing to excess extracellular glutamate as the target, these arguments greatly strengthen the case, put now for many years, to test appropriately delivered ant-TNF agents to treat neurodegenerative diseases in randomly controlled trials.