Intermediary metabolism in sea urchin: the first inferences from the genome sequence

Astragalus polysaccharide attenuates bleomycin-induced pulmonary fibrosis by inhibiting TLR4/ NF-κB signaling pathway and regulating gut microbiota

PURPOSE

Astragalus polysaccharide (APS) is a naturally-occurring compound derived from Astragalus membranaceus with anti-inflammatory and antioxidant properties. However, its beneficial effects and mechanisms on pulmonary fibrosis are unknown. Gut microbiota impact lung diseases via the gut-lung axis. Herein, we investigated APS progression to intervene in pulmonary fibrosis via the toll-like receptor 4(TLR4)/nuclear factor-kappa B(NF-κB) signaling pathway and gut microbiota homeostasis regulation.

METHODS

We used bleomycin (BLM) to construct an idiopathic pulmonary fibrosis (IPF) mouse model and assessed the pathology with Masson, hematoxylin-eosin (HE), and Sirius red staining. Enzyme-linked immunosorbent assay (ELISA) kits were employed to evaluate the inflammatory cytokine levels. Western blot evaluated TLR4/NF-κB signaling pathway expression. TUNEL staining to detect apoptosis. Mice feces samples were gathered for 16S rRNA gene sequencing.

RESULTS

Our findings revealed that APS ameliorated the extent of damage and collagen deposition in lung tissues, reduced inflammatory cytokines TNF-α, IL-6, and IL-1β levels, and decreased apoptosis. APS might attenuate the inflammatory response through TLR4/NF-κB signaling pathway inhibition. Meanwhile, the IPF mice model exhibited dysregulation of gut microbiota, and these changes were restored after APS intervention. APS may increase the proportion of probiotics, decrease that of harmful bacteria, and balance the gut microbiota via regulating metabolic pathways.

CONCLUSION

APS ameliorated lung tissue injury in the IPF mice model, inhibited TLR4/NF-κB signaling pathway, suppressed inflammatory cytokines activation, and reduced apoptosis. Moreover, APS regulated the metabolism of gut microbiota besides beneficial bacteria content elevation.

Metabolomics Unravels Grazing Interactions under Nutrient Enrichment from Aquaculture

Our goal was to understand the mechanisms behind the impact of nutrient enrichment at intermediate distances from aquaculture on the interactions of a subtidal macroalgae community with its main grazer, the sea urchin Paracentrotus lividus. We assessed the diversity and cover of the macroalgal community, the abundance and biometrics of the sea urchins, the carbon and nitrogen elemental and isotopic compositions, and their metabolome in two stations, at an intermediate distance (station A) and away (station B) from a fish cage facility in the Aegean Sea (Greece), during the warm and cold seasons. The nutrient input at station A favored a shift to a macroalgal assemblage dominated by turf-forming species, depleted of native-erected species and with a higher abundance of invasive algae. A stable isotope analysis showed fish-farm-associated nitrogen enrichment of the macroalgae and trophic transfer to P. lividus. A decrease in metabolites related to grazing, reproduction, and energy reserves was found in P. lividus at station A. Furthermore, the metabolomic analysis was able to pinpoint stress in P. lividus at an intermediate distance from aquaculture. The chosen combination of traditional ecology with omics technology could be used to uncover not only the sublethal effects of nutrient loading but also the pathways for species interactions.

Lipid metabolism of sea urchin Paracentrotus lividus in two contrasting natural habitats

Sea urchins Paracentrotus lividus were harvested monthly from April 2015 to March 2016 from two sites in Sardinia (Italy). The two sites, a Posidonia oceanica meadow and a rocky bottom habitat, were naturally characterized by different food sources and availability, being mainly populated by the sea grass Posidonia oceanica and the brown algae Halopteris scoparia, respectively. Total lipids showed a minimum during winter in mature gonads, and a maximum in the summer (recovery stage). Fatty acid (FA) profiles of gut contents and gonads differed from those of the most available food sources. Levels of C18:3 (n-3) (ALA) discriminated samples from the two sites. Despite the very low amounts of C20:5 (n-3) (EPA) and C20:4 (n-6) (ARA) in P. oceanica, the main FA in gonads and gut contents were EPA and ARA in both sites. Increase in green algae intake prior to gametogenesis, especially C. cylindracea, likely affected EPA and ARA levels in gonads. The results show that P. lividus is able to concentrate lipids in gut contents and also to selectively store EPA, ARA and their precursors ALA and 18:2 (n-6) (LA). Moreover, bioconversion of ALA to EPA and of LA to ARA in P. lividus is suggested.

De novo transcriptomic analysis of gonad of Strongylocentrotus nudus and gene discovery for biosynthesis of polyunsaturated fatty acids

BACKGROUND

Strongylocentrotus nudus is an important cultured sea urchin species in north China, because its gonad is rich in unsaturated fatty acids, particularly long polyunsaturated fatty acids (LC-PUFAs). These PUFAs play pleiotropic and crucial roles in a wide range of biological process.

OBJECTIVE

However, the genes contributing to biosynthesis PUFAs have not been elucidated yet, and the molecular mechanism relative to the difference in PUFA composition between male and female gonad as been revealed but the corresponding has not been understood.

METHODS

In this paper, solexa sequencing based transcriptomic approach was used to identify and characterize the key genes relative to PUFA synthesis and further conducted different expressed genes between male and female gonad.

RESULTS

A total of 130,124 transcripts and 189330 unigenes were de novo assembled from 64.32 Gb data. Next, these unigenes were subjected to functional annotation by mapping to six public databases, and this process revealed a lot of genes involving in lipid metabolism. In addition, three types of fatty acids front-end desaturase and three species of very long fatty acids elongase were identified and the pathway for PUFA biosynthesis was hypothesized. Last, comparative analysis revealed the higher expression level of Δ5 desaturase, Δ6 desaturase, ELOVL-4, -6 and -7 in male gonad compared with female.

CONCLUSION

This results could plausible explain the differ in composition of PUFAs between male and female gonad of sea urchin.

The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s

The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.

Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification

Ocean acidification from the uptake of anthropogenic CO2 is expected to have deleterious consequences for many calcifying marine animals. Forecasting the vulnerability of these marine organisms to climate change is linked to an understanding of whether species possess the physiological capacity to compensate for the potentially adverse effects of ocean acidification. We carried out a microarray-based transcriptomic analysis of the physiological response of larvae of a calcifying marine invertebrate, the purple sea urchin, Strongylocentrotus purpuratus, to CO2-driven seawater acidification. In lab-based cultures, larvae were raised under conditions approximating current ocean pH conditions (pH 8.01) and at projected, more acidic pH conditions (pH 7.96 and 7.88) in seawater aerated with CO2 gas. Targeting expression of ∼1000 genes involved in several biological processes, this study captured changes in gene expression patterns that characterize the transcriptomic response to CO2-driven seawater acidification of developing sea urchin larvae. In response to both elevated CO2 scenarios, larvae underwent broad scale decreases in gene expression in four major cellular processes:biomineralization, cellular stress response, metabolism and apoptosis. This study underscores that physiological processes beyond calcification are impacted greatly, suggesting that overall physiological capacity and not just a singular focus on biomineralization processes is essential for forecasting the impact of future CO2 conditions on marine organisms. Conducted on targeted and vulnerable species, genomics-based studies, such as the one highlighted here, have the potential to identify potential `weak links' in physiological function that may ultimately determine an organism's capacity to tolerate future ocean conditions.

The sea urchin genome as a window on function

The emphasis on the sequencing of genomes seems to make this task an end in itself. However, genome sequences and the genes that are predicted from them are really an opportunity to examine the biological function of the organism constructed by that genome. This point is illustrated here by examples in which the newly annotated gene complement reveals surprises about the way Strongylocentrotus purpuratus, the purple sea urchin, goes about its business. The three topics considered here are the nature of the innate immune system; the unexpected complexity of sensory function implied by genes encoding sensory proteins; and the remarkable intricacy of the regulatory gene complement in embryogenesis.