Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus

Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of Strongylocentrotus purpuratus. The most prevalent among these elements were the unknown elements—in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the de novo transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level.

Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid—Novel Insights into Echinodermata Biology

The purple sea urchin (Strongylocentrotus purpuratus) is a marine invertebrate of the class Echinoidea that serves as an important research model for developmental biology, cell biology, and immunology, as well as for understanding regenerative responses and ageing. Peptidylarginine deiminases (PADs) are calcium-dependent enzymes that mediate post-translational protein deimination/citrullination. These alterations affect protein function and may also play roles in protein moonlighting. Extracellular vesicles (EVs) are membrane-bound vesicles that are released from cells as a means of cellular communication. Their cargo includes a range of protein and RNA molecules. EVs can be isolated from many body fluids and are therefore used as biomarkers in physiological and pathological responses. This study assessed EVs present in the coelomic fluid of the purple sea urchin (Strongylocentrotus purpuratus), and identified both total protein cargo as well as the deiminated protein cargo. Deiminated proteins in coelomic fluid EVs were compared with the total deiminated proteins identified in coelomic fluid to assess putative differences in deiminated protein targets. Functional protein network analysis for deiminated proteins revealed pathways for immune, metabolic, and gene regulatory functions within both total coelomic fluid and EVs. Key KEGG and GO pathways for total EV protein cargo furthermore showed some overlap with deimination-enriched pathways. The findings presented in this study add to current understanding of how post-translational deimination may shape immunity across the phylogeny tree, including possibly via PAD activity from microbiota symbionts. Furthermore, this study provides a platform for research on EVs as biomarkers in sea urchin models.

Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics

This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.

Exploring impacts of marine heatwaves: paternal heat exposure diminishes fertilization success in the purple sea urchin (Strongylocentrotus purpuratus)

Marine heatwaves (MHWs) are projected to increase in intensity and frequency over the coming decades, and it is imperative to assess the adaptive capacity of marine organisms to these extreme temperature events. Given the nature of MHWs to last days to weeks in a region, these events may have overarching impacts on phenological events like reproduction and development. Here, the role of adult thermal history and transgenerational plasticity may be an important pathway by which MHWs are transduced to impact community structure. In this study, we sought to explore the effects of paternal thermal history in the purple urchin, Strongylocentrotus purpuratus, on a crucial aspect of reproduction, fertilization. Using ecologically relevant temperatures representative of both MHW events that occurred in 2014–2020 and non-MHW temperatures in our region of the California Large Marine Ecosystem, we conditioned male S. purpuratus for 28 days to either a high, MHW or a low, non-MHW temperature. Following the temperature acclimation of adults, sperm performance was tested for individual males by conducting fertilization success trials at varying temperatures and sperm concentrations. While sperm appeared robust to elevated temperature during fertilization, sperm produced by high-temperature-acclimated males had overall diminished performance as compared to those acclimated to non-MHW temperatures. These results suggest MHW events will have a negative impact on fertilization in situ for S. purpuratus populations. Furthermore, these results highlight the importance of considering both male and female environmental history in projections of reproduction under climate change scenarios.

Energetic context determines the effects of multiple upwelling-associated stressors on sea urchin performance

Globally, kelp forests are threatened by multiple stressors, including increasing grazing by sea urchins. With coastal upwelling predicted to increase in intensity and duration in the future, understanding whether kelp forest and urchin barren urchins are differentially affected by upwelling-related stressors will give insight into how future conditions may affect the transition between kelp forests and barrens. We assessed how current and future-predicted changes in the duration and magnitude of upwelling-associated stressors (low pH, dissolved oxygen, and temperature) affected the performance of purple sea urchins (Strongylocentrotus purpuratus) sourced from rapidly-declining bull kelp (Nereocystis leutkeana) forests and nearby barrens and maintained on habitat-specific diets. Kelp forest urchins were of superior condition to barrens urchins, with ~ 6–9 times more gonad per body mass. Grazing and condition in kelp forest urchins were more negatively affected by distant-future and extreme upwelling conditions, whereas grazing and survival in urchins from barrens were sensitive to both current-day and all future-predicted upwelling, and to increases in acidity, hypoxia, and temperature regardless of upwelling. We conclude that urchin barren urchins are more susceptible to increases in the magnitude and duration of upwelling-related stressors than kelp forest urchins. These findings have important implications for urchin population dynamics and their interaction with kelp.

The zombification and reanimation of purple urchins (Strongylocentrotus purpuratus) in response to food availability

To survive periods of starvation, organisms can reduce their metabolism and/or decrease energy allocation to reproduction. This is especially important for coastal rocky reefs where widespread kelp deforestation has become increasingly common in recent decades. This deforestation often results in the formation of urchin barrens that have high densities of herbivorous sea urchins and little macroalgae for them to consume. While it is clear that these barrens can persist for years to decades, it is unclear how the urchins within them survive such prolonged periods without regular access to macroalgae. Here, we show that urchin metabolism and gonad mass both decrease significantly when the urchins are starved, and that these urchins regain normal metabolic activity and gonad masses when access to food is restored. However, if urchins occur in barren areas that receive drift algae from nearby kelp forests, it appears they can maintain normal metabolic activity and gonad mass. Together, our results provide experimental evidence that reducing metabolism may be a primary strategy for avoiding starvation in urchins occurring within barrens. Our results can be especially important to researchers looking to restore kelp forests and to urchin fishers who seek to harvest these urchins for their gonads but currently cannot because their gonads are of poor quality. Additionally, this has important implications for consumers in other ecosystems where access to energetic resources is spatially or temporally variable and can point to new avenues of research to explain how organisms adjust their energetic needs to survive extended periods of starvation.