Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts.

Most autotrophic organisms possess a single carbon fixation pathway. The chemoautotrophic symbionts of the hydrothermal vent tubeworm Riftia pachyptila, however, possess two functional pathways: the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. How these two pathways are coordinated is unknown. Here we measured net carbon fixation rates, transcriptional/metabolic responses and transcriptional co-expression patterns of Riftia pachyptila endosymbionts by incubating tubeworms collected from the East Pacific Rise at environmental pressures, temperature and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes; the rTCA is allied to hydrogenases and dissimilatory nitrate reduction, whereas the CBB is allied to sulfide oxidation and assimilatory nitrate reduction, suggesting distinctive yet complementary roles in metabolic function. Furthermore, our network analysis implicates the rTCA and a group 1e hydrogenase as key players in the physiological response to limitation of sulfide and oxygen. Net carbon fixation rates were also exemplary, and accordingly, we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.

Combined effects of organic and mineral UV-filters on the lugworm Arenicola marina.

Pollution from personal care products, such as UV-filters like avobenzone and nano-zinc oxide (nZnO), poses a growing threat to marine ecosystems. To better understand this hazard, especially for lesser-studied sediment-dwelling marine organisms, we investigated the physiological impacts of simultaneous exposure to nZnO and avobenzone on the lugworm Arenicola marina. Lugworms were exposed to nZnO, avobenzone, or their combination for three weeks. We assessed pollutant-induced metabolic changes by measuring key metabolic intermediates in the body wall and coelomic fluid, and oxidative stress by analyzing antioxidant levels and oxidative lesions in proteins and lipids of the body wall. Exposure to UV filters resulted in shifts in the concentrations of Krebs' cycle and urea cycle intermediates, as well as alterations in certain amino acids in the body wall and coelomic fluid of the lugworms. Pathway enrichment analyses revealed that nZnO induced more pronounced metabolic shifts compared to avobenzone or their combination. Exposure to avobenzone or nZnO alone prompted an increase in tissue antioxidant capacity, indicating a compensatory response to restore redox balance, which effectively prevented oxidative damage to proteins or lipids. However, co-exposure to nZnO and avobenzone suppressed superoxide dismutase and lead to accumulation of lipid peroxides and methionine sulfoxide, indicating oxidative stress and damage to lipids and proteins. Our findings highlight oxidative stress as a significant mechanism of toxicity for both nZnO and avobenzone, especially when combined, and underscores the importance of further investigating the fitness implications of oxidative stress induced by these common UV filters in benthic marine organisms.

Metal bioaccumulation and effects of olivine sand exposure on benthic marine invertebrates.

Due to the anthropogenic increase of atmospheric CO2 emissions, humanity is facing the negative effects of rapid global climate change. Both active emission reduction and carbon dioxide removal (CDR) technologies are needed to meet the Paris Agreement and limit global warming to 1.5 °C by 2050. One promising CDR approach is coastal enhanced weathering (CEW), which involves the placement of sand composed of (ultra)mafic minerals like olivine in coastal zones. Although the large-scale placement of olivine sand could beneficially impact the planet through the consumption of atmospheric CO2 and reduction in ocean acidification, it may also have physical and geochemical impacts on benthic communities. The dissolution of olivine can release dissolved constituents such as trace metals that may affect marine organisms. Here we tested acute and chronic responses of marine invertebrates to olivine sand exposure, as well as examined metal accumulation in invertebrate tissue resulting from olivine dissolution. Two different ecotoxicological experiments were performed on a range of benthic marine invertebrates (amphipod, polychaete, bivalve). The first experiment included acute and chronic survival and growth tests (10 and 20 days, respectively) of olivine exposure while the second had longer (28 day) exposures to measure chronic survival and bioaccumulation of trace metals (e.g. Ni, Cr, Co) released during olivine sand dissolution. Across all fauna we observed no negative effects on acute survival or chronic growth resulting solely from olivine exposure. However, over 28 days of exposure, the bent-nosed clam Macoma nasuta experienced reduced burrowing and accumulated 4.2 ± 0.7 µg g ww-1 of Ni while the polychaete Alitta virens accumulated 3.5 ± 0.9 µg g ww-1 of Ni. No significant accumulation of any other metals was observed. Future work should include longer-term laboratory studies as well as CEW field studies to validate these findings under real-world scenarios.

Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes.

Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.

Exposure to hull cleaning wastewater induces mortality through oxidative stress and cholinergic disturbance in the marine polychaete Perinereis aibuhitensis.

While wastewater and paint particles discharged from the in-water cleaning process of ship hulls are consistently released into benthic ecosystems, their hazardous effects on non-target animals remain largely unclear. In this study, we provide evidence on acute harmful effects of hull cleaning wastewater in marine polychaete Perinereis aibuhitensis by analyzing physiological and biochemical parameters such as survival, burrowing activity, and oxidative status. Raw wastewater samples were collected during ship hull cleaning processes in the field. Two wastewater samples for the exposure experiment were prepared in the laboratory: 1) mechanically filtered in the in-water cleaning system (MF) and 2) additionally filtered with a 0.45 µm filter in the laboratory (LF). These wastewater samples contained high concentrations of metals (zinc and copper) and metal-based booster biocides (copper pyrithione and zinc pyrithione) compared to those analyzed in seawater. Polycheates were exposed to different concentrations of the two wastewater samples for 96 h. Higher mortality was observed in response to MF compared to LF-exposed polychaetes. Both wastewater samples dose-dependently decreased burrowing activity and AChE activity. Drastic oxidative stress was observed in response to the two wastewater samples. MDA levels were significantly increased by MF and LF samples. Significant GSH depletion was observed with MF exposure, while increased and decreased GSH contents were observed in LF-exposed polychaetes. Enzymatic activities of antioxidant components, catalase, superoxide dismutase, and glutathione S-transferase were significantly modulated by both wastewater samples. These results indicate that even filtered hull cleaning wastewater can have deleterious effects on the health status of polychaetes.

Purification and Properties of a Plasmin-like Marine Protease from Clamworm (Perinereis aibuhitensis).

Marine organisms are a rich source of enzymes that exhibit excellent biological activity and a wide range of applications. However, there has been limited research on the proteases found in marine mudflat organisms. Based on this background, the marine fibrinolytic enzyme FELP, which was isolated and purified from clamworm (Perinereis aibuhitensis), has exhibited excellent fibrinolytic activity. We demonstrated the FELP with a purification of 10.61-fold by precipitation with ammonium sulfate, ion-exchange chromatography, and gel-filtration chromatography. SDS-PAGE, fibrin plate method, and LC-MS/MS indicated that the molecular weight of FELP is 28.9 kDa and identified FELP as a fibrinolytic enzyme-like protease. FELP displayed the maximum fibrinolytic activity at pH 9 (407 ± 16 mm2) and 50 °C (724 ± 27 mm2) and had excellent stability at pH 7-11 (50%) or 30-60 °C (60%), respectively. The three-dimensional structure of some amino acid residues of FELP was predicted with the SWISS-MODEL. The fibrinolytic and fibrinogenolytic assays showed that the enzyme possessed direct fibrinolytic activity and indirect fibrinolysis via the activation of plasminogen; it could preferentially degrade Aα-chains of fibrinogen, followed by Bß- and γ-chains. Overall, the fibrinolytic enzyme was successfully purified from Perinereis aibuhitensis, a marine Annelida (phylum), with favorable stability that has strong fibrinolysis activity in vitro. Therefore, FELP appears to be a potent fibrinolytic enzyme with an application that deserves further investigation.

Behavioral and biochemical responses of the marine polychaete Perinereis aibuhitensis to 2-ethylhexyl-4-methoxycinnamate (EHMC) exposure.

2-ethylhexyl-4-methoxycinnamate (EHMC) is a commonly used UV filter, and is receiving increasing concerns due to its ubiquitous occurrence in a variety of environmental media and potential adverse effects. This study was aimed to assess the ecotoxicological potentials of EHMC on the marine polychaete Perinereis aibuhitensis. To this end, ragworms were exposed to 2, 20, 200 µg/L EHMC for 14 days and multiple toxicological endpoints were investigated. The results showed that EHMC significantly reduced burrowing rate, but did not affect AChE activity. Exposure to EHMC significantly elevated the activities of SOD and CAT and decreased the levels of lipid peroxidation. Besides, the induction of AKP activity indicated a stimulated immune response in the ragworms when exposed to high concentration of EHMC. Furthermore, the upregulated expression of caspase-8 suggested that EHMC might induce apoptosis in ragworms via the death receptor-mediated extrinsic pathway. Our findings highlight the potential environmental risks of EHMC to marine ecosystems.

Toxic effect of chromium on nonspecific immune, bioaccumulation, and tissue structure of Urechis unicinctus.

The contamination of toxic heavy metals in aquatic environments has garnered significant global attention due to its detrimental effects on marine organisms and human health. Hexavalent chromium is a typical environmental and occupational heavy metal pollutant, identified as carcinogenic heavy metal. This study aimed to assess the impact of different Cr (VI) concentrations (0.05-2.5 mg/L) on Urechis unicinctus (U. unicinctus) by investigating bioaccumulation, antioxidant defense system, expression of resistance-related genes, and histological issues. A clear concentration-effect relationship was observed in the bioaccumulation of Cr (VI) in muscle tissues of U. unicinctus. Moreover, exposure to Cr (VI) can alter the activities of lysozyme (LSZ), catalase (CAT), and superoxide dismutase (SOD) to enhance cellular defense mechanisms in U. unicinctus. Likewise, maintained the normal protein structure and functional stability by regulating protein folding. The heat shock cognitive protein (HSC70) gene showed an upward and then downward trend after Cr (VI) exposure. At 12 h, the HSC70 gene expression reached the maximum values of 4.75 and 4.61-fold in the 0.1 and 1.5 mg/L groups, respectively. The organism produced a large number of free radicals, and elevated level of metallothionein (MT) was used to scavenge free radicals and alleviate oxidative stress. Additionally, histopathological examination revealed disorganization in the midgut, atrophic changes in intestinal connective tissue, uneven distribution in respiratory tissues, and irregular shape with a significant reduction in epithelial cells within the gastric cavity. These findings can serve as a valuable reference for elucidating the toxicity mechanisms of heavy metals towards marine benthic organisms and enhancing water environment monitoring strategies.

A single coelomic cell type is involved in both immune and respiratory functions of the coastal bioindicator annelid: Capitella C-Channel1 from the English Channel.

The polychaete Capitella is a typical member of the 'thiobiome', and is commonly used as an eutrophication indicator species in environmental assessment studies. To deal with a sulfide-rich and poisonous surrounding, cells in close contact with the environment, and thus able to play a major role in detoxication and survival, are circulating cells. This work aimed to morpho-functionally describe the circulating coelomic cells of Capitella from the English Channel inhabiting the sulfide-rich mud in Roscoff Harbor. In general, worms have three types of circulating cells, granulocytes involved in bacterial clearance and defense against microorganisms, eleocytes with an essentially trophic role and elimination of cellular waste, and erythrocytes which play a role in detoxification and respiration via their intracellular hemoglobin. By combining diverse microscopic and cellular approaches, we provide evidence that Capitella does not possess granulocytes and eleocytes, but rather a single abundant rounded cell type with the morphological characteristics of erythrocytes i.e. small size and production of intracellular hemoglobin. Surprisingly, our data show that in addition to their respiratory function, these red cells could exert phagocytic activities, and produce an antimicrobial peptide. This latter immune role is usually supported by granulocytes. Our data highlight that the erythrocytes of Capitella from the English Channel differ in morphology and bear more functions than the erythrocytes of other annelids. The simplicity of this multi-task (or polyvalent) single-cell type makes Capitella an interesting model for studies of the impact of the environment on the immunity of this bioindicator species.

Third-Generation Sequencing Reveals the Adaptive Role of the Epigenome in Three Deep-Sea Polychaetes.

The roles of DNA methylation in invertebrates are poorly characterized, and critical data are missing for the phylum Annelida. We fill this knowledge gap by conducting the first genome-wide survey of DNA methylation in the deep-sea polychaetes dominant in deep-sea vents and seeps: Paraescarpia echinospica, Ridgeia piscesae, and Paralvinella palmiformis. DNA methylation calls were inferred from Oxford Nanopore sequencing after assembling high-quality genomes of these animals. The genomes of these worms encode all the key enzymes of the DNA methylation metabolism and possess a mosaic methylome similar to that of other invertebrates. Transcriptomic data of these polychaetes support the hypotheses that gene body methylation strengthens the expression of housekeeping genes and that promoter methylation acts as a silencing mechanism but not the hypothesis that DNA methylation suppresses the activity of transposable elements. The conserved epigenetic profiles of genes responsible for maintaining homeostasis under extreme hydrostatic pressure suggest DNA methylation plays an important adaptive role in these worms.

Hot and heavy: Responses of ragworms (Hediste diversicolor) to copper-spiked sediments and elevated temperature.

Sediment contamination and seawater warming are two major stressors to macrobenthos in estuaries. However, little is known about their combined effects on infaunal organisms. Here we investigated the responses of an estuarine polychaete Hediste diversicolor to metal-contaminated sediment and increased temperature. Ragworms were exposed to sediments spiked with 10 and 20 mg kg-1 of copper at 12 and 20 °C for three weeks. No considerable changes were observed in the expression of genes related to copper homeostasis and in the accumulation of oxidative stress damage. Dicarbonyl stress was attenuated by warming exposure. Whole-body energy reserves in the form of carbohydrates, lipids and proteins were little affected, but the energy consumption rate increased with copper exposure and elevated temperature, indicating higher basal maintenance costs of ragworms. The combined effects of copper and warming exposures were mostly additive, with copper being a weak stressor and warming a more potent stressor. These results were replicable, as confirmed by two independent experiments of similar settings conducted at two different months of the year. This study suggests the higher sensitivity of energy-related biomarkers and the need to search for more conserved molecular markers of metal exposure in H. diversicolor.

Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms.

Bacterial symbioses allow annelids to colonise extreme ecological niches, such as hydrothermal vents and whale falls. Yet, the genetic principles sustaining these symbioses remain unclear. Here, we show that different genomic adaptations underpin the symbioses of phylogenetically related annelids with distinct nutritional strategies. Genome compaction and extensive gene losses distinguish the heterotrophic symbiosis of the bone-eating worm Osedax frankpressi from the chemoautotrophic symbiosis of deep-sea Vestimentifera. Osedax's endosymbionts complement many of the host's metabolic deficiencies, including the loss of pathways to recycle nitrogen and synthesise some amino acids. Osedax's endosymbionts possess the glyoxylate cycle, which could allow more efficient catabolism of bone-derived nutrients and the production of carbohydrates from fatty acids. Unlike in most Vestimentifera, innate immunity genes are reduced in O. frankpressi, which, however, has an expansion of matrix metalloproteases to digest collagen. Our study supports that distinct nutritional interactions influence host genome evolution differently in highly specialised symbioses.

Biochemical and Behavioural Alterations Induced by Arsenic and Temperature in Hediste diversicolor of Different Growth Stages.

Contamination with Arsenic, a toxic metalloid, is increasing in the marine environment. Additionally, global warming can alter metalloids toxicity. Polychaetes are key species in marine environments. By mobilizing sediments, they play vital roles in nutrient and element (including contaminants) cycles. Most studies with marine invertebrates focus on the effects of metalloids on either adults or larvae. Here, we bring information on the effects of temperature increase and arsenic contamination on the polychaete Hediste diversicolor in different growth stages and water temperatures. Feeding activity and biochemical responses-cholinesterase activity, indicators of cell damage, antioxidant and biotransformation enzymes and metabolic capacity-were evaluated. Temperature rise combined with As imposed alterations on feeding activity and biochemical endpoints at different growth stages. Small organisms have their antioxidant enzymes increased, avoiding lipid damage. However, larger organisms are the most affected class due to the inhibition of superoxide dismutase, which results in protein damage. Oxidative damage was observed on smaller and larger organisms exposed to As and temperature of 21 °C, demonstrating higher sensibility to the combination of temperature rise and As. The observed alterations may have ecological consequences, affecting the cycle of nutrients, sediment oxygenation and the food chain that depends on the bioturbation of this polychaete.

Gotta Go Slow: Two Evolutionarily Distinct Annelids Retain a Common Hedgehog Pathway Composition, Outlining Its Pan-Bilaterian Core.

Hedgehog signaling is one of the key regulators of morphogenesis, cell differentiation, and regeneration. While the Hh pathway is present in all bilaterians, it has mainly been studied in model animals such as Drosophila and vertebrates. Despite the conservatism of its core components, mechanisms of signal transduction and additional components vary in Ecdysozoa and Deuterostomia. Vertebrates have multiple copies of the pathway members, which complicates signaling implementation, whereas model ecdysozoans appear to have lost some components due to fast evolution rates. To shed light on the ancestral state of Hh signaling, models from the third clade, Spiralia, are needed. In our research, we analyzed the transcriptomes of two spiralian animals, errantial annelid Platynereis dumerilii (Nereididae) and sedentarian annelid Pygospio elegans (Spionidae). We found that both annelids express almost all Hh pathway components present in Drosophila and mouse. We performed a phylogenetic analysis of the core pathway components and built multiple sequence alignments of the additional key members. Our results imply that the Hh pathway compositions of both annelids share more similarities with vertebrates than with the fruit fly. Possessing an almost complete set of single-copy Hh pathway members, lophotrochozoan signaling composition may reflect the ancestral features of all three bilaterian branches.

Tyre particle exposure affects the health of two key estuarine invertebrates.

Tyre wear particles may be the largest source of microplastic to the natural environment, yet information on their biological impacts is inadequate. Two key estuarine invertebrates; the clam Scrobicularia plana and the ragworm Hediste diversicolor were exposed to 10% tyre particles in sediment for three days. Both species consumed the particles, although S. plana consumed 25x more than H. diversicolor (967 compared with 35 particles.g-1 wet weight, respectively). We then investigated the impact of 21 days exposure to different concentrations of tyre particles in estuarine sediments (0.2, 1, and 5% dry weight sediment) on aspects of the health of S. plana and H. diversicolor. Reductions in feeding and burial rates were observed for S. plana but not H. diversicolor, whilst both species showed a decrease in protein content in response to the greatest tyre particle concentration (5%), linked to an 18% decrease in energy reserves for H. diversicolor. Five percent tyre particle exposure led to an increase in total glutathione in the tissues of H. diversicolor, whilst lipid peroxidation decreased in the digestive glands of S. plana, possibly due to an increase in cell turnover. This study found that S. plana's health was impacted at lower concentrations than H. diversicolor, likely due to its consumption of large quantities of sediment. At the high exposure concentration (5%), the health of both invertebrates was impacted. This study did not separate the effects caused by the microplastic particles versus the effects of the chemical additives leaching from these particles, but our results do indicate that future studies should investigate effects in isolation and in combination, to determine the main drivers of toxicity.

Bioaccumulation of polycyclic aromatic hydrocarbons (PAH) in Polychaeta Marphysa sanguinea in the anthropogenically impacted Tunis Lagoon: DNA damage and immune biomarkers.

This work assessed the impact of polycyclic aromatic hydrocarbons (PAHs) on the polychaeta Marphysa sanguinea in Tunis Lagoon. Highest PAHs concentrations were accumulated at station E with maximum Σ PAH of 6028,87 ng/g DW. Changes in animal physiology were clearly related to bioaccumulated PAH. In fact, high levels of immune biomarkers (cyclooxygenase [COX] and lysozyme activity with maximum of 44631,10 FU/mn/mg protein and 0,017 lysozyme activity/mn/mg protein, respectively) were recorded at stations B and E. Triacylglycerol (TAG), the energy source, was lowest at the most polluted stations (E and B), while phospholipids (PL) were highest at the control station. Statistical analysis revealed a probable effect of both low and high molecular weight PAHs on variations in energy storage lipids (TAG and sterol and wax esters [SE/WE]) and membrane lipids, particularly PL. Our results encourage the use of M. sanguinea to assess pollution levels in coastal ecosystems.

A drug discovery approach based on comparative transcriptomics between two toxin-secreting marine annelids: Glycera alba and Hediste diversicolor.

Most animal toxins evolved to interact with specific molecular targets, which makes them highly-prized bioactives for drug development. Marine toxins, in particular, due to their wide chemical diversity, offer a new range of possibilities, a few of which have already been translated into approved drugs. Glycera alba and Hediste diversicolor are sympatric Polychaeta with distinct ecology and behavior suspected to secrete toxins that evolved to interact with distinct molecular targets, thus with differential selectivity and potential applications in drug discovery. Comparative transcriptomics revealed that while G. alba's venom apparatus is localized in the proboscis and neurotoxins are secreted to overtake prey, H. diversicolor secretes fewer and less specific toxins that are seemingly a defense. Human interactome-directed analysis unraveled novel toxins and other bioactives with potential biomedical applications, like proteins from G. alba's venom that can regulate apoptosis, whereas H. diversicolor yielded proteins that may control inflammation and cell proliferation in humans. Omics and bioinformatics appear to be powerful tools for marine bioprospecting and drug discovery, enabling molecular mining through transcriptomes of non-model organisms and link their ecology and physiology with protein's specificity and bioreactivity. Interactome-directed analysis against the human proteome seems an efficient alternative to the design of synthetic drugs.

Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola).

Sirsoe methanicola, commonly known as the methane ice worm, is the only macrofaunal species known to inhabit the Gulf of Mexico methane hydrates. Little is known about this elusive marine polychaete that can colonize rich carbon and energy reserves. Metagenomic analysis of gut contents and worm fragments predicted diverse metabolic capabilities with the ability to utilize a range of nitrogen, sulfur, and organic carbon compounds through microbial taxa affiliated with Campylobacterales, Desulfobacterales, Enterobacterales, SAR324, Alphaproteobacteria, and Mycoplasmatales. Entomoplasmatales and Chitinivibrionales were additionally identified from extracted full-length 16S rRNA sequences, and read analysis identified 196 bacterial families. Overall, the microbial community appeared dominated by uncultured Sulfurospirillum, a taxon previously considered free-living rather than host-associated. Metagenome-assembled genomes (MAGs) classified as uncultured Sulfurospirillum predicted thiosulfate disproportionation and the reduction of tetrathionate, sulfate, sulfide/polysulfide, and nitrate. Microbial amino acid and vitamin B12 biosynthesis genes were identified in multiple MAGs, suggesting nutritional value to the host. Reads assigned to aerobic or anaerobic methanotrophic taxa were rare. IMPORTANCE Methane hydrates represent vast reserves of natural gas with roles in global carbon cycling and climate change. This study provided the first analysis of metagenomes associated with Sirsoe methanicola, the only polychaete species known to colonize methane hydrates. Previously unrecognized participation of Sulfurospirillum in a gut microbiome is provided, and the role of sulfur compound redox reactions within this community is highlighted. The comparative biology of S. methanicola is of general interest given research into the adverse effects of sulfide production in human gut microbiomes. In addition, taxonomic assignments are provided for nearly 200 bacterial families, expanding our knowledge of microbiomes in the deep sea.

Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog.

The extremophile Alvinella pompejana, an annelid worm living on the edge of hydrothermal vents in the Pacific Ocean, is an excellent model system for studying factors that govern protein stability. Low intrinsic stability is a crucial factor for the susceptibility of the transcription factor p53 to inactivating mutations in human cancer. Understanding its molecular basis may facilitate the design of novel therapeutic strategies targeting mutant p53. By analyzing expressed sequence tag (EST) data, we discovered a p53 family gene in A. pompejana. Protein crystallography and biophysical studies showed that it has a p53/p63-like DNA-binding domain (DBD) that is more thermostable than all vertebrate p53 DBDs tested so far, but not as stable as that of human p63. We also identified features associated with its increased thermostability. In addition, the A. pompejana homolog shares DNA-binding properties with human p53 family DBDs, despite its evolutionary distance, consistent with a potential role in maintaining genome integrity. Through extensive structural and phylogenetic analyses, we could further trace key evolutionary events that shaped the structure, stability, and function of the p53 family DBD over time, leading to a potent but vulnerable tumor suppressor in humans.

Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura).

The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.