The characterization of toll-like receptor repertoire in Pinna nobilis after mass mortality events suggests adaptive introgression

The fan mussel Pinna nobilis is currently on the brink of extinction due to a multifactorial disease mainly caused to the highly pathogenic parasite Haplosporidium pinnae, meaning that the selection pressure outweighs the adaptive potential of the species. Hopefully, rare individuals have been observed somehow resistant to the parasite, stretching the need to identify the traits underlying this better fitness. Among the candidate to explore at first intention are fast-evolving immune genes, of which toll-like receptor (TLR). In this study, we examined the genetic diversity at 14 TLR loci across P. nobilis, Pinna rudis and P. nobilis × P. rudis hybrid genomes, collected at four physically distant regions, that were found to be either resistant or sensitive to the parasite H. pinnae. We report a high genetic diversity, mainly observed at cell surface TLRs compared with that of endosomal TLRs. However, the endosomal TLR-7 exhibited unexpected level of diversity and haplotype phylogeny. The lack of population structure, associated with a high genetic diversity and elevated dN/dS ratio, was interpreted as balancing selection, though both directional and purifying selection were detected. Interestingly, roughly 40% of the P. nobilis identified as resistant to H. pinnae were introgressed with P. rudis TLR. Specifically, they all carried a TLR-7 of P. rudis origin, whereas sensitive P. nobilis were not introgressed, at least at TLR loci. Small contributions of TLR-6 and TLR-4 single-nucleotide polymorphisms to the clustering of resistant and susceptible individuals could be detected, but their specific role in resistance remains highly speculative. This study provides new information on the diversity of TLR genes within the P. nobilis species after MME and additional insights into adaptation to H. pinnae that should contribute to the conservation of this Mediterranean endemic species.

RNA-Seq comparative study reveals molecular effectors linked to the resistance of Pinna nobilis to Haplosporidium pinnae parasite

With the intensification of maritime traffic, recently emerged infectious diseases have become major drivers in the decline and extinction of species. Since 2016, mass mortality events have decimated the endemic Mediterranean Sea bivalve Pinna nobilis, affecting ca. 100% of individuals. These events have largely been driven by Haplosporidium pinnae's infection, an invasive species which was likely introduced by shipping. While monitoring wild populations of P. nobilis, we observed individuals that survived such a mass mortality event during the summer of 2018 (France). We considered these individuals resistant, as they did not show any symptoms of the disease, while the rest of the population in the area was devastated. Furthermore, the parasite was not detected when we conducted a PCR amplification of a species-specific fragment of the small subunit ribosomal DNA. In parallel, the transcriptomic analysis showed evidence of some parasite RNA indicating that the resistant individuals had been exposed to the parasite without proliferating. To understand the underlying mechanisms of resistance in these individuals, we compared their gene expression with that of susceptible individuals. We performed de novo transcriptome assembly and annotated the expressed genes. A comparison of the transcriptomes in resistant and susceptible individuals highlighted a gene expression signature of the resistant phenotype. We found significant differential expressions of genes involved in immunity and cell architecture. This data provides the first insights into how individuals escape the pathogenicity associated with infection.

Mitogenome sequence comparison in the endangered congeneric Pinna nobilis and Pinna rudis bivalves

BACKGROUND

The pen shells Pinna nobilis and Pinna rudis are large wedge-shaped bivalve molluscs. Both species are threatened by different anthropogenic pressures. In the last few years, P. nobilis populations have significantly reduced due to massive mortality events. The complete mitochondrial DNA sequences of these congeneric species have been determined and compared for the first time.

RESULTS

The mitogenome sequences of P. nobilis and P. rudis were 18,919 bp and 18,264 bp in length, respectively. Each mitogenome is composed of 12 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA (tRNAs) genes and non-coding regions. A putative Adenosine Triphosphate synthase subunit 8 gene could only be proposed for P. nobilis. Both newly sequenced mitogenomes present a conserved gene order between them, comparable to the closely related Atrina pectinata, but global arrangement greatly differs from other available bivalve mitochondrial sequences. Multiple copies of tRNA-Cys were identified, located in different positions probably due to mechanisms of mitochondrial genome rearrangements, and detected 2 and 3 times in P. rudis and in P. nobilis, respectively.

CONCLUSION

A close relationship was shown between Pinna species and Atrina pectinata and a consistent clustering showing a monophyletic origin of Pinnidae family sequences was evidenced. The mitochondrial genomes will provide a valuable genetic resource for further studies on population genetics and species identification.

When male seahorses take the female contraceptive pill

17α-ethinylestradiol (EE2), the female contraceptive pill, has been detected in mediterranean coasts where seahorse populations, Hippocampus guttulatus, live. Low environmental concentrations have the potential to disrupt growth but also endocrine metabolism, and this imbalance is all the more critical in early life stage. To investigate the impact of EE2 in reared seahorses, we exposed aged 2 months and sexually undifferentiated seahorses to an environmental concentration of 21 ng/L of EE2 for a period of 30 days. EE2 exposure led to a 19% reduction in weight, but also a mortality rate of 27%. This exposure predicted demasculinization of male individuals with a late onset of secondary sexual characteristics. EE2 exposure led to an increase of the free androgen index, but significant reductions of estradiol and testosterone in males were observed. This low estrogen concentration seemed to impact the positive feedback on luteinizing hormone (LH) with a decrease in LH production. Added to this, synthetic estrogen had a negative impact on the production and the release of follicle-stimulating hormone. Contrary to all expectations, females demonstrated a significant decrease in vitellogenin, following exposure to EE2 at 21 ng/L, while no changes were detected in males. This first study on the European long-snouted seahorses confirmed the deleterious impact of the female contraceptive pill with a real impact on growth, sexual differentiation, and maturation in young immature seahorses.

Amphiphilic hydrolyzable polydimethylsiloxane-b-poly(ethyleneglycol methacrylate-co-trialkylsilyl methacrylate) block copolymers for marine coatings. II. Antifouling laboratory tests and field trials

Poly(dimethylsiloxane) (PDMS) elastomer coatings containing an amphiphilic hydrolyzable diblock copolymer additive were prepared and their potential as marine antifouling and antiadhesion materials was tested. The block copolymer additive consisted of a PDMS first block and a random poly(trialkylsilyl methacrylate (TRSiMA, R = butyl, isopropyl)-co-poly(ethyleneglycol) methacrylate (PEGMA) copolymer second block. PDMS-b-TRSiMA block copolymer additives without PEGMA units were also used as additives. The amphiphilic character of the coating surface was assessed in water using the captive air bubble technique for measurements of static and dynamic contact angles. The attachment of macro- and microorganisms on the coatings was evaluated by field tests and by performing adhesion tests to the barnacle Amphibalanus amphitrite and the green alga Ulva rigida. All the additive-based PDMS coatings showed better antiadhesion properties to A. amphitrite larvae than to U. rigida spores. Field tests provided meaningful information on the antifouling and fouling release activity of coatings over an immersion period of 23 months.

Hydrolyzable Additive-Based Silicone Elastomers: A New Approach for Antifouling Coatings

Fouling Release Coatings are marine antifouling coatings based on silicone elastomers. Contrary to commonly used biocide-based antifouling coatings, they do not release biocides into the marine environment, however, they suffer from poor antifouling efficacy during idle periods. To improve their antifouling performances in static conditions, various amounts of hydrolyzable polymers were incorporated within a silicone matrix. These hydrolyzable polymers were chosen for the well-known hydrolytic degradation mechanism of their main chain, e.g. poly(ε-caprolactone) (PCL), or of their ester pending groups, e.g. poly(bis(trimethylsilyloxy)methylsilyl methacrylate) (PMATM2). The degradation kinetics of such hydrolyzable silicone coatings were assessed by mass loss measurements during immersion in deionized water. Coatings containing PMATM2 exhibited a maximum mass loss after 12 weeks, whereas PCL-based coatings showed no significant mass loss after 24 weeks. Dynamic contact angle measurements revealed the modifications of the coatings surface chemistry with an amphiphilic behavior after water exposure. The attachment of macrofoulers on these coatings were evaluated by field tests in the Mediterranean Sea, demonstrating the short or long-term antifouling effect of these hydrolyzable polymers embedded in the silicone matrix. The settlement of A. amphitrite barnacles on the different coatings indicated inhospitable behaviors towards larval barnacles for coatings with at least 15 wt % of additives.

Effect of a glyphosate-based herbicide on gene expressions of the cytokines interleukin-1β and interleukin-10 and of heme oxygenase-1 in European sea bass, Dicentrarchus labrax L

Glyphosate-based herbicides are the most frequently used herbicides in the world. We evaluated the effect of Roundup 360 SL on the expression of interleukin-1β (il-1β), interleukin-10 (il-10) and heme-oxygenase-1 (ho-1) in the gills, intestines and spleen of young European sea bass (Dicentrachus labrax L.), aged 8 mo. A group of fish was exposed to 647 mg/L of Roundup for 96 h. This treatment did not alter gene expression levels of il-1β and il-10 cytokine in the intestines, but significantly lowered both levels in the gills (p = 0.02 and p = 0.04 respectively). Expression levels of ho-1 were increased significantly in the three organs of fish from the treated group (the gills p = 0.04, the intestines p = 0.004 and the spleen p < 0.001). These changes may in turn negatively impact the immune system of European sea bass exposed to Roundup.

A single Sfp-type phosphopantetheinyl transferase plays a major role in the biosynthesis of PKS and NRPS derived metabolites in Streptomyces ambofaciens ATCC23877

The phosphopantetheinyl transferases (PPTases) are responsible for the activation of the carrier protein domains of the polyketide synthases (PKS), non ribosomal peptide synthases (NRPS) and fatty acid synthases (FAS). The analysis of the Streptomyces ambofaciens ATCC23877 genome has revealed the presence of four putative PPTase encoding genes. One of these genes appears to be essential and is likely involved in fatty acid biosynthesis. Two other PPTase genes, samT0172 (alpN) and samL0372, are located within a type II PKS gene cluster responsible for the kinamycin production and an hybrid NRPS-PKS cluster involved in antimycin production, respectively, and their products were shown to be specifically involved in the biosynthesis of these secondary metabolites. Surprisingly, the fourth PPTase gene, which is not located within a secondary metabolite gene cluster, appears to play a pleiotropic role. Its product is likely involved in the activation of the acyl- and peptidyl-carrier protein domains within all the other PKS and NRPS complexes encoded by S. ambofaciens. Indeed, the deletion of this gene affects the production of the spiramycin and stambomycin macrolide antibiotics and of the grey spore pigment, all three being PKS-derived metabolites, as well as the production of the nonribosomally produced compounds, the hydroxamate siderophore coelichelin and the pyrrolamide antibiotic congocidine. In addition, this PPTase seems to act in concert with the product of samL0372 to activate the ACP and/or PCP domains of the antimycin biosynthesis cluster which is also responsible for the production of volatile lactones.

Acute toxicity of a commercial glyphosate formulation on European sea bass juveniles (Dicentrarchus labrax L.): gene expressions of heme oxygenase-1 (ho-1), acetylcholinesterase (AChE) and aromatases (cyp19a and cyp19b)

Acute toxicity of Roundup, a commercial glyphosate--based herbicide, was evaluated in a teleost marine fish, the European sea bass, after 96 h of exposure. The LC50 96-h value of Roundup was 529 mg/L. Juveniles (Dicentrarchus labrax L.) were exposed to a sublethal concentration (35% of the LC50, i.e. 193 mg/L) of Roundup for 96-h. The study of heme oxygenase-1 (ho-1) gene expression was performed in four tissues (liver, gills, brain and gonads) and highlighted the disruption of antioxidant defence system. Results showed that ho-1 mRNA levels in liver and gills significantly decreased (p<0.001 and p<0.01 respectively) in fish exposed to 193 mg/L of Roundup, whereas in brain and gonads, ho-1 mRNA level was not altered. The analysis of acetylcholinesterase expression was used to evaluate the overall neurotoxicity of the herbicide and aromatase genes to assess the alteration of the endocrine system. Results showed that AChE and cyp19b gene transcriptions significantly increased (p<0.01) in brain of sea bass, whereas aromatase gene expression (cyp19a) in gonads was not significantly altered. Our results showed complex tissue-specific transcriptional responses after 96 h of exposure to a sublethal concentration. All these disruptions confirmed the deleterious effects of this glyphosate-based herbicide in a marine species.

Characterisation of a natural variant of the γ-butyrolactone signalling receptor

Background

The control of antibiotic production in Streptomyces coelicolor A3(2) involves complicated regulatory networks with multiple regulators controlling the expression of antibiotic biosynthetic pathways. One such regulatory network is that of the γ-butyrolactones, the so-called S. coelicolor butanolide (SCB) system. The γ-butyrolactones in this system serve as signalling molecules and bind to the receptor protein ScbR, releasing the repression of its target genes. The resulting expression changes affect the production of the two pigmented antibiotics Act and Red, as well as the transcription of the cpk antibiotic biosynthesis gene cluster and the synthesis of the γ-butyrolactones themselves.

Results

We identified a natural variant of ScbR in S. coelicolor (ScbR_M600) that differs from ScbR in the genome-sequenced strain M145 (ScbR_M145) by a single amino acid change, R120S. ScbR_M600 is impaired in its DNA binding ability and alters the expression of the pathway-specific regulatory genes of the red and cpk antibiotic biosynthesis gene clusters. Also, expression of the γ-butyrolactone biosynthesis gene scbA and production of the signalling molecules is slightly reduced.

Conclusions

The γ-butyrolactone receptor, ScbR, plays a key role in the SCB regulatory cascade and in determining the onset of the expression of the antibiotic regulatory genes.

Identification of genes involved in siderophore transport inStreptomyces coelicolorA3(2)

The potential iron siderophore transporter genes have been determined from the genome sequence of Streptomyces coelicolor A3(2). One of these gene clusters, cdtABC, was disrupted and characterized to determine its role in the uptake of the siderophores produced by S. coelicolor. Resistance to the siderophore-like antibiotics, salmycin and albomycin, was tested in the parent and cdtABC mutant, showing that the parent, but not the mutant, was sensitive to salmycin, while both were resistant to albomycin. Ferrioxamine competition assays against salmycin suggest that the uptake of salmycin is via a ferrioxamine transport system. However, Fe-55 ferrioxamine B uptake experiments did not reveal any difference between the parent and mutant. This suggests that CdtABC specifically transports salmycin, while ferrioxamine uptake maybe substituted by another transport system.

Differential and cross-transcriptional control of duplicated genes encoding alternative sigma factors in Streptomyces ambofaciens

The duplicated hasR and hasL genes of Streptomyces ambofaciens encode alternative sigma factors (named sigma(B(R)) and sigma(B(L))) belonging to the sigma(B) general stress response family in Bacillus subtilis. The duplication appears to be the result of a recent event that occurred specifically in S. ambofaciens. The two genes are 98% identical, and their deduced protein products exhibit 97% identity at the amino acid level. In contrast with the coding sequences, their genetic environments and their transcriptional control are strongly divergent. While hasL is monocistronic, hasR is arranged in a polycistronic unit with two upstream open reading frames, arsR and prsR, that encode putative anti-anti-sigma and anti-sigma factors, respectively. Transcription of each has gene is initiated from two promoters. In each case, one promoter was shown to be developmentally controlled and to be similar to those recognized by the B. subtilis general stress response sigma factor sigma(B). Expression from this type of promoter for each of the has genes dramatically increases during the course of growth in liquid or on solid media and following oxidative and osmotic stresses. Reverse transcription-PCR measurements indicate that hasR is 100 times more strongly expressed than hasL from the sigma(B)-like promoter. Transcription from the second promoter of each gene (located upstream of arsR in the case of the hasR locus) appears to be constitutive and weak. Quantitative transcriptional analysis in single and double has mutant strains revealed that sigma(B(R)) and sigma(B(L)) direct their own transcription as well as that of their duplicates. Only a slight sensitivity in response to oxidative conditions could be assigned to either single or double mutants, revealing the probable redundancy of the sigma factors implied in stress response in Streptomyces.