Immune-related genes in gastropods and bivalves: a comparative overview

The biological diversity of molluscs and their adaptation to highly diverse environments offer a unique opportunity for studying the evolution of the innate immune system in invertebrates. This review provides an updated account about the progresses made over the past few years in the study of the molecular players involved in the recognition of pathogen associated molecular patters (PAMPs), in the transduction of immune signaling and in the elimination of potentially pathogenic microbes in gastropod and bivalve molluscs. A major focus will be put on the differences and peculiarities of the molecular immune system of the two major molluscan classes, which have developed specific adaptations to cope with diverse living environments, pathogenic and non-pathogenic microbes over the course of several hundred million years of independent evolution. Intriguing but still poorly understood aspects, such as antiviral response and immune priming, will be also explored, highlighting the present challenges and opportunities connected to the application of modern genomics techniques to the study of the immune system in these fascinating metazoans

An updated molecular basis for mussel immunity

Non-self recognition with the consequent tolerance or immune reaction is a crucial process to succeed as living organisms. At the same time the interactions between host species and their microbiome, including potential pathogens and parasites, significantly contribute to animal life diversity. Marine filter-feeding bivalves, mussels in particular, can survive also in heavily anthropized coastal waters despite being constantly surrounded by microorganisms. Based on the first outline of the Mytilus galloprovincialis immunome dated 2011, the continuously growing transcript data and the recent release of a draft mussel genome, we explored the available sequence data and scientific literature to reinforce our knowledge on the main gene-encoded elements of the mussel immune responses, from the pathogen recognition to its clearance. We carefully investigated molecules specialized in the sensing and targeting of potential aggressors, expected to show greater molecular diversification, and outlined, whenever relevant, the interconnected cascades of the intracellular signal transduction. Aiming to explore the diversity of extracellular, membrane-bound and intracellular pattern recognition receptors in mussel, we updated a highly complex immune system, comprising molecules which are described here in detail for the first time (e.g. NOD-like receptors) or which had only been partially characterized in bivalves (e.g. RIG-like receptors). Overall, our comparative sequence analysis supported the identification of over 70 novel full-length immunity-related transcripts in M. galloprovincialis. Nevertheless, the multiplicity of gene functions relevant to immunity, the involvement of part of them in other vital processes, and also the lack of a refined mussel genome make this work still not-exhaustive and support the development of more specific studies

The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family

Argonaute (AGO) family proteins play many roles in epigenetic programming, genome rearrangement, mRNA breakdown, inhibition of translation, and transposon silencing. Despite being a hotspot in current scientific research, their evolutionary history is still poorly understood and consequently the identification of evolutionary conserved structural features should also generate useful information for better understanding their functions. We report here for the first time the transcript sets of the two subfamilies, Ago and Piwi, in the West African lungfish Protopterus annectens and in the Indonesian coelacanth Latimeria menadoensis, two key species in the evolutionary lineage leading to tetrapods. The phylogenetic analysis of 142 inferred protein sequences in 22 fully sequenced species and the analysis of microsynteny performed in the major vertebrate lineages indicate an intricate pattern for the evolution of both subfamilies that has been shaped by whole genome duplications and lineage specific gains and losses. The argonaute subfamily was additionally expanded by local gene duplications at the base of the jawed vertebrate lineage. The subfamily of Piwi proteins is involved in several processes such as spermatogenesis, piRNA biogenesis, and transposon repression. Expression assessment of AGO genes and genes coding for proteins involved in small RNA biogenesis suggests a limited activity of the Piwi pathway in lungfish in agreement with the lungfish genome containing mainly old and inactive transposons

IL-17 signaling components in bivalves: Comparative sequence analysis and involvement in the immune responses

The recent discovery of soluble immune-regulatory molecules in invertebrates takes advantage of the rapid growth of next generation sequencing datasets. Following protein domain searches in the transcriptomes of 31 bivalve spp. and in few available mollusk genomes, we retrieved 59 domains uniquely identifying interleukin 17 (IL-17) and 96 SEFIR domains typical of IL-17 receptors and CIKS/ACT1 proteins acting downstream in the IL-17 signaling pathway. Compared to the Chordata IL-17 family members, we confirm a separate clustering of the bivalve domain sequences and a consistent conservation pattern of amino acid residues. Analysis performed at transcript and genome level allowed us to propose an updated view of the components outlining the IL-17 signaling pathway in Mytilus galloprovincialis and Crassostrea gigas (in both species, homology modeling reduced the variety of IL-17 domains to only two 3D structures). Digital expression analysis indicated more heterogeneous expression levels for the mussel and oyster IL-17 ligands than for IL-17 receptors and CIKS/CIKSL proteins. Besides, new qPCR analyses confirmed such gene expression trends in hemocytes and gills of mussels challenged with heat-killed bacteria. These results uphold the involvement of an ancient IL-17 signaling pathway in the bivalve immune responses and, likewise in humans, suggest the possibility of distinctive modulatory roles of individual IL-17s/IL-17 receptors. Overall, the common evidence of pro-inflammatory cytokines and inter-related intracellular signaling pathways in bivalves definitely adds complexity to the invertebrate immunity

First Insights into the Repertoire of Secretory Lectins in Rotifers

Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties

Mytilus galloprovincialis carbonic anhydrase II: Activity and cDNA sequence analysis

The esterase activity of carbonic anhydrase (CA) was investigated in mussels sampled at 24 locations along the Croatian coast of Adriatic Sea. The gills were the target tissue because the respiratory, ionic transport and pH regulatory enzyme function of CA and its potential usage as biomarkers of environmental pollution was the main topic. Total esterase activity was measured in cytosolic fraction by colorimetric end-point reaction using p-nitrophenyl acetate as enzyme substrate. CA activity was estimated by the same enzymatic reaction using acetazolamide as a specific CA inhibitor. The results of total esterase activities in winter (March; all sites average value 0.137\ub10.057) were lower than determined for summer season (August; 0.153\ub10.036) at almost all investigated locations. CA activities determined in gills of mussel sampled in winter ranged from 1.75% to 24.65% of total esterase activities and in summer samples were lower (0.83 to 13.45%). Although recent research showed potential application of CA activity in bioassay and biomarker in pollution studies, further research is needed. Here we report a short-term simple colorimetric microplate method which can be applied for analyses of large numbers of samples. Furthermore in this study we characterized full length coding sequence (cDNA) of M. galloprovincialis carbonic anhydrase II (CAII). The CAII cDNA (with the 5\u2019 and 3\u2019 untranslated regions) is 1317 bp long. The putative open reading frame encodes a polypeptide of 256 amino acids, with a theoretical pI/Mw 5.87/28.416 kDa and conserved domains (active site and zinc binding site)

RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum

Background The Mediterranean mussel Mytilus galloprovincialis is marine bivalve with a relevant commercial importance as well as a key sentinel organism for the biomonitoring of environmental pollution. Here we report the RNA sequencing of the mussel digestive gland, performed with the aim: a) to produce a high quality de novo transcriptome assembly, thus improving the genetic and molecular knowledge of this organism b) to provide an initial assessment of the response to paralytic shellfish poisoning (PSP) on a molecular level, in order to identify possible molecular markers of toxin accumulation. Results The comprehensive de novo assembly and annotation of the transcriptome yielded a collection of 12,079 non-redundant consensus sequences with an average length of 958 bp, with a high percentage of full-length transcripts. The whole-transcriptome gene expression study indicated that the accumulation of paralytic toxins produced by the dinoflagellate Alexandrium minutum over a time span of 5 days scarcely affected gene expression, but the results need further validation with a greater number of biological samples and naturally contaminated specimens. Conclusion The digestive gland reference transcriptome we produced significantly improves the data collected from previous sequencing efforts and provides a basic resource for expanding functional genomics investigations in M. galloprovincialis. Although not conclusive, the results of the RNA-seq gene expression analysis support the classification of mussels as bivalves refractory to paralytic shellfish poisoning and point out that the identification molecular biomarkers of PSP in the digestive gland of this organism is problematic

Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage

Although the major SARS-CoV-2 omicron lineages share over 30 non-synonymous substitutions in the spike glycoprotein, they show several unique mutations that were acquired after their ancestral split. One of the most intriguing mutations associated with BA.1 is the presence of the inserted tripeptide Glu-Pro-Glu within the N-terminal domain, at a site that had previously independently acquired short insertions in several other SARS-CoV-2 lineages. Although the functional implications of the small nucleotide sequences found at this insertion hotspot, named RIR1, are still unclear, we have previously hypothesized that they may play a compensatory role in counterbalancing minor fitness deficits associated with other co-occurring spike non-synonymous mutations. Here, we show that similar insertion events have independently occurred at RIR1 at least 20 times in early 2022 within the BA.2 lineage, being occasionally associated with significant community transmission. One of these omicron sublineages, characterized by a Ser-Gly-Arg insertion in position 212, has been responsible for over 4000 documented COVID-19 cases worldwide between January and July 2022, for the most part concentrated in Denmark, where it reached a national prevalence close to 4% (10% in the Nordjylland region) in mid-May. Although the concurrent spread of the BA.2.12.1, BA.4 and BA.5 lineages led to the rapid decline of this BA.2 sublineage, the independent acquisition of several other RIR1 insertions on a BA.2 genomic background suggests that these events may provide a slight fitness advantage. Therefore, they should be carefully monitored in the upcoming months in other emerging omicron-related lineages, including BA.5

Un approccio trascrittomico per delineare i meccanismi molecolari alla base della risposta del mitilo Mytilus galloprovincialis a patogeni e alla contaminazione da biotossine algali

2010/2011L’avvento delle tecniche di sequenziamento di nuova generazione ha reso recentemente disponibile l’opportunità di analizzare su scala genomica e trascrittomica organismi non modello, anche nel caso in cui virtualmente non sia disponibile alcuna informazione pregressa. Il mitilo mediterraneo Mytilus galloprovincialis è un organismo di grande importanza economica ed è considerato un utile bioindicatore, ma nonostante ciò fino a questo momento gli studi molecolari sono stati fortemente limitati proprio dalla limitata conoscenza genomica di questo importante bivalve. In questa tesi sono state utilizzate tecniche di sequenziamento di nuova generazione per analizzare la risposta del mitilo a biotossine algali paralitiche (PSP) su scala trascrittomica a livello della ghiandola digestiva. L’enorme mole di dati di sequenza ottenuti ha permesso di studiare in modo approfondito alcune famiglie di geni di grande importanza nella risposta immune del mitilo. In particolare sono state individuate e descritte l’ampia famiglia di lectine C1q-like, coinvolte nel riconoscimento dei patogeni, e due nuove famiglie di peptidi antimicrobici, le big defensine e le mitimacine.XXIV Ciclo198

Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves

C1q-domain-containing (C1qDC) proteins are rapidly emerging as key players in the innate immune response of bivalve mollusks. Growing experimental evidence suggests that these highly abundant secretory proteins are involved in the recognition of microbe-associated molecular patterns, serving as lectin-like molecules in the bivalve proto-complement system. While a large amount of functional data concerning the binding specificity of the globular head C1q domain and on the regulation of these molecules in response to infection are quickly accumulating, the genetic mechanisms that have led to the extraordinary lineage-specific expansion of the C1qDC gene family in bivalves are still largely unknown. The analysis of the chromosome-scale genome assembly of the Eastern oyster Crassostrea virginica revealed that the 476 oyster C1qDC genes, far from being uniformly distributed along the genome, are located in large clusters of tandemly duplicated paralogs, mostly found on chromosomes 7 and 8. Our observations point out that the evolutionary process behind the development of a large arsenal of C1qDC lectin-like molecules in marine bivalves is still ongoing and likely based on an unequal crossing over