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International Journal of Molecular... Aug 2021Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell...
Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative and atypical genes were found in the genome. Multiple related transcripts of were identified in the transcriptome. Expression of was much higher than that of in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the and promotor regions and the IRE motif in mRNAs of and indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research.
Topics: Animals; Conserved Sequence; Ferritins; Iron; Metabolic Networks and Pathways; Models, Molecular; Phylogeny; Porifera; Protein Domains; Sequence Analysis, DNA; Transcriptome
PubMed: 34445356
DOI: 10.3390/ijms22168635 -
Genome Biology and Evolution Apr 2019Addressing the origin of axial-patterning machinery is essential for understanding the evolution of animal form. Historically, sponges, a lineage that branched off early...
Addressing the origin of axial-patterning machinery is essential for understanding the evolution of animal form. Historically, sponges, a lineage that branched off early in animal evolution, were thought to lack Hox and ParaHox genes, suggesting that these critical axial-patterning genes arose after sponges diverged. However, a recent study has challenged this long-held doctrine by claiming to identify ParaHox genes (Cdx family) in two calcareous sponge species, Sycon ciliatum and Leucosolenia complicata. We reanalyzed the main data sets in this paper and analyzed an additional data set that expanded the number of bilaterians represented and removed outgroup homeodomains. As in the previous study, our Neighbor-Joining analyses of the original data sets recovered a clade that included sponge and Cdx genes, whereas Bayesian analyses placed these sponge genes within the NKL subclass of homeodomains. Unlike the original study, only one of our two maximum-likelihood analyses was congruent with Cdx genes in sponges. Our analyses of our additional data set led to the sponge genes consistently being placed within the NKL subclass of homeodomains regardless of method or model. Our results show more support for these sponge genes belonging to the NKL subclass, and therefore imply that Hox and ParaHox genes arose after Porifera diverged from the rest of animals.
Topics: Animals; Homeodomain Proteins; Models, Genetic; Porifera
PubMed: 30859199
DOI: 10.1093/gbe/evz052 -
Marine Drugs Dec 2018Marine sponges are a very attractive and rich source in the production of novel bioactive compounds. The sponges exhibit a wide range of pharmacological activities. The... (Review)
Review
Marine sponges are a very attractive and rich source in the production of novel bioactive compounds. The sponges exhibit a wide range of pharmacological activities. The genus consists of various species, such as , , , and , along with a handful of undescribed species. The genus is a rich source of secondary metabolites containing diverse chemical classes, including alkaloids, ceramides, cerebrososides, and terpenes, with various valuable biological activities. This review covers the literature from January 1983 until January 2018 and provides a complete survey of all the compounds isolated from the genus and the associated microbiota, along with their corresponding biological activities, whenever applicable.
Topics: Alkaloids; Animals; Biological Products; Ceramides; Porifera; Terpenes
PubMed: 30598005
DOI: 10.3390/md17010019 -
Integrative and Comparative Biology Oct 2019The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms... (Review)
Review
The chemical ecology and chemical defenses of sponges have been investigated for decades; consequently, sponges are among the best understood marine organisms in terms of their chemical ecology, from the level of molecules to ecosystems. Thousands of natural products have been isolated and characterized from sponges, and although relatively few of these compounds have been studied for their ecological functions, some are known to serve as chemical defenses against predators, microorganisms, fouling organisms, and other competitors. Sponges are hosts to an exceptional diversity of microorganisms, with almost 40 microbial phyla found in these associations to date. Microbial community composition and abundance are highly variable across host taxa, with a continuum from diverse assemblages of many microbial taxa to those that are dominated by a single microbial group. Microbial communities expand the nutritional repertoire of their hosts by providing access to inorganic and dissolved sources of nutrients. Not only does this continuum of microorganism-sponge associations lead to divergent nutritional characteristics in sponges, these associated microorganisms and symbionts have long been suspected, and are now known, to biosynthesize some of the natural products found in sponges. Modern "omics" tools provide ways to study these sponge-microbe associations that would have been difficult even a decade ago. Metabolomics facilitate comparisons of sponge compounds produced within and among taxa, and metagenomics and metatranscriptomics provide tools to understand the biology of host-microbe associations and the biosynthesis of ecologically relevant natural products. These combinations of ecological, microbiological, metabolomic and genomics tools, and techniques provide unprecedented opportunities to advance sponge biology and chemical ecology across many marine ecosystems.
Topics: Animals; Aquatic Organisms; Genome; Host Microbial Interactions; Microbiota; Porifera; Transcriptome
PubMed: 30942859
DOI: 10.1093/icb/icz014 -
Journal of Natural Products May 2022Investigation of the marine sponge MeOH fractions using feature-based molecular networking, dereplication, and isolation led to the discovery of new... (Review)
Review
Investigation of the marine sponge MeOH fractions using feature-based molecular networking, dereplication, and isolation led to the discovery of new bromopyrrole-derived metabolites. An in-house library of bromopyrrole alkaloids previously isolated from and sp. was utilized, along with the investigation of an MS/MS fragmentation of these compounds. Our strategy led to the isolation and identification of the disparamides A-C (-), with a novel carbon skeleton. Additionally, new dispyrins B-F (-) and nagelamides H2 and H3 ( and ) and known nagelamide H (), citrinamine B (), ageliferin (), bromoageliferin (), and dibromoageliferin () were also isolated and identified by analysis of spectroscopic data. Analysis of MS/MS fragmentation data and molecular networking analysis indicated the presence of hymenidin (), oroidin (), dispacamide (), monobromodispacamide (), keramadine (), longamide B (), methyl ester of longamide B (), hanishin (), methyl ester of 3-debromolongamide B (), and 3-debromohanishin (). Antibacterial activity of ageliferin (), bromoageliferin (), and dibromoageliferin () was evaluated against susceptible and multi-drug-resistant ESKAPE pathogenic bacteria , , , , , and . Dibromoageliferin () displayed the most potent antimicrobial activity against all tested susceptible and MDR strains. Compounds - presented no significant hemolytic activity up to 100 μM.
Topics: Agelas; Alkaloids; Animals; Anti-Bacterial Agents; Escherichia coli; Esters; Molecular Structure; Porifera; Pyrroles; Tandem Mass Spectrometry
PubMed: 35427139
DOI: 10.1021/acs.jnatprod.2c00094 -
GigaScience Oct 2017Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms....
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
Topics: Animals; Microbiota; Porifera; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29020741
DOI: 10.1093/gigascience/gix077 -
Microbiome Mar 2018The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now... (Review)
Review
The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.
Topics: Animals; Aquatic Organisms; Bacteria; Carbon; Climate Change; Dysbiosis; Ecosystem; Microbiota; Nitrogen; Oceans and Seas; Phosphorus; Porifera; Symbiosis
PubMed: 29523192
DOI: 10.1186/s40168-018-0428-1 -
Molecules (Basel, Switzerland) Jan 2017: This extensive review covers research published between 2010 and 2012 regarding new compounds derived from marine sponges, including 62 species from 60 genera... (Review)
Review
: This extensive review covers research published between 2010 and 2012 regarding new compounds derived from marine sponges, including 62 species from 60 genera belonging to 33 families and 13 orders of the Demospongia class (Porifera). The emphasis is on the cytotoxic activity that bioactive metabolites from sponges may have on cancer cell lines. At least 197 novel chemical structures from 337 compounds isolated have been found to support this work. Details on the source and taxonomy of the sponges, their geographical occurrence, and a range of chemical structures are presented. The compounds discovered from the reviewed marine sponges fall into mainly four chemical classes: terpenoids (41.9%), alkaloids (26.2%), macrolides (8.9%) and peptides (6.3%) which, along with polyketides, sterols, and others show a range of biological activities. The key sponge orders studied in the reviewed research were Dictyoceratida, Haplosclerida, Tetractinellida, Poecilosclerida, and Agelasida. , (Haplosclerida), (Tetractinellida), and (Dictyioceratida), were found to be the most promising genera because of their capacity for producing new bioactive compounds. Several of the new compounds and their synthetic analogues have shown in vitro cytotoxic and pro-apoptotic activities against various tumor/cancer cell lines, and some of them will undergo further in vivo evaluation.
Topics: Animals; Aquatic Organisms; Biological Products; Cell Line, Tumor; Cell Survival; Humans; Porifera
PubMed: 28134844
DOI: 10.3390/molecules22020208 -
Molecules (Basel, Switzerland) Jan 2021Glycan-to-glycan binding was shown by biochemical and biophysical measurements to mediate xenogeneic self-recognition and adhesion in sponges, stage-specific cell... (Review)
Review
Glycan-to-glycan binding was shown by biochemical and biophysical measurements to mediate xenogeneic self-recognition and adhesion in sponges, stage-specific cell compaction in mice embryos, and in vitro tumor cell adhesion in mammals. This intermolecular recognition process is accepted as the new paradigm accompanying high-affinity and low valent protein-to-protein and protein-to-glycan binding in cellular interactions. Glycan structures in sponges have novel species-specific sequences. Their common features are the large size >100 kD, polyvalency >100 repeats of the specific self-binding oligosaccharide, the presence of fucose, and sulfated and/or pyruvylated hexoses. These structural and functional properties, different from glycosaminoglycans, inspired their classification under the glyconectin name. The molecular mechanism underlying homophilic glyconectin-to-glyconectin binding relies on highly polyvalent, strong, and structure-specific interactions of small oligosaccharide motifs, possessing ultra-weak self-binding strength and affinity. Glyconectin localization at the glycocalyx outermost cell surface layer suggests their role in the initial recognition and adhesion event during the complex and multistep process. In mammals, Le-to-Le homophilic binding is structure-specific and has ultra-weak affinity. Cell adhesion is achieved through highly polyvalent interactions, enabled by clustering of small low valent structure in plasma membranes.
Topics: Animals; Binding Sites; Cell Adhesion; Particle Size; Polymers; Polysaccharides; Porifera
PubMed: 33451117
DOI: 10.3390/molecules26020397 -
MBio Dec 2022Chemists have studied marine animals for the better part of a century because they contain a diverse array of bioactive compounds. Tens of thousands of compounds have...
Chemists have studied marine animals for the better part of a century because they contain a diverse array of bioactive compounds. Tens of thousands of compounds have been reported, many with elaborate structural motifs and biological mechanisms of action found nowhere else. The challenge holding back the field has long been that of supply. Compounds are sometimes obtained by cultivating marine animals or by wild harvest, but this often presents logistical and environmental challenges. Some of the most medically important marine animal compounds are supplied by synthesis, often through multistep procedures that delay drug development. A relatively small number of such agents have been approved by the U.S. Food and Drug Administration, often after a heroic effort. In a recent paper, Uppal and coworkers (https://doi.org/10.1128/mBio.01524-22) address key hurdles underlying the supply issue, discovering an uncultivated new bacterial genus from a marine sponge and reconstituting the biosynthetic pathway for expression.
Topics: Animals; Porifera; Bacteria; Drug Development; Drug Discovery; Biological Products
PubMed: 36314838
DOI: 10.1128/mbio.02499-22