| a post-synaptic scaffold at the origin of the animal kingdom. | the evolution of complex sub-cellular structures such as the synapse requires the assembly of multiple proteins, each conferring added functionality to the integrated structure. tracking the early evolution of synapses has not been possible without genomic information from the earliest branching animals. as the closest extant relatives to the eumetazoa, porifera (sponges) represent a pivotal group for understanding the evolution of nervous systems, because sponges lack neurons with clearly recog ... | 2007 | 17551586 |
| demosponge and sea anemone fibrillar collagen diversity reveals the early emergence of a/c clades and the maintenance of the modular structure of type v/xi collagens from sponge to human. | collagens are often considered a metazoan hallmark, with the fibril-forming fibrillar collagens present from sponges to human. from evolutionary studies, three fibrillar collagen clades (named a, b, and c) have been defined and shown to be present in mammals, whereas the emergence of the a and b clades predates the protostome/deuterostome split. moreover, several c clade fibrillar collagen chains are present in some invertebrate deuterostome genomes but not in protostomes whose genomes have been ... | 2008 | 18697744 |
| biological characterisation of haliclona (?gellius) sp.: sponge and associated microorganisms. | we have characterised the northern pacific undescribed sponge haliclona (?gellius) sp. based on rdna of the sponge and its associated microorganisms. the sponge is closely related to amphimedon queenslandica from the great barrier reef as the near-complete 18s rdna sequences of both sponges were identical. the microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. most bacterial phyla were de ... | 2009 | 19471996 |
| evolutionary history of the hap2/gcs1 gene and sexual reproduction in metazoans. | the hap2/gcs1 gene first appeared in the common ancestor of plants, animals, and protists, and is required in the male gamete for fusion to the female gamete in the unicellular organisms chlamydomonas and plasmodium. we have identified a hap2/gcs1 gene in the genome sequence of the sponge amphimedon queenslandica. this finding provides a continuous evolutionary history of hap2/gcs1 from unicellular organisms into the metazoan lineage. divergent versions of the hap2/gcs1 gene are also present in ... | 2009 | 19888453 |
| structure and expression of conserved wnt pathway components in the demosponge amphimedon queenslandica. | wnt-signalling plays a critical role in animal development, and its misregulation results in serious human diseases, including cancer. while the wnt pathway is well studied in eumetazoan models, little is known about the evolutionary origin of its components and their functions. here, we have identified key machinery of the wnt-β-catenin (canonical)-signalling pathway that is encoded in the amphimedon queenslandica (demospongiae; porifera) genome, namely wnt, fzd, sfrp, lrp5/6, dvl, axin, apc, g ... | 2010 | 20883218 |
| diversity of mycobacterium species from marine sponges and their sensitivity to antagonism by sponge-derived rifamycin-synthesizing actinobacterium in the genus salinispora. | eleven isolates of mycobacterium species as well as an antimycobacterial salinispora arenicola strain were cultured from the sponge amphimedon queenslandica. the 16s rrna, rpob, and hsp65 genes from these mycobacterium isolates were sequenced, and phylogenetic analysis of a concatenated alignment showed the formation of a large clade with mycobacterium poriferae isolated previously from another sponge species. the separation of these mycobacterium isolates into three species-level groups was evi ... | 2010 | 20883497 |
| the homeodomain complement of the ctenophore mnemiopsis leidyi suggests that ctenophora and porifera diverged prior to the parahoxozoa. | abstract: | 2010 | 20920347 |
| origin of animal epithelia: insights from the sponge genome. | epithelial tissues are a key metazoan cell type, providing a basic structural unit for the construction of diverse animal body plans. historically, an epithelial grade of organization was considered to be restricted to the eumetazoa, with the majority of cell layers described for porifera lacking any of the conserved ultrastructural characteristics of epithelia. now with the use of genomic information from the demosponge, amphimedon queenslandica, we identify orthologs of bilaterian genes that d ... | 2010 | 21040426 |
| evolution of rna-binding proteins in animals: insights from genome-wide analysis in the sponge amphimedon queenslandica. | rna-binding proteins (rbps) are key players in various biological processes, most notably regulation of gene expression at the posttranscriptional level. although many rbps have been carefully studied in model organisms, very few studies have addressed the evolution of these proteins at the scale of the animal kingdom. we identified a large set of putative rbps encoded by the genome of the demosponge amphimedon queenslandica, a species representing a basal animal lineage. we compared the amphime ... | 2011 | 21325094 |
| genome-wide analysis of the sox family in the calcareous sponge sycon ciliatum: multiple genes with unique expression patterns. | | 2012 | 22824100 |
| the evolutionary diversification of lsf and grainyhead transcription factors preceded the radiation of basal animal lineages. | the transcription factors of the lsf/grainyhead (grh) family are characterized by the possession of a distinctive dna-binding domain that bears no clear relationship to other known dna-binding domains, with the possible exception of the p53 core domain. in triploblastic animals, the lsf and grh subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of dna binding. for example, grainyhead (grh) homologs are expressed primarily in t ... | 2010 | 20398424 |
| phylogenetic analysis of cdk and cyclin proteins in premetazoan lineages. | the molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. in this study, we conducted a comprehensive evolutionary analysis of cdk and cyclin proteins in metazoans and their unicellular relatives. | 2014 | 24433236 |
| the insect chemoreceptor superfamily is ancient in animals. | the insect chemoreceptor superfamily consists of 2 gene families, the highly diverse gustatory receptors (grs) found in all arthropods with sequenced genomes and the odorant receptors that evolved from a gr lineage and have been found only in insects to date. here, i describe relatives of the insect chemoreceptor superfamily, specifically the basal gr family, in diverse other animals, showing that the superfamily dates back at least to early animal evolution. gr-like (grl) genes are present in t ... | 2015 | 26354932 |
| genomics, phylogeny and in silico analysis of mitochondrial glutathione s-transferase-kappa from the camel camelus dromedarius. | the domesticated one-humped camel, camelus dromedarius, is one of the most important animals in the arabian peninsula. for most of its life, this species is exposed to both intrinsic and extrinsic genotoxic factors that cause gross dna alterations in many organisms. gst enzymes constitute an important supergene family involved in protection against the deleterious effects of oxidative stress and xenobiotics. cloning the camel mitochondrial gst kappa (gstk) gene and comparing its structural simil ... | 2014 | 24810173 |
| landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. | combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. by analysing histone modifications in a morphologically-simple, early branching animal, the sponge amphimedon queenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. this includes distal enhancers, repressive chromati ... | 2017 | 28395144 |
| origin and evolution of the sponge aggregation factor gene family. | although discriminating self from nonself is a cardinal animal trait, metazoan allorecognition genes do not appear to be homologous. here we characterise the aggregation factor (af) gene family, which encodes putative allorecognition factors in the demosponge amphimedon queenslandica, and trace its evolution across 24 sponge (porifera) species. the af locus in amphimedon is comprised of a cluster of five similar genes that encode calx-beta and von willebrand domains and a newly defined wreath do ... | 2017 | 28104746 |
| an ancient role for nitric oxide in regulating the animal pelagobenthic life cycle: evidence from a marine sponge. | in many marine invertebrates, larval metamorphosis is induced by environmental cues that activate sensory receptors and signalling pathways. nitric oxide (no) is a gaseous signalling molecule that regulates metamorphosis in diverse bilaterians. in most cases no inhibits or represses this process, although it functions as an activator in some species. here we demonstrate that no positively regulates metamorphosis in the poriferan amphimedon queenslandica. high rates of a. queenslandica metamorpho ... | 2016 | 27874071 |
| conservation and divergence of bhlh genes in the calcisponge sycon ciliatum. | basic helix-loop-helix (bhlh) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group b involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups c and f involved in development and maintenance of homeostasis; and metazoan-specific groups a, d and e including well-studied genes, such as atonal, twist and hairy, with diverse developmental roles including control of morphogenesis and specificati ... | 2016 | 27757221 |
| surprisingly rich repertoire of wnt genes in the demosponge halisarca dujardini. | wnt proteins are secreted signalling molecules found in all animal phyla. in bilaterian animals, including humans, wnt proteins play key roles in development, maintenance of homeostasis and regeneration. while wnt gene repertoires and roles are strongly conserved between cnidarians and bilaterians, wnt genes from basal metazoans (sponges, ctenophores, placozoans) are difficult or impossible to assign to the bilaterian + cnidarian orthologous groups. moreover, dramatic differences in wnt numbers ... | 2016 | 27287511 |
| purification and partial characterization of a lectin protein complex, the clathrilectin, from the calcareous sponge clathrina clathrus. | carbohydrate-binding proteins were purified from the marine calcareous sponge clathrina clathrus via affinity chromatography on lactose and n-acetyl glucosamine-agarose resins. proteomic analysis of acrylamide gel separated protein subunits obtained in reducing conditions pointed out several candidates for lectins. based on amino-acid sequence similarity, two peptides displayed homology with the jack bean lectin concanavalin a, including a conserved domain shared by proteins in the l-type lectin ... | 2016 | 27113336 |
| retracing the path of planar cell polarity. | the planar cell polarity pathway (pcp) has been described as the main feature involved in patterning cell orientation in bilaterian tissues. recently, a similar phenomenon was revealed in cnidarians, in which the inhibition of this pathway results in the absence of cilia orientation in larvae, consequently proving the functional conservation of pcp signaling between cnidaria and bilateria. nevertheless, despite the growing accumulation of databases concerning basal lineages of metazoans, very fe ... | 2016 | 27039172 |
| detection of prokaryotic genes in the amphimedon queenslandica genome. | horizontal gene transfer (hgt) is common between prokaryotes and phagotrophic eukaryotes. in metazoans, the scale and significance of hgt remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. marine sponges (porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. in this study, we identified a number of potential horizontally transferred genes withi ... | 2016 | 26959231 |
| the ontogeny of choanocyte chambers during metamorphosis in the demosponge amphimedon queenslandica. | the aquiferous body plan of poriferans revolves around internal chambers comprised of choanocytes, a cell type structurally similar to choanoflagellates. these choanocyte chambers perform a range of physiological and developmental functions, including the capture of food and the generation of stem cells. despite the increasing interest for choanocytes as sponge stem cells, there is limited knowledge on the development of choanocyte chambers. using a combination of cell lineage tracing, antibody ... | 2016 | 26958337 |
| bilaterian-like promoters in the highly compact amphimedon queenslandica genome. | the regulatory systems underlying animal development must have evolved prior to the emergence of eumetazoans (cnidarians and bilaterians). although representatives of earlier-branching animals - sponges ctenophores and placozoans - possess most of the developmental transcription factor families present in eumetazoans, the dna regulatory elements that these transcription factors target remain uncharted. here we characterise the core promoter sequences, u1 snrnp-binding sites (5' splice sites; 5's ... | 2016 | 26931148 |
| transcriptome changes during the life cycle of the red sponge, mycale phyllophila (porifera, demospongiae, poecilosclerida). | sponges are an ancient metazoan group with broad ecological, evolutionary, and biotechnological importance. as in other marine invertebrates with a biphasic life cycle, the developing sponge undergoes a significant morphological, physiological, and ecological transformation during settlement and metamorphosis. in this study, we compare new transcriptome datasets for three life cycle stages of the red sponge (mycale phyllophila) to test whether gene expression (as in the model poriferan, amphimed ... | 2015 | 26492274 |
| comparative analyses of developmental transcription factor repertoires in sponges reveal unexpected complexity of the earliest animals. | developmental transcription factors (dtfs) control development of animals by affecting expression of target genes, some of which are transcription factors themselves. in bilaterians and cnidarians, conserved dtfs are involved in homologous processes such as gastrulation or specification of neurons. the genome of amphimedon queenslandica, the first sponge to be sequenced, revealed that only a fraction of these conserved dtf families are present in demosponges. this finding was in line with the vi ... | 2015 | 26253310 |
| dynamic and widespread lncrna expression in a sponge and the origin of animal complexity. | long noncoding rnas (lncrnas) are important developmental regulators in bilaterian animals. a correlation has been claimed between the lncrna repertoire expansion and morphological complexity in vertebrate evolution. however, this claim has not been tested by examining morphologically simple animals. here, we undertake a systematic investigation of lncrnas in the demosponge amphimedon queenslandica, a morphologically simple, early-branching metazoan. we combine rna-seq data across multiple devel ... | 2015 | 25976353 |
| deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge amphimedon queenslandica. | the demosponge amphimedon queenslandica is amongst the few early-branching metazoans with an assembled and annotated draft genome, making it an important species in the study of the origin and early evolution of animals. current gene models in this species are largely based on in silico predictions and low coverage expressed sequence tag (est) evidence. | 2015 | 25975661 |
| mutations in nature conferred a high affinity phosphatidylinositol 4,5-bisphosphate-binding site in vertebrate inwardly rectifying potassium channels. | all vertebrate inwardly rectifying potassium (kir) channels are activated by phosphatidylinositol 4,5-bisphosphate (pip2) (logothetis, d. e., petrou, v. i., zhang, m., mahajan, r., meng, x. y., adney, s. k., cui, m., and baki, l. (2015) annu. rev. physiol. 77, 81-104; fürst, o., mondou, b., and d'avanzo, n. (2014) front. physiol. 4, 404-404). structural components of a pip2-binding site are conserved in vertebrate kir channels but not in distantly related animals such as sponges and sea anemones ... | 2015 | 25957411 |
| sensory flask cells in sponge larvae regulate metamorphosis via calcium signaling. | the porifera (sponges) is one of the earliest phyletic lineages to branch off the metazoan tree. although the body-plan of sponges is among the simplest in the animal kingdom and sponges lack nervous systems that communicate environmental signals to other cells, their larvae have sensory systems that generate coordinated responses to environmental cues. in eumetazoans (cnidaria and bilateria), the nervous systems of larvae often regulate metamorphosis through ca(2+)-dependent signal transduction ... | 2015 | 25898842 |
| insights into frizzled evolution and new perspectives. | the frizzled proteins (fzds) are a family of trans-membrane receptors that play pivotal roles in wnt pathways and thus in animal development. based on evaluation of the amphimedon queenslandica genome, it has been proposed that two fzd genes may have been present before the split between demosponges and other animals. the major purpose of this study is to go deeper into the evolution of this family of proteins by evaluating an extended set of available data from bilaterians, cnidarians, and diff ... | 2015 | 25801223 |
| the role of g protein-coupled receptors in the early evolution of neurotransmission and the nervous system. | the origin and evolution of the nervous system is one of the most intriguing and enigmatic events in biology. the recent sequencing of complete genomes from early metazoan organisms provides a new platform to study the origins of neuronal gene families. this review explores the early metazoan expansion of the largest integral transmembrane protein family, the g protein-coupled receptors (gpcrs), which serve as molecular targets for a large subset of neurotransmitters and neuropeptides in higher ... | 2015 | 25696819 |
| the gpcr repertoire in the demosponge amphimedon queenslandica: insights into the gpcr system at the early divergence of animals. | g protein-coupled receptors (gpcrs) play a central role in eukaryotic signal transduction. however, the gpcr component of this signalling system, at the early origins of metazoans is not fully understood. here we aim to identify and classify gpcrs in amphimedon queenslandica (sponge), a member of an earliest diverging metazoan lineage (porifera). furthermore, phylogenetic comparisons of sponge gpcrs with eumetazoan and bilaterian gpcrs will be essential to our understanding of the gpcr system at ... | 2014 | 25528161 |
| spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. | the concept of germ layers has been one of the foremost organizing principles in developmental biology, classification, systematics and evolution for 150 years (refs 1 - 3). of the three germ layers, the mesoderm is found in bilaterian animals but is absent in species in the phyla cnidaria and ctenophora, which has been taken as evidence that the mesoderm was the final germ layer to evolve. the origin of the ectoderm and endoderm germ layers, however, remains unclear, with models supporting the ... | 2015 | 25487147 |
| calcisponges have a parahox gene and dynamic expression of dispersed nk homeobox genes. | sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the antennapedia (antp) class, which in bilaterians encompass hox, parahox and nk genes. in the genome of the demosponge amphimedon queenslandica, no hox or parahox genes are present, but nk genes are linked in a tight cluster similar to the nk clusters of bilaterians. it has been proposed that hox and parahox genes o ... | 2014 | 25355364 |
| determining the biomass composition of a sponge holobiont for flux analysis. | the first step on the path of flux analysis of a new organism with little available literature is the determination of the biomass composition. once the content of the macromolecular components (protein, rna, dna, carbohydrates, lipids) and their composition is known, this composition can be converted into a biomass equation. the biomass equation is an important part of metabolic flux analysis. this equation provides the information about the precursor and energy needs for growth. in many experi ... | 2014 | 25178787 |
| the surprisingly complex immune gene repertoire of a simple sponge, exemplified by the nlr genes: a capacity for specificity? | most bacteria are not pathogenic to animals, and may instead serve beneficial functions. the requisite need for animals to differentiate between microbial friend and foe is likely borne from a deep evolutionary imperative to recognise self from non-self, a service ably provided by the innate immune system. recent findings from an ancient lineage of simple animals - marine sponges - have revealed an unexpectedly large and diverse suite of genes belonging to one family of pattern recognition recep ... | 2015 | 25058852 |
| analysis of the biomass composition of the demosponge amphimedon queenslandica on heron island reef, australia. | marine sponges are a potential source of important pharmaceutical drugs, the commercialisation of which is restricted by the difficulties of obtaining a sufficient and regular supply of biomass. one way to optimize commercial cell lines for production is the in-depth characterization and target identification through genome scale metabolic modeling and flux analysis. by applying these tools to a sponge, we hope to gain insights into how biomass is formed. we chose amphimedon queenslandica as it ... | 2014 | 24960461 |
| genome-wide analysis of simple sequence repeats in marine animals-a comparative approach. | tandem simple sequence repeats (ssrs) are one of the most popular molecular markers in genetic analysis owing to their ubiquitous occurrence,high reproducibility, multiallelic nature, and codominant mode. high mutability makes ssrs play a role in genome evolution and correspondingly show different patterns. comparative analysis of genomic ssrs in different taxonomic groups usually focuses on land species, while marine animals have been neglected. this study examined the abundance of genomic ssrs ... | 2014 | 24939717 |
| pan-metazoan phylogeny of the dmrt gene family: a framework for functional studies. | the family of doublesex-mab-3 related transcription factors (dmrts) includes key regulators of sexual differentiation and neurogenesis. to help understand the functional diversification of this gene family, we examined dmrt gene complements from the whole genome sequences and predicted gene models of 32 animal species representing 12 different phyla and from several non-metazoan outgroups. dmrts are present in all animals except the sponge amphimedon queenslandica, but are not found in any of th ... | 2014 | 24903586 |
| evolutionary origin of gastrulation: insights from sponge development. | the evolutionary origin of gastrulation--defined as a morphogenetic event that leads to the establishment of germ layers--remains a vexing question. central to this debate is the evolutionary relationship between the cell layers of sponges (poriferans) and eumetazoan germ layers. despite considerable attention, it remains unclear whether sponge cell layers undergo progressive fate determination akin to eumetazoan primary germ layer formation during gastrulation. | 2014 | 24678663 |
| blind ordering of large-scale transcriptomic developmental timecourses. | rna-seq enables the efficient transcriptome sequencing of many samples from small amounts of material, but the analysis of these data remains challenging. in particular, in developmental studies, rna-seq is challenged by the morphological staging of samples, such as embryos, since these often lack clear markers at any particular stage. in such cases, the automatic identification of the stage of a sample would enable previously infeasible experimental designs. here we present the 'basic linear in ... | 2014 | 24504336 |
| identification and characterization of transforming growth factor β induced gene (tgfbig) from branchiostoma belcheri: insights into evolution of tgfbi family. | the transforming growth factor β induced gene (tgfbig) encodes a protein (tgfbi) which plays important roles in many biological processes. however, no tgfbig homolog has been reported in b. belcheri. here, we identified a tgfbi-like gene from b. belcheri and extensively studied the evolutionary history of tgfbi family. we found that the amphioxus genome contains a tgfbig homolog designated as amphitgfbi which encodes a protein with 5 fas1 domains. the tgfbigs were present in a common ancestor wi ... | 2014 | 24140261 |
| the characterization of sponge nlrs provides insight into the origin and evolution of this innate immune gene family in animals. | the "nucleotide-binding domain and leucine-rich repeat" (nlr) genes are a family of intracellular pattern recognition receptors (prr) that are a critical component of the metazoan innate immune system, involved in both defense against pathogenic microorganisms and in beneficial interactions with symbionts. to investigate the origin and evolution of the nlr gene family, we characterized the full nacht domain-containing gene complement in the genome of the sponge, amphimedon queenslandica. as sist ... | 2014 | 24092772 |
| genomic organization, evolution, and expression of photoprotein and opsin genes in mnemiopsis leidyi: a new view of ctenophore photocytes. | calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (phylum cnidaria) and comb jellies (phylum ctenophora). the complete genomic sequence from the ctenophore mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. to determine when photoprotein ... | 2012 | 23259493 |
| the way wnt works: components and mechanism. | the canonical wnt/β-catenin pathway is an ancient and evolutionarily conserved signaling pathway that is required for the proper development of all metazoans, from the basal demosponge amphimedon queenslandica to humans. misregulation of wnt signaling is implicated in many human diseases, making this pathway an intense area of research in industry as well as academia. in this review, we explore our current understanding of the molecular steps involved in the transduction of a wnt signal. we will ... | 2013 | 23256519 |
| evolution of selenoproteins in the metazoan. | the selenocysteine (sec) containing proteins, selenoproteins, are an important group of proteins present throughout all 3 kingdoms of life. with the rapid progression of selenoprotein research in the post-genomic era, application of bioinformatics methods to the identification of selenoproteins in newly sequenced species has become increasingly important. although selenoproteins in human and other vertebrates have been investigated, studies of primitive invertebrate selenoproteomes are rarely re ... | 2012 | 22943432 |
| structural and functional characterization of ribosomal protein gene introns in sponges. | ribosomal protein genes (rpgs) are a powerful tool for studying intron evolution. they exist in all three domains of life and are much conserved. accumulating genomic data suggest that rpg introns in many organisms abound with non-protein-coding-rnas (ncrnas). these ancient ncrnas are small nucleolar rnas (snornas) essential for ribosome assembly. they are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms ... | 2012 | 22880015 |
| genomic insights into the marine sponge microbiome. | marine sponges (phylum porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. the genome of one sponge, amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. the remarkable microbial and chemical diversity of t ... | 2012 | 22842661 |
| the expression of delta ligands in the sponge amphimedon queenslandica suggests an ancient role for notch signaling in metazoan development. | intercellular signaling via the notch pathway regulates cell fate, patterning, differentiation and proliferation, and is essential for the proper development of bilaterians and cnidarians. to investigate the origins of the notch pathway, we are studying its deployment in a representative of an early branching lineage, the poriferan amphimedon queenslandica. the a. queenslandica genome encodes a single notch receptor and five membrane-bound delta ligands, as well as orthologs of many genes that e ... | 2012 | 22824137 |
| a unique alkaline ph-regulated and fatty acid-activated tandem pore domain potassium channel (k₂p) from a marine sponge. | a cdna encoding a potassium channel of the two-pore domain family (k(2p), kcnk) of leak channels was cloned from the marine sponge amphimedon queenslandica. phylogenetic analysis indicated that aquk(2p) cannot be placed into any of the established functional groups of mammalian k(2p) channels. we used the xenopus oocyte expression system, a two-electrode voltage clamp and inside-out patch clamp electrophysiology to determine the physiological properties of aquk(2p). in whole cells, non-inactivat ... | 2012 | 22723483 |
| the physiology and molecular biology of sponge tissues. | sponges have become the focus of studies on molecular evolution and the evolution of animal body plans due to their ancient branching point in the metazoan lineage. whereas our former understanding of sponge function was largely based on a morphological perspective, the recent availability of the first full genome of a sponge (amphimedon queenslandica), and of the transcriptomes of other sponges, provides a new way of understanding sponges by their molecular components. this wealth of genetic in ... | 2012 | 22664120 |
| transcriptome profiling of the demosponge amphimedon queenslandica reveals genome-wide events that accompany major life cycle transitions. | the biphasic life cycle with pelagic larva and benthic adult stages is widely observed in the animal kingdom, including the porifera (sponges), which are the earliest branching metazoans. the demosponge, amphimedon queenslandica, undergoes metamorphosis from a free-swimming larva into a sessile adult that bears no morphological resemblance to other animals. while the genome of a. queenslandica contains an extensive repertoire of genes very similar to that of complex bilaterians, it is as yet unc ... | 2012 | 22646746 |
| blue-light-receptive cryptochrome is expressed in a sponge eye lacking neurons and opsin. | many larval sponges possess pigment ring eyes that apparently mediate phototactic swimming. yet sponges are not known to possess nervous systems or opsin genes, so the unknown molecular components of sponge phototaxis must differ fundamentally from those in other animals, inspiring questions about how this sensory system functions. here we present molecular and biochemical data on cryptochrome, a candidate gene for functional involvement in sponge pigment ring eyes. we report that amphimedon que ... | 2012 | 22442365 |
| origin and evolution of laminin gene family diversity. | laminins are a family of multidomain glycoproteins that are important contributors to the structure of metazoan extracellular matrices. to investigate the origin and evolution of the laminin family, we characterized the full complement of laminin-related genes in the genome of the sponge, amphimedon queenslandica. as a representative of the demospongiae, a group consistently placed within the earliest diverging branch of animals by molecular phylogenies, amphimedon is uniquely placed to provide ... | 2012 | 22319142 |
| domain combination of the vertebrate-like tlr gene family: implications for their origin and evolution. | domain shuffling, which is an important mechanism in the evolution of multi-domain proteins, has shaped the evolutionary development of the immune system in animals. toll and toll-like receptors (tlrs) are a class of proteins that play a key role in the innate and adaptive immune systems. draft genome sequences provide the opportunity to compare the toll/tlr gene repertoire among representative metazoans. in this study, we investigated the combination of toll/interleukin-1 receptor (tir) and leu ... | 2011 | 22227927 |
| phylogenetic relationships of the marine haplosclerida (phylum porifera) employing ribosomal (28s rrna) and mitochondrial (cox1, nad1) gene sequence data. | the systematics of the poriferan order haplosclerida (class demospongiae) has been under scrutiny for a number of years without resolution. molecular data suggests that the order needs revision at all taxonomic levels. here, we provide a comprehensive view of the phylogenetic relationships of the marine haplosclerida using many species from across the order, and three gene regions. gene trees generated using 28s rrna, nad1 and cox1 gene data, under maximum likelihood and bayesian approaches, are ... | 2011 | 21931685 |
| a horizontal gene transfer supported the evolution of an early metazoan biomineralization strategy. | the synchronous and widespread adoption of the ability to biomineralize was a defining event for metazoan evolution during the late precambrian/early cambrian 545 million years ago. however our understanding on the molecular level of how animals first evolved this capacity is poor. because sponges are the earliest branching phylum of biomineralizing metazoans, we have been studying how biocalcification occurs in the coralline demosponge astrosclera willeyana. | 2011 | 21838889 |
| [the genome of the sponge amphimedon queenslandica is helping us to reconstruct our precambrian ancestor]. | | 2011 | 21382321 |
| freshwater sponges have functional, sealing epithelia with high transepithelial resistance and negative transepithelial potential. | epithelial tissue - the sealed and polarized layer of cells that regulates transport of ions and solutes between the environment and the internal milieu - is a defining characteristic of the eumetazoa. sponges, the most ancient metazoan phylum, are generally believed to lack true epithelia, but their ability to occlude passage of ions has never been tested. here we show that freshwater sponges (demospongiae, haplosclerida) have functional epithelia with high transepithelial electrical resistance ... | 2010 | 21124779 |
| the genome of the sponge amphimedon queenslandica provides new perspectives into the origin of toll-like and interleukin 1 receptor pathways. | members of the toll-like receptor (tlr) and the interleukin 1 receptor (il1r) superfamilies activate various signaling cascades that are evolutionarily conserved in eumetazoans. in this study, we have searched the genome and expressed sequence tags of the demosponge amphimedon queenslandica for molecules involved in tlr and il1r signaling. although we did not identify a conventional tlr or ilr, the amphimedon genome encodes two related receptors, amqigtirs, which are comprised of at least three ... | 2011 | 20883219 |
| numts in the sponge genome reveal conserved transposition mechanisms in metazoans. | the transposition of parts of the mitochondrial (mt) genetic material into the nuclear genome (numts) occurs in a wide range of eukaryotes. here, we show that numts exist for nearly all regions of the mt genome in the demosponge amphimedon queenslandica, a representative of the oldest phyletic lineage of animals. because the sponge numts are small and noncoding, and transposed via a dna intermediate, as in eumetazoans, we infer that the transpositonal processes underlying numt formation in conte ... | 2011 | 20720154 |
| the amphimedon queenslandica genome and the evolution of animal complexity. | sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. here we present the draft genome sequence of amphimedon queenslandica, a demosponge from the great barrier reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion a ... | 2010 | 20686567 |
| the initiation of metamorphosis as an ancient polyphenic trait and its role in metazoan life-cycle evolution. | comparative genomics of representative basal metazoans leaves little doubt that the most recent common ancestor to all modern metazoans was morphogenetically complex. here, we support this interpretation by demonstrating that the demosponge amphimedon queenslandica has a biphasic pelagobenthic life cycle resembling that present in a wide range of bilaterians and anthozoan cnidarians. the a. queenslandica life cycle includes a compulsory planktonic larval phase that can end only once the larva de ... | 2010 | 20083639 |
| early evolution of the lim homeobox gene family. | lim homeobox (lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the lhx family during development in non-bilaterian phyla are not known. | 2010 | 20082688 |
| wnt/beta-catenin signalling and epithelial patterning in the homoscleromorph sponge oscarella. | sponges branch basally in the metazoan phylogenetic tree and are thus well positioned to provide insights into the evolution of mechanisms controlling animal development, likely to remain active in adult sponges. of the four sponge clades, the homoscleromorpha are of particular interest as they alone show the "true" epithelial organization seen in other metazoan phyla (the eumetazoa). we have examined the deployment in sponges of wnt signalling pathway components, since this pathway is an import ... | 2009 | 19503791 |
| the evolution of runx genes ii. the c-terminal groucho recruitment motif is present in both eumetazoans and homoscleromorphs but absent in a haplosclerid demosponge. | the runt dna binding domain (runx) defines a metazoan family of sequence-specific transcription factors with essential roles in animal ontogeny and stem cell based development. depending on cis-regulatory context, runx proteins mediate either transcriptional activation or repression. in many contexts runx-mediated repression is carried out by groucho/tle, recruited to the transcriptional complex via a c-terminal wrpy sequence motif that is found encoded in all heretofore known runx genes. | 2009 | 19374764 |
| multiple dicer genes in the early-diverging metazoa. | dicer proteins are highly conserved, are present in organisms ranging from plants to metazoans, and are essential components of the rna interference pathway. although the complement of dicer proteins has been investigated in many "higher" metazoans, there has been no corresponding characterization of dicer proteins in any early-branching metazoan. we cloned partial cdnas of genes belonging to the dicer family from the anthozoan cnidarian nematostella vectensis and two distantly related haplotype ... | 2009 | 19276153 |
| expression of a poriferan potassium channel: insights into the evolution of ion channels in metazoans. | ion channels establish and regulate membrane potentials in excitable and non-excitable cells. how functional diversification of ion channels contributed to the evolution of nervous systems may be understood by studying organisms at key positions in the evolution of animal multicellularity. we have carried out the first analysis of ion channels cloned from a marine sponge, amphimedon queenslandica. phylogenetic comparison of sequences encoding for poriferan inward-rectifier k(+) (kir) channels su ... | 2009 | 19251990 |
| early origins and evolution of micrornas and piwi-interacting rnas in animals. | in bilaterian animals, such as humans, flies and worms, hundreds of micrornas (mirnas), some conserved throughout bilaterian evolution, collectively regulate a substantial fraction of the transcriptome. in addition to mirnas, other bilaterian small rnas, known as piwi-interacting rnas (pirnas), protect the genome from transposons. here we identify small rnas from animal phyla that diverged before the emergence of the bilateria. the cnidarian nematostella vectensis (starlet sea anemone), a close ... | 2008 | 18830242 |
| sponge oas has a distinct genomic structure within the 2-5a synthetase family. | 2',5'-oligoadenylate synthetases (2-5a synthetases, oas) are enzymes that play an important role in the interferon-induced antiviral defense mechanisms in mammals. sponges, the evolutionarily lowest multicellular animals, also possess oas; however, their function is presently unclear. low homology between primary structures of 2-5a synthetases from vertebrates and sponges renders their evolutionary relationship obscure. the genomic structure of vertebrate oass has been thoroughly examined, makin ... | 2008 | 18797928 |
| sponge genes provide new insight into the evolutionary origin of the neurogenic circuit. | the nerve cell is a eumetazoan (cnidarians and bilaterians) synapomorphy [1]; this cell type is absent in sponges, a more ancient phyletic lineage. here, we demonstrate that despite lacking neurons, the sponge amphimedon queenslandica expresses the notch-delta signaling system and a proneural basic helix loop helix (bhlh) gene in a manner that resembles the conserved molecular mechanisms of primary neurogenesis in bilaterians. during amphimedon development, a field of subepithelial cells express ... | 2008 | 18674909 |
| does the high gene density in the sponge nk homeobox gene cluster reflect limited regulatory capacity? | a huge discrepancy in morphological diversity exists between poriferans and eumetazoans. the disparate evolutionary outcomes of these two ancient metazoan lineages may be reflected in the composition, architecture, and regulation of genomes of modern representatives. as a case study, we compare the sizes of upstream intergenic regions of genes found within the nk homeobox cluster of the demosponge amphimedon queenslandica with eumetazoan orthologs. this analysis includes nk genes as well as five ... | 2008 | 18574099 |
| partitioning of genetically distinct cell populations in chimeric juveniles of the sponge amphimedon queenslandica. | natural chimerism, the fusion between genetically distinct conspecifics, is a process known to occur in various marine benthic invertebrates. sponges (phylum porifera) have proven to be a useful model to study the origin and evolution of allorecognition. like some other invertebrates, they display an ontogenetic shift in their allorecognition response: genetically different individuals can fuse during early development, but, in most instances, not as adults. however, there is a limited understan ... | 2008 | 18514309 |
| genesis and expansion of metazoan transcription factor gene classes. | we know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. many transcription factor genes that play critical roles in bilaterian development largely appear to have ... | 2008 | 18296413 |
| the transcription factor nf-kappab in the demosponge amphimedon queenslandica: insights on the evolutionary origin of the rel homology domain. | the rel/nuclear factor-kappa b (nf-kappab) and nuclear factor of activated t-cells (nfat) transcription factors contribute to the regulation of an assortment of biological processes by binding dna with high specificity using their rel homology domain (rhd). recently, it has been shown that members of these gene families are present in the genome of the anthozoan cnidarian nematostella vectensis, indicating that they predate the evolution of the most recent ancestor to living bilaterians. by iden ... | 2008 | 18175145 |
| genotyping individual amphimedon embryos, larvae, and adults. | introductionthe distribution of amphimedon queenslandica is patchy on coral reefs in the great barrier reef, with small, localized populations detected in shallow, still water reef-flat environments. a. queenslandica is a spermcast spawner, in which fertilization occurs internally. sperm presumably originate from neighboring reproductive individuals within the population. the ability to genotype individual embryos within a single brood chamber has the potential to shed light on the fertilization ... | 2008 | 21356744 |
| whole-mount in situ hybridization in amphimedon. | introductiondevelopmental gene expression is analyzed predominantly via whole-mount in situ hybridization using digoxigenin-labeled rna probes. this protocol describes how to perform this procedure in amphimedon queenslandica, including fixation, hybridization, and sectioning of embryonic, larval, and post-larval juvenile stages. | 2008 | 21356742 |
| the demosponge amphimedon queenslandica: reconstructing the ancestral metazoan genome and deciphering the origin of animal multicellularity. | introductionsponges are one of the earliest branching metazoans. in addition to undergoing complex development and differentiation, they can regenerate via stem cells and can discern self from nonself ("allorecognition"), making them a useful comparative model for a range of metazoan-specific processes. molecular analyses of these processes have the potential to reveal ancient homologies shared among all living animals and critical genomic innovations that underpin metazoan multicellularity. amp ... | 2008 | 21356734 |
| wnt and tgf-beta expression in the sponge amphimedon queenslandica and the origin of metazoan embryonic patterning. | the origin of metazoan development and differentiation was contingent upon the evolution of cell adhesion, communication and cooperation mechanisms. while components of many of the major cell signalling pathways have been identified in a range of sponges (phylum porifera), their roles in development have not been investigated and remain largely unknown. here, we take the first steps toward reconstructing the developmental signalling systems used in the last common ancestor to living sponges and ... | 2007 | 17925879 |
| the nk homeobox gene cluster predates the origin of hox genes. | hox and other antennapedia (antp)-like homeobox gene subclasses - parahox, ehgbox, and nk-like - contribute to key developmental events in bilaterians [1-4]. evidence of physical clustering of antp genes in multiple animal genomes [4-9] suggests that all four subclasses arose via sequential cis-duplication events. here, we show that hox genes' origin occurred after the divergence of sponge and eumetazoan lineages and occurred concomitantly with a major evolutionary transition in animal body-plan ... | 2007 | 17379523 |
| origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. | molecular and genetic analyses conducted in model organisms such as drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. much less is known, however, about the evolutionary origin of these elaborated networks and their large-scale evolution. here we report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loop-helix (bhlh) proteins, at the scale ... | 2007 | 17335570 |
| mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge. | the first mitochondrial (mt) genomes of demosponges have recently been sequenced and appear to be markedly different from published eumetazoan mt genomes. here we show that the mt genome of the haplosclerid demosponge amphimedon queenslandica has features that it shares with both demosponges and eumetazoans. although the a. queenslandica mt genome has typical demosponge features, including size, long noncoding regions, and bacterialike rrna genes, it lacks atp9, which is found in the other demos ... | 2007 | 17053047 |