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Amphimedon

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Bernard M. Degnan – 1st expert on this subject based on the ideXlab platform

  • A Post-Synaptic Scaffold at the Origin of the Animal
    , 2020
    Co-Authors: Sakarya, Bernard M. Degnan, Maja Adamska, Marcin Adamski, Kathryn A. Armstrong, I-fan Wang, Bruce Tidor, H Todd, Kenneth S. Kosik

    Abstract:

    Background. 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 recognizable synapses, in contrast to eumetazoan animals. Methodology/Principal Findings. We show that the genome of the demosponge Amphimedon queenslandica possesses a nearly complete set of post-synaptic protein homologs whose conserved interaction motifs suggest assembly into a complex structure. In the critical synaptic scaffold gene, dlg, residues that make hydrogen bonds and van der Waals interactions with the PDZ ligand are 100% conserved between sponge and human, as is the motif organization of the scaffolds. Expression in Amphimedon of multiple post-synaptic gene homologs in larval flask cells further supports the existence of an assembled structure. Among the few post-synaptic genes absent from Amphimedon, but present in Eumetazoa, are receptor genes including the entire ionotropic glutamate receptor family. Conclusions/Significance. Highly conserved protein interaction motifs and co-expression in sponges of multiple proteins whose homologs interact in eumetazoan synapses indicate that a complex protein scaffold was present at the origin of animals, perhaps predating nervous systems. A relatively small number of crucial innovations to this pre-existing structure may represent the founding changes that led to a post-synaptic element.

  • co expression of synaptic genes in the sponge Amphimedon queenslandica uncovers ancient neural submodules
    Scientific Reports, 2019
    Co-Authors: Eunice Wong, Sandie M Degnan, Jan Molter, Victor Anggono, Bernard M. Degnan

    Abstract:

    The synapse is a complex cellular module crucial to the functioning of neurons. It evolved largely through the exaptation of pre-existing smaller submodules, each of which are comprised of ancient sets of proteins that are conserved in modern animals and other eukaryotes. Although these ancient submodules themselves have non-neural roles, it has been hypothesized that they may mediate environmental sensing behaviors in aneural animals, such as sponges. Here we identify orthologues in the sponge Amphimedon queenslandica of genes encoding synaptic submodules in neural animals, and analyse their cell-type specific and developmental expression to determine their potential to be co-regulated. We find that genes comprising certain synaptic submodules, including those involved in vesicle trafficking, calcium-regulation and scaffolding of postsynaptic receptor clusters, are co-expressed in adult choanocytes and during metamorphosis. Although these submodules may contribute to sensory roles in this cell type and this life cycle stage, total synaptic gene co-expression profiles do not support the existence of a functional synapse in A. queenslandica. The lack of evidence for the co-regulation of genes necessary for pre- and post-synaptic functioning in A. queenslandica suggests that sponges, and perhaps the last common ancestor of sponges and other extant animals, had the ability to promulgate sensory inputs without complete synapse-like functionalities. The differential co-expression of multiple synaptic submodule genes in sponge choanocytes, which have sensory and feeding roles, however, is consistent with the metazoan ancestor minimally being able to undergo exo- and endocytosis in a controlled and localized manner.

  • Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks
    Non-Coding RNA, 2018
    Co-Authors: Federico Gaiti, William L. Hatleberg, Miloš Tanurdžić, Bernard M. Degnan

    Abstract:

    Although developmental regulation by long non-coding RNAs (lncRNAs) appears to be a widespread feature amongst animals, the origin and level of evolutionary conservation of this mode of regulation remain unclear. We have previously demonstrated that the sponge Amphimedon queenslandica—a morphologically-simple animal—developmentally expresses an array of lncRNAs in manner akin to more complex bilaterians (insects + vertebrates). Here, we first show that Amphimedon lncRNAs are expressed in specific cell types in larvae, juveniles and adults. Thus, as in bilaterians, sponge developmental regulation involves the dynamic, cell type- and context-specific regulation of specific lncRNAs. Second, by comparing gene co-expression networks between Amphimedon queenslandica and Sycon ciliatum—a distantly-related calcisponge—we identify several putative co-expression modules that appear to be shared in sponges; these network-embedded sponge lncRNAs have no discernable sequence similarity. Together, these results suggest sponge lncRNAs are developmentally regulated and operate in conserved gene regulatory networks, as appears to be the case in more complex bilaterians.

Junichi Kobayashi – 2nd expert on this subject based on the ideXlab platform

  • zamamidine d a manzamine alkaloid from an okinawan Amphimedon sp marine sponge
    Journal of Natural Products, 2017
    Co-Authors: Takaaki Kubota, Jane Fromont, Tohru Gonoi, Kenta Nakamura, Shinichiro Kurimoto, Kanae Sakai, Junichi Kobayashi

    Abstract:

    A new manzamine alkaloid, zamamidine D (1), was isolated from an Okinawan Amphimedon sp. marine sponge. The structure of zamamidine D (1) including the relative configuration was elucidated on the basis of spectroscopic data. Zamamidine D (1) is the first manzamine alkaloid possessing a 2,2′-methylenebistryptamine unit as the aromatic moiety instead of a β-carboline unit. Zamamidine D (1) showed antimicrobial activity against several bacteria and fungi.

  • zamamiphidin a a new manzamine related alkaloid from an okinawan marine sponge Amphimedon sp
    Organic Letters, 2013
    Co-Authors: Takaaki Kubota, Jane Fromont, Yuki Kamijyo, Azusa Takahashinakaguchi, Tohru Gonoi, Junichi Kobayashi

    Abstract:

    A manzamine related alkaloid, zamamiphidin A (1), consisting of a new heptacyclic ring system has been isolated from an Okinawan marine sponge Amphimedon sp. The structure of 1 including the relative stereochemistry was elucidated on the basis of the spectroscopic data. Compound 1 showed antibacterial activity against Staphylococcus aureus (MIC, 32 μg/mL).

  • Pyrinodemins G–I, new bis-3-alkylpyridine alkaloids from a marine sponge Amphimedon sp.
    Tetrahedron, 2013
    Co-Authors: Takaaki Kubota, Jane Fromont, Kenichi Kura, Junichi Kobayashi

    Abstract:

    Three new bis-3-alkylpyridine alkaloids, pyrinodemins G–I (1–3), were isolated from an Okinawan marine sponge Amphimedon sp. and the structures of 1–3 were elucidated on the basis of spectroscopic data. Pyrinodemins G–I (1–3) were novel bis-3-alkylpyridine alkaloids possessing an N-methoxy amide moiety, an α,β-unsaturated 3,5-disubstituted γ-lactone moiety, and a 2,3-di-substituted acrolein at a junction of two 3-alkylpyridines, respectively. Pyrinodemins G (1) and H (2) showed cytotoxicity against P388 murine leukemia cells.

Takaaki Kubota – 3rd expert on this subject based on the ideXlab platform

  • zamamidine d a manzamine alkaloid from an okinawan Amphimedon sp marine sponge
    Journal of Natural Products, 2017
    Co-Authors: Takaaki Kubota, Jane Fromont, Tohru Gonoi, Kenta Nakamura, Shinichiro Kurimoto, Kanae Sakai, Junichi Kobayashi

    Abstract:

    A new manzamine alkaloid, zamamidine D (1), was isolated from an Okinawan Amphimedon sp. marine sponge. The structure of zamamidine D (1) including the relative configuration was elucidated on the basis of spectroscopic data. Zamamidine D (1) is the first manzamine alkaloid possessing a 2,2′-methylenebistryptamine unit as the aromatic moiety instead of a β-carboline unit. Zamamidine D (1) showed antimicrobial activity against several bacteria and fungi.

  • zamamiphidin a a new manzamine related alkaloid from an okinawan marine sponge Amphimedon sp
    Organic Letters, 2013
    Co-Authors: Takaaki Kubota, Jane Fromont, Yuki Kamijyo, Azusa Takahashinakaguchi, Tohru Gonoi, Junichi Kobayashi

    Abstract:

    A manzamine related alkaloid, zamamiphidin A (1), consisting of a new heptacyclic ring system has been isolated from an Okinawan marine sponge Amphimedon sp. The structure of 1 including the relative stereochemistry was elucidated on the basis of the spectroscopic data. Compound 1 showed antibacterial activity against Staphylococcus aureus (MIC, 32 μg/mL).

  • pyrinodemins g i new bis 3 alkylpyridine alkaloids from a marine sponge Amphimedon sp
    Tetrahedron, 2013
    Co-Authors: Takaaki Kubota, Jane Fromont, Kenichi Kura, Junichi Kobayashi

    Abstract:

    Three new bis-3-alkylpyridine alkaloids, pyrinodemins G–I (1–3), were isolated from an Okinawan marine sponge Amphimedon sp. and the structures of 1–3 were elucidated on the basis of spectroscopic data. Pyrinodemins G–I (1–3) were novel bis-3-alkylpyridine alkaloids possessing an N-methoxy amide moiety, an α,β-unsaturated 3,5-disubstituted γ-lactone moiety, and a 2,3-di-substituted acrolein at a junction of two 3-alkylpyridines, respectively. Pyrinodemins G (1) and H (2) showed cytotoxicity against P388 murine leukemia cells.