Exploration of Genes Associated with Sponge Silicon Biomineralization in the Whole Genome Sequence of the Hexactinellid Euplectella curvistellata

Shimizu, Katsuhiko; Kobayashi, Hiroki; Nishi, Michika; Tsukahara, Masatoshi; Bito, Tomohiro; Arima, Jiro

doi:10.1007/978-981-13-1002-7_16

Cited by 7 publications

(8 citation statements)

References 17 publications

(29 reference statements)

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“…The genomics of biomineralization has advanced rapidly and is a topic of active work, however mostly in such directions as calcification, biosilicification, and the formation of biomagnetic structures. Thus, genomic architectures within diverse genetic toolkits have been intensively studied in calcifying organisms (i.e., bacteria], corals, sea urchins, hemichordates, mollusks [ 289 ], biosilicifiers (i.e., diatoms [ 290 ], sponges [ 18 , 291 , 292 , 293 ], and especially magnetotactic microorganisms) to carry out the understanding of biomineralization. However, we cannot exclude the occurrence of so-called “gene-independent biomineralization” [ 294 ] in the case of forced biomineralization.…”

Section: Discussionmentioning

confidence: 99%

Forced Biomineralization: A Review

2021

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Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of “forced biomineralization”, which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.

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Section: Discussionmentioning

confidence: 99%

Forced Biomineralization: A Review

2021

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“…In addition, we found a homolog of conventional actin , which has been recently reported to be important for spicule scaffolding [ 159 ]. Shimizu and collaborators [ 156 ] tried unsuccessfully to isolate silicatein proteins from the spicules of the glass sponge Euplectella aspergillum and failed to recover any sequence belonging to the silicatein family in this species. Similarly, we did not find any silicatein ortholog (except cathepsin L).…”

Section: Resultsmentioning

confidence: 99%

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

et al. 2023

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Background Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology—evodevo—and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera. Results We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species. Conclusions The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.

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“…One gene thought to be involved in silica biomineralization in hexactinellids is glassin, a novel histidine-rich protein containing HX or HHX repeats [ 9 , 43 ]. Considering this, we first searched for homologues of Euplectella glassin in the A. vastus genome and were able to identify a complete orthologue of this gene both in this (Avas.s014.g618) and in the O. minuta genome (LOD99_3750).…”

Section: Resultsmentioning

confidence: 99%

The genome of the reef-building glass spongeAphrocallistes vastusprovides insights into silica biomineralization

et al. 2023

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Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus , a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO 2 ), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO 2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.

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Exploration of Genes Associated with Sponge Silicon Biomineralization in the Whole Genome Sequence of the Hexactinellid Euplectella curvistellata

Cited by 7 publications

References 17 publications

Forced Biomineralization: A Review

Forced Biomineralization: A Review

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

The genome of the reef-building glass spongeAphrocallistes vastusprovides insights into silica biomineralization

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