Genetic mechanisms of calcareous sponge biomineralization

• Applicant: Dr. Oliver Voigt
• Subject Area: Animal Physiology and Biochemistry ; Evolutionary Cell and Developmental Biology (Zoology) ; Palaeontology
• Term: from 2016 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 319411146

• Final Report Year: 2021

Final Report Abstract

Biomineralization is the biological controlled formation of mineral structures. Many animal groups use biomineralization to form functional structures like skeletons, shells, or teeth. Biominerals are often composite materials of organic and inorganic compounds, with different material characteristics than their purely mineral counterparts. In the project, we studied the genetic basis of carbonate biomineralization in calcareous sponges (Phylum Porifera, Class Calcarea) using RNA-Seq, proteomics of spicules matrix proteins and RNA in situ hybridisation. Calcareous sponges produce calcite spicules, which can be needle-shaped diactines (growing initially at two tips), triactines with three actines, or tetractines. Few specific cells, the sclerocytes, act together to secrete these spicules into an extracellular space enclosed between them. Two cells are involved in the formation of each actine; the founder cell promotes actine growth, the thickener cell moves along the produced actine in the later spicule formation stage towards the growing tip, secreting additional spicule material. Our studies included sponges of both subclasses (Calcaronea and Calcinea) to identify essential genes of the genetic biomineralization machinery of calcareous sponges. We studied their spatial and temporal expression to learn more about these genes functions. Finally, we screened additional transcriptomes to address which genes date back to the last common ancestor of calcareous sponges and which are lineage-specific innovations. The project provided the first analysis of spicule matrix proteins isolated from calcareous sponge spicules. This approach was challenging because of the unexpected low concentrations of (soluble) spicule matrix proteins. Finally, we identified many proteins (83). Another applied method was to identify genes overexpressed in body parts of calcareous sponges with increased spicule formation. In some species, we could not succeed, probably because of the too low abundance of sclerocytes or preparational difficulties. In the model species Sycon ciliatum, 430 genes were overexpressed in a growth zone with increased spicule formation, including known biomineralization genes. Both approaches identified a group of proteins with some similarities to coral skeletal matrix protein Galaxin as essential components of the spicule matrix in both subclasses of calcareous sponges. Eight of these galaxin-like proteins were overexpressed in the spicule formation zone in Sycon ciliatum. RNA in situ hybridisation experiments showed very specific expression patterns, expressed either in founder cells or thickener cells; in some cases, they were spicule-type-specific. Spicule formation is therefore again shown to be coordinated by a change of expression of specific biominerlization genes. Additionally, spicules with different shapes involve specific spicule matrix proteins. Results of this project complement the knowledge of the genetic bases of biomineralization in calcareous sponges and their evolution. We conclude that the biomineralization machinery of the last common ancestor of calcareous sponges already possessed components of the biomineralization machinery found in extant species. Two enzymatic carbonic anhydrases (one mitochondrial and one secreted membrane-bound) and two bicarbonate transporter (AE-like1, NBT-like1) are essential elements of the calcareous sponge genetic biomineralization toolkit. Of the identified spicule matrix proteins, orthologs can only be found for one of the galaxin-like proteins in all studied sponges, suggesting it also dates back to an ancestral matrix protein of the last common ancestor of extant calcareous sponges. In contrast, other spicule matrix proteins seem to be lineage- or even species-specific or too fast evolving to track their evolution. Only these genes showed a spicule-type specific expression. Future research on calcareous sponges could provide even a more fine-grained picture of the genetic control over the formation of biominerals. Finally, our specific expression patterns for different spicule formation stages could be helpful in other approaches, e.g., identifying these stages in single-cell sequencing data. Such data allows studying the differentiation and expression changes of sclerocytes types and identify sclerocyte precursors.

Publications

• Evolution of key biomineralization genes in calcareous sponges, 10th World Sponge Conference, Galway, Ireland, Jun 25-30 2017
  Voigt O, Adamska M, Adamski M, Miller DJ, Wörheide, G., Fortunato S
  
• Identification of spicule matrix proteins of calcareous sponges, 10th World Sponge Conference, Galway, Ireland, Jun 25-30 2017
  Fraduso B, Fortunato S, Adamska M, Adamski M, Voigt O
  
• (2018): A new species of the calcareous sponge genus Leuclathrina (Calcarea: Calcinea: Clathrinida) from the Maldives. Zootaxa 4382 (1), 147–158
  Voigt O, Ruthensteiner B, Leiva L, Fradusco B, Wörheide G
  
• (2021): Carbonic anhydrases: An ancient tool in calcareous sponge biomineralization. Frontiers in Genetics 12:383
  Voigt O, Fradusco B, Gut C, Kevrekidis C, Vargas S, Wörheide G