The Role of Enzymes in Biomineralization Processes

Weiss, Ingrid M.; Marin, Frédéric

doi:10.1002/9780470986325.ch3

Cited by 13 publications

(5 citation statements)

References 220 publications

(219 reference statements)

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“…Enzymes are crucial for the production of all biominerals (Weiss and Marin, 2008), they can be categorized in many different ways based on type of biochemical catalytic activity, or biological function carried out, from protein synthesis to signalling cascades, ion transport and mineral nucleation. Here we describe the genes in modules 1 and 2 encoding enzymes that can be categorized as specific to mineralization [according to Weiss and Marin (2008)].…”

Section: Biomineralization-specific Enzymesmentioning

confidence: 99%

Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways

et al. 2019

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Motivation The molecular processes regulating molluscan shell production remain relatively uncharacterized, despite the clear evolutionary and societal importance of biomineralization. Results Here we built the first computationally predicted gene regulatory network (GRN) for molluscan biomineralization using Antarctic clam (Laternula elliptica) mantle gene expression data produced over an age-categorized shell damage-repair time-course. We used previously published in vivo in situ hybridization expression data to ground truth gene interactions predicted by the GRN and show that candidate biomineralization genes from different shell layers, and hence microstructures, were connected in unique modules. We characterized two biomineralization modules of the GRN and hypothesize that one module is responsible for translating the extracellular proteins required for growing, repairing or remodelling the nacreous shell layer, whereas the second module orchestrates the transport of both ions and proteins to the shell secretion site, which are required during normal shell growth, and repair. Our findings demonstrate that unbiased computational methods are particularly valuable for studying fundamental biological processes and gene interactions in non-model species where rich sources of gene expression data exist, but annotation rates are poor and the ability to carry out true functional tests are still lacking. Availability and implementation The raw RNA-Seq data is freely available for download from NCBI SRA (Accession: PRJNA398984), the assembled and annotated transcriptome can be viewed and downloaded from molluscDB (ensembl.molluscdb.org) and in addition, the assembled transcripts, reconstructed GRN, modules and detailed annotations are all available as Supplementary Files. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Biomineralization-specific Enzymesmentioning

confidence: 99%

Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways

et al. 2019

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“…It is practically impossible to observe the complexity of organic matrix deposition during adult shell formation on an enzymatic level (e.g., chitin synthases, chitin deacetylases) in situ (see Fig. 1 for details, compare also (Bevelander and Nakahara, 1969;Jackson et al, 2006;Weiss and Marin, 2008)). To date, most in vitro experiments with ''purified" compounds indicated an intercalation of the silk into the chitins.…”

Section: Introductionmentioning

confidence: 99%

Covalent modification of chitin with silk-derivatives acts as an amphiphilic self-organizing template in nacre biomineralisation

Weiss

Kaufmann

Heiland

et al. 2009

Journal of Structural Biology

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“…However, common binding principles and motifs are hard to identify since biomineralization proteins interact with a range of different materials, at different environmental conditions and at various levels of regulation [ 7 , 8 ]. They can function as enzymes or structural proteins [ 9 ], promote or inhibit crystal growth and they can be incorporated as intracrystalline biomolecules [ 10 ]. Available data on biomineralization proteins offer the possibility to compare mineral-associated proteins and to search for unifying principles like conserved sequence regions, certain domains like C-type lectin domains, acidic or disordered domains, to mention only a few.…”

Section: Resultsmentioning

confidence: 99%

Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization

et al. 2017

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Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO2 mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.

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The Role of Enzymes in Biomineralization Processes

Abstract: 72

Cited by 13 publications

References 220 publications

Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways

Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways

Covalent modification of chitin with silk-derivatives acts as an amphiphilic self-organizing template in nacre biomineralisation

Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization

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