Identification of the Domains Involved in Promotion of Silica Formation in Glassin, a Protein Occluded in Hexactinellid Sponge Biosilica, for Development of a Tag for Purification and Immobilization of Recombinant Proteins

Abstract

Glassin, a protein occluded in biosilica of the hexactinellid sponge Euplectela, promotes silica formation from silicic acid at room temperature and neutral pH and is characterized by its primary structure which consists of a tandem repeat carrying three distinct domains, histidine and aspartic acid-rich (HD) domain, proline-rich (P) domain, and histidine and threonine-rich (HT) domain. The present study aims to clarify the domain responsible for the promotion of silica formation and to demonstrate usefulness of glassin and its domain as a tag for purification and immobilization of recombinant proteins. When each domain was mixed with silicic acid at neutral pH, silica was formed with HD domain as well as glassin, or a single repeat, but not with P or HT domain. Neither of amino or carboxy-terminal half of HD domain induced silica formation. The amount of silica formed with HD domain was significantly lower than that of glassin or a single repeat. HD domain fused with HT domain raised the amount of silica formed, while a HD domain fused with P domain, a mixture of HD and P domains, or a mixture of HD and HT domains has little effect on the promotion of silica formation. Collectively, a minimum sequence for promotion of silica formation is HD domain, whose activity can be enhanced by HT domain through a topological effect. In addition, practicality of glassin and HD domain was demonstrated by fusion of these sequences to green fluorescent protein which was successfully purified with Ni affinity chromatography and immobilized on silica.

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Data Availability

DNA sequences are deposited in DDBJ/EMBL/GenBank accession nos. LC520255–LC520266.

References

  1. Aguilar-Camacho JM, McCormack GP (2019) Silicatein expression in Haliclona indistincta (phylum Porifera, order Haplosclerida) at different developmental stages. Dev Genes Evol 229:35–41

    CAS  Article  Google Scholar 

  2. Arnold FH, Haymore BL (1991) Engineered metal-binding proteins: purification to protein folding. Science 252:1796–1797

    CAS  Article  Google Scholar 

  3. Brinker CJ, Scherer GW (1990) Sol-gel science: the physics and chemistry of sol-gel processing. Academic Press, Inc, San Diego

    Google Scholar 

  4. Brutchey RL, Morse DE (2008) Silicatein and the translation of its molecular mechanism of Biosilicification into low temperature nanomaterial synthesis. Chem Rev 108:4915–4934

    CAS  Article  Google Scholar 

  5. Cha JN, Shimizu K, Zhou Y, Christiansen SC, Chmelka BF, Stucky DS, Morse DE (1999) Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro. PNAS 96:361–365

    CAS  Article  Google Scholar 

  6. Chaga G, Bochkariov DE, Jokhadze GG, Hopp J, Nelson P (1999) Natural poly-histidine affinity tag for purification of recombinant proteins on cobalt (II)-carboxymethylaspartate crosslinked agarose. J Chromatogr A 864:247–256

    CAS  Article  Google Scholar 

  7. Davis AK, Hildebrand M, Palenik B (2005) A stress-induced protein associated with the girdle band region of the diatom Thalassiosira pseudonana (Bacillariophyta). J Phycol 41:577–589

    CAS  Article  Google Scholar 

  8. Dickerson MB, Sandhage KH, Naik RR (2008) Protein- and peptide-directed syntheses of inorganic materials. Chem Rev 108:4935–4978

    CAS  Article  Google Scholar 

  9. Ehrlich H, Maldonado M, Spindler KD, Eckert C, Hanke T, Born R, Goebel C, Simon P, Heinemann S, Worch H (2007) First evidence of chitin as a component of the skeletal fibers of marine sponges. Part I. Verongidae (demospongia: Porifera). J Exp Zool B Mol Dev Evol 308:347–356

    Article  Google Scholar 

  10. Ehrlich H, Demadis KD, Pokrovsky OS, Koutsoukos PG (2010) Modern views on desilicification: biosilica and abiotic silica dissolution in natural and artificial environments. Chem Rev 110:4656–4689

    CAS  Article  Google Scholar 

  11. Hochuli E, Bannwarth W, Döbeli H (1988) Genetic approach to facilitate purification of recombinant proteins with a novel metal chelate adsorbent. Nat Biotechnol 6:1321–1325

    CAS  Article  Google Scholar 

  12. Iler RK (1979) The chemistry of silica: solubility, polymerization, colloid and surface properties, and biochemistry. Wiley, New York

    Google Scholar 

  13. Kaluzhnaya OV, Belikova AS, Podolskaya EP, Krasko AG, Müller WEG, Belikov SI (2007) Identification of silicateins in freshwater sponge Lubomirskia baicalensis. Mol Biol 41:554–561

    CAS  Article  Google Scholar 

  14. Kotzsch A, Gröger P, Pawolski D, Bomans PHH, Sommerdijk NAJM, Schlierf M, Kröger N (2017) Silicanin-1 is a conserved diatom membrane protein involved in silica biomineralization. BMC Biol 15:65

    Article  Google Scholar 

  15. Kozhemyako VB, Veremeichik GN, Shkryl YN, Kovalchuk SN, Krasokhin VB, Rasskazov VA, Zhuravlev YN, Bulgakov VP, Kulchin YN (2010) Silicatein genes in spicule-forming and nonspicule-forming pacific demosponges. Mar Biotechnol (NY) 12:403–409

    CAS  Article  Google Scholar 

  16. Kröger N, Deutzmann R, Sumper M (1999) Polycationic peptides from diatom biosilica that direct silica nanosphere formation. Science 286:1129–1132

    Article  Google Scholar 

  17. Kröger N, Deutzmann R, Bergsdorf C, Sumper M (2000) Species-specific polyamines from diatoms control silica morphology. PNAS 97:14133–14138

    Article  Google Scholar 

  18. Kröger N, Lorenz S, Brunner E, Sumper M (2002) Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis. Science 298:584–586

    Article  Google Scholar 

  19. Kuno T, Nonoyama T, Hirao K, Kato K (2011) Influence of the charge relay effect on the silanol condensation reaction as a model for silica biomineralization. Langmuir 27:13154–13158

    CAS  Article  Google Scholar 

  20. Liang MK, Patwardhan SV, Danilovtseva EN, Annenkov VV, Perry CC (2009) Imidazole catalyzed silica synthesis: progress toward understanding the role of histidine in (bio)silicification. J Mater Res 24:1700–1708

    CAS  Article  Google Scholar 

  21. Luckarift H, Spain J, Naik R (2004) Enzyme immobilization in a biomimetic silica support. Nat Biotechnol 22:211–213

    CAS  Article  Google Scholar 

  22. Marron AO, Ratcliffe S, Wheeler GL, Goldstein RE, Nicole K, Not F, Vargas C, Richte DJ (2016) The evolution of silicon transport in eukaryotes. Mol Biol Evol 33:3226–3248

    CAS  Article  Google Scholar 

  23. Matsunaga S, Sakai R, Jimbo M, Kamiya H (2007) Long-chain polyamines (LCPAs) from marine sponge: possible implication in spicule formation. Chembiochem 8:1729–1735

    CAS  Article  Google Scholar 

  24. Mohri K, Nakatsukasa M, Masuda Y, Agata K, Funayama N (2008) Toward understanding the morphogenesis of siliceous spicules in freshwater sponge: differential mRNA expression of spicule-type-specific silicatein genes in Ephydatia fluviatilis. Dev Dyn 237:3024–3039

    CAS  Article  Google Scholar 

  25. Morse DE (1999) Silicon biotechnology: harnessing biological silica production to construct new materials. Trends Biotechnol 17:230–232

    CAS  Article  Google Scholar 

  26. Müller WE, Rothenberger M, Boreiko A, Tremel W, Reiber A, Schröder HC (2005) Formation of siliceous spicules in the marine demosponge Suberites domuncula. Cell Tissue Res 321:285–297

    Article  Google Scholar 

  27. Müller WE, Schlossmacher U, Eckert C, Krasko A, Boreiko A, Ushijima H, Wolf SE, Tremel W, Müller IM, Schröder HC (2007) Analysis of the axial filament in spicules of the demosponge Geodia cydonium: different silicatein composition in microscleres (asters) and megascleres (Oxeas and Triaenes). Eur J Cell Biol 86:473–487

    Article  Google Scholar 

  28. Nemoto M, Maeda Y, Muto M, Tanaka M, Yoshino T, Mayama S, Tanaka T (2014) Identification of a frustule-associated protein of the marine pennate diatom Fistulifera sp. strain JPCC DA0580. Mar Genomics 16:39–44

    Article  Google Scholar 

  29. Pozzolini M, Sturla L, Cerrano C, Bavestrello G, Camardella L, Parodi AM, Raheli F, Benatti U, Müller WEG, Giovine M (2004) Molecular cloning of silicatein gene from marine sponge Petrosia ficiformis (Porifera, Demospongiae) and development of primmorphs as a model for biosilicification studies. Mar Biotechnol 6:594–603

    CAS  Article  Google Scholar 

  30. Riesgo A, Maldnado M, López-Legentil S (2015) A proposal for the evolution of cathepsin and silicatein in sponges. J Mol Evol 80:278–291

    CAS  Article  Google Scholar 

  31. Scheffel A, Poulsen N, Shian S, Kröger N (2011) Nanopatterned protein microrings from a diatom that direct silica morphogenesis. PNAS 108:3175–3180

    CAS  Article  Google Scholar 

  32. Schlossmacher U, Wiens M, Schröder HC, Wang X, Jochum KP, Müller WEG (2011) Silintaphin-1--interaction with silicatein during structure-guiding bio-silica formation. FEBS J 278:1145–1155

    CAS  Article  Google Scholar 

  33. Shimizu K (2015) Marine silicon biotechnology. In: Kim SK (ed) Springer handbook of marine biotechnology. Springer Handbooks. Springer, Berlin

    Google Scholar 

  34. Shimizu K, Morse DE (2018) In: Moore BS (ed) Methods in enzymology, vol 605. Academic Press

  35. Shimizu K, Cha J, Stucky GD, Morse DE (1998) Silicatein alpha: cathepsin L-like protein in sponge biosilica. PNAS 95:6234–6238

    CAS  Article  Google Scholar 

  36. Shimizu K, Amano T, Bari MR, Weaver JC, Arima J, Mori N (2015) Glassin, a histidine-rich protein from the siliceous skeletal system of the marine sponge Euplectella, directs silica polycondensation. PNAS 112:11449–11454

    CAS  Article  Google Scholar 

  37. Tesson B, Lerch SJL, Hildebrand M (2017) Characterization of a new protein family associated with the silica deposition vesicle membrane enables genetic manipulation of diatom silica. Sci Rep 7:13457

    Article  Google Scholar 

  38. Wenzl S, Hett R, Richthammer P, Sumper M (2008) Silacidins: highly acidic phosphopeptides from diatom shells assist in silica precipitation in vitro. Angew Chem Int Ed 47:1729–1732

    CAS  Article  Google Scholar 

  39. Wiens M, Schröder HC, Wang X, Link T, Steindorf D, Müller WEG (2011) Isolation of the silicatein-a interactor silintaphin-2 by a novel solid-phase pull-down assay. Biochemistry 50:1981–1990

    CAS  Article  Google Scholar 

  40. Zhou Y, Shimizu K, Cha JN, Stucky GD, Morse DE (1999) Efficient catalysis of polysiloxane synthesis by Silicatein α requires specific Hydroxy and imidazole functionalities. Angew Chem Int Ed 38:779–782

    Article  Google Scholar 

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Funding

This work was supported by JSPS KAKENHI grant number JP15K06581.

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Correspondence to Katsuhiko Shimizu.

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Nishi, M., Kobayashi, H., Amano, T. et al. Identification of the Domains Involved in Promotion of Silica Formation in Glassin, a Protein Occluded in Hexactinellid Sponge Biosilica, for Development of a Tag for Purification and Immobilization of Recombinant Proteins. Mar Biotechnol 22, 739–747 (2020). https://doi.org/10.1007/s10126-020-09967-2

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Keywords

  • Biosilica
  • Porifera
  • Immobilization
  • Protein purification
  • Histidine
  • Metal affinity