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Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science

Abstract

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

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Figure 1: Integrating RNA-seq, proteomics and material science.
Figure 2: Marine snail egg-case bioelastomeric membranes and proteins.
Figure 3: Identification of green mussel (P. viridis) adhesive protein sequences.
Figure 4: Sucker ring teeth biomaterials from jumbo squid.
Figure 5: Solvent-free processing of thermoplastic suckerin.
Figure 6: Engineering of recombinant suckerin-39.

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Acknowledgements

We are grateful to H. Waite and S. Brenner for insightful discussions and suggestions. We thank J. Weaver, C. Salinas and D. DeMartini for help with Jumbo squid sucker teeth sample collection. G. Muniraj, L. Sellou and C. Sutanto assisted with extraction and purification of P. viridis and squid sucker teeth proteins. V. Gangu provided informatics support and S. Seah provided assistance with tyrosinase modeling. V. Lipik assisted with the acquisition of MALDI-TOF data. W.M. Guo helped with cell culture experiments. We thank K.S. Tan for his advice on snail biology and animal collection. V. Seow, E. Tay and A. Hermawan helped with sample collection and mechanical testing of P. cochlidium egg cases. This research was funded by the Singapore National Research Foundation (NRF) through a NRF Fellowship (A. Miserez), a Singapore Ministry of Education Tier 2 grant (A. Miserez, MOE2011-T2-2-044) and the Agency for Science, Technology and Research (A*Star) of Singapore (S.H., Y.S., F.T.W., V.H.B.H.). M.C.D. and A.P.-F. were supported by US National Institutes of Health grant no. 1R21HL112114-01.

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Contributions

P.A.G. and S.H. conducted molecular experiments and analyzed sequencing data. S.H. and K.W.K. generated and compiled RNA-seq data. A. Miserez and S.A. conducted and analyzed mechanical testing experiments. Y.S. conducted tyrosinase assays, conducted and analyzed qPCR data, and provided editorial comments. M.R. performed LC MS/MS experiments and analyzed the data with PEAKS. A. Masic conducted and interpreted Raman spectroscopy data. M.C.D. developed the idea of microwave heating of SRT proteins. A.P.-F. and M.C.D. conducted and analyzed the template wetting experiments with native and recombinant proteins and provided editorial comments. P.A.G. conceived and conducted the suckerin fiber and film engineering and characterization experiments and developed and conducted the photo cross-linking experiments. S.A. and G.Z.T. conducted Raman and FTIR experiments on drawn fibers. F.T.W. performed structural modeling of tyrosinases. K.W.K. and D.D. expressed and purified recombinant proteins. V.H.B.H. helped perform and analyze cell culture experiments. A. Miserez, P.A.G. and S.H. designed the study and wrote the paper.

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Correspondence to Ali Miserez.

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The authors declare no competing financial interests.

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Guerette, P., Hoon, S., Seow, Y. et al. Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science. Nat Biotechnol 31, 908–915 (2013). https://doi.org/10.1038/nbt.2671

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