Genetically encoded click chemistry, an enabling tool for materials synthetic biology

doi:10.12211/2096-8280.2021-076

Abstract

Abstract:

Precise control over the structure and function of a material constitutes a fundamental challenge facing materials science. Due to the diverse specific interactions among biomolecules, direct assembly of biomolecules or even living cells into higher-order structures may provide a solution to this. In recent years, genetically encoded click chemistries (GECCs)-a collection of new protein chemistries that are inspired by the spontaneous isopeptide bond formation within naturally occurring microbial proteins-have gained traction among materials scientists. They are able to covalently assemble functional protein molecules directly into advanced architectures, with efficiency and selectivity rivaling traditional click reactions, while conferring genetic programmability on the resulting materials. These tools have facilitated the integration of protein engineering, materials science, and synthetic biology, and thus have opened enormous opportunities for the cross-disciplinary research. Here, we provide a concise review and discussion over the recent developments and applications of these protein chemistries, and the trends thereof. We compare the GECCs of different generations in reactivities, examine the synthesis of various uncommon protein molecule enabled by protein topology engineering, glance over the entirely protein-based hydrogels with dynamically tunable properties or underwater adhesiveness assembled via GECCs, glimpse into the design of subunit vaccines, especially those against COVID-19, and further explore the modulation of genetically engineered living materials by GECCs, featuring self-production, micropatterning, and self-assembly. Despite the tangible potential held by these molecular tools, unceasing protein engineering efforts remain necessary to further optimize and expand the arsenal of GECCs. As their chemical reactivities are fully encoded within the information (i.e., the amino acid sequence), GECCs may also serve as a source of inspiration to develop new chemistries for other synthetic information polymers in a broader term. Together, this emerging GECC toolbox has greatly empowered materials synthetic biology and will continue to provide solutions and inspirations for new biotechnologies.

Key words: genetically encoded click chemistry, hydrogel, vaccine, protein topology engineering, living material

摘要：

对材料的结构与功能实现精准控制是材料学领域的根本挑战之一。很多生物大分子之间具有多种特异性的反应，利用这些特异性反应将生物大分子乃至活体细胞直接组装成更高级的结构提供了一种可能的解决方案。为了实现这种特异有效的组装，借鉴于传统的点击化学，可基因编码点击化学应运而生。这套新的蛋白质化学源于自然界微生物中的异肽键化学，通过基因编辑的方式控制功能化蛋白质分子的自组装反应，同时具有点击化学的高效等优点，经过多种优化之后在合成生物学中被广泛运用。其发展和应用有力促进了蛋白质工程、材料学与合成生物学的交叉融合。本文简要介绍了可基因编码点击化学在近年的应用，包括以多种非线性蛋白质分子为代表的蛋白质拓扑工程产物、多种具有不同功能的全蛋白质水凝胶材料、重组疫苗及工程活体材料等，并总结了其发展潜力。

关键词: 可基因编码点击化学, 水凝胶, 疫苗, 蛋白质拓扑工程, 活体材料

CLC Number:

Q816

Qikun YI, Chenbo SUN, Zhongguang YANG, Ri WANG, Songzi KOU, Zhaoxia LI, Fei SUN. Genetically encoded click chemistry, an enabling tool for materials synthetic biology[J]. Synthetic Biology Journal, 2022, 3(4): 690-708.

易琪昆, 孙晨博, 杨中光, 王日, 寇松姿, 李朝霞, 孙飞. 可基因编码点击化学在材料合成生物学中的应用[J]. 合成生物学, 2022, 3(4): 690-708.

Figures/Tables 9

Fig. 2 Controlling the protein topological structures

Fig. 3 Development of entirely protein-based hydrogels based on GECC(Adapted from Ref. 49 with permission from National Academy of Sciences, copyright 2014.)LIF—Leukemia inhibitory factor; A-LIF-A—SpyTag-ELP-LIF-LEP-SpyTag

Fig. 4 Development of smart photo-responsive hydrogel based on GECCAdapted from Ref. 52 with permission from National Academy of Sciences, copyright 2017.(a) Constructing CarHc into linear polymer utilizing SpyChemistry, which can undergo liquid-to-solid phase transition induced by AdoB12, and solid-to-liquid phase transition induced by light. (b) Photo-induced release of 3T3 cells or hMSCs.

Fig. 5 Applying GECC to develop heavy-metal binding protein hydrogelAdapted from Ref. 51 with permission from The Royal Society of Chemistry, copyright 2017.(a) Synthesis of super uranyl-binding protein (SUP) materials and chromate-binding protein materials. (b) Uranium extraction from seawater using the hydrogels comprising SUP or its mutant, SUP-E64D, which exhibits stronger uranyl binding. Enrichment index was calculated as the ratio of uranium concentration in protien material to that in water body after enrichment. (c) Removal of chromate from tap water using ModA hydrogels. Removal percentage was calculated as the reduced percentage of chromate in water body after removal. Removal efficiency was calculated as the ratio of the actual amount of chromate absorbed by the material to the theoretical maximum by the material.

Fig. 6 Application of GECC in recombinant protein vaccines

Fig. 7 GECC and engineered living materials(a) Features of engineered living materials. (b) Decoration of E. coli biofilm via GECC. (c) Decoration of 2D hexameric protein lattice (S-layer) on the surface of C. crescentus via GECC. Left: SpyTagged S-layer visualized by AFM. Scale bar: 40 nm. Right: the C. crescentus material labelled with SpyCatcher-mRFP1 imaged via fluorescence microscopy. Scale bar: 3 μm.

Fig. 8 Smart production platform enabled by GECC.

Fig. 9 GECC-based self-assembled E. coli living material and its features(a) Diagram of GECC-based self-assembled E. coli living material[118]. (b) Self-assembled engineered living materials with core-shell structure, scale bar: 100 μm. (c) Intercellular assembly enabled by Spy chemistry activates quorum sensing. AHL, N-Acyl-Homoserine Lactone, an autoinducer of quorum sening. The green fluorescent protein, mWasabi, served as a reporter of quorum sensing. L-Arabinose (L-Ara) was used to induce the expression of SpyTag and SpyCatcher. Scale bar: 100 μm.

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