Department of Biotechnology

Cell-free translation systems for bioengineering and synthetic biology

Description

The project is aimed at bioengineering developments and optimization of cell-free expression systems for the production of protein products. Using methods of genetic engineering, bioengineering, and synthetic biology, the capabilities of cell-free translation systems in biotechnology and the production of non-protein products are investigated

Goal

Bioengineering development and optimization of cell-free expression systems for the efficient production of protein products and non-protein compounds

Key objectives

1. Development and optimization of cell-free expression systems for the production of target protein products
2. Application of genetic engineering methods to improve the components of cell-free translation systems
3. Investigation of the capabilities of cell-free translation systems in biotechnology
4. Study of the potential of cell-free systems for the production of non-protein products
5. Integration of synthetic biology approaches to expand the functionality of cell-free expression systems

Partner organizations

• Lomonosov Moscow State University
• Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences
• Research Institute of Systems Biology and Medicine of Rospotrebnadzor

Publications

• Khabibullina NF, Tereshchenkov AG, Komarova ES, Syroegin EA, Shiriaev DI, Paleskava A, Kartsev VG, Bogdanov AA, Konevega AL, Dontsova OA, Sergiev PV, Osterman IA, Polikanov YS. Structure of Dirithromycin Bound to the Bacterial Ribosome Suggests New Ways for Rational Improvement of Macrolides. Antimicrob Agents Chemother. 2019 May 24;63(6):e02266-18. doi: 10.1128/AAC.02266-18
• Travin DY, Watson ZL, Metelev M, Ward FR, Osterman IA, Khven IM, Khabibullina NF, Serebryakova M, Mergaert P, Polikanov YS, Cate JHD, Severinov K. Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition. Nat Commun. 2019 Oct 8;10(1):4563. doi: 10.1038/s41467-019-12589-5.
• Metelev M, Osterman IA, Ghilarov D, Khabibullina NF, Yakimov A, Shabalin K, Utkina I, Travin DY, Komarova ES, Serebryakova M, Artamonova T, Khodorkovskii M, Konevega AL, Sergiev PV, Severinov K, Polikanov YS. Klebsazolicin inhibits 70S ribosome by obstructing the peptide exit tunnel. Nat Chem Biol. 2017 Oct;13(10):1129-1136. doi: 10.1038/nchembio.2462
• Osterman IA, Khabibullina NF, Komarova ES, Kasatsky P, Kartsev VG, Bogdanov AA, Dontsova OA, Konevega AL, Sergiev PV, Polikanov YS. Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state. Nucleic Acids Res. 2017 Jul 7;45(12):7507-7514. doi: 10.1093/nar/gkx413
• Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS. Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site. Nucleic Acids Res. 2019 Feb 28;47(4):2089-2100. doi: 10.1093/nar/gky1211
• Almutairi MM, Svetlov MS, Hansen DA, Khabibullina NF, Klepacki D, Kang HY, Sherman DH, Vázquez-Laslop N, Polikanov YS, Mankin AS. Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res. 2017 Sep 19;45(16):9573-9582. doi: 10.1093/nar/gkx673
• Khabibullina NF, Liukmanova EN, Kopeina GS, Shenkarev ZO, Arsen'ev AS, Dolgikh DA, Kirpichnikov MP. [The development and optimization of coupled cell-free expression system for production of the transmembrane domain of the receptor tyrosine kinase ErbB3]. Bioorg Khim. 2010 Sep-Oct;36(5):654-60. Russian. doi: 10.1134/s1068162010050080
• Lyukmanova EN, Shenkarev ZO, Khabibullina NF, Kulbatskiy DS, Shulepko MA, Petrovskaya LE, Arseniev AS, Dolgikh DA, Kirpichnikov MP. N-terminal fusion tags for effective production of g-protein-coupled receptors in bacterial cell-free systems. Acta Naturae. 2012 Oct;4(4):58-64
• Lyukmanova EN, Shenkarev ZO, Khabibullina NF, Kopeina GS, Shulepko MA, Paramonov AS, Mineev KS, Tikhonov RV, Shingarova LN, Petrovskaya LE, Dolgikh DA, Arseniev AS, Kirpichnikov MP. Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes. Biochim Biophys Acta. 2012 Mar;1818(3):349-58. doi: 10.1016/j.bbamem.2011.10.020
• Mineev KS, Khabibullina NF, Lyukmanova EN, Dolgikh DA, Kirpichnikov MP, Arseniev AS. Spatial structure and dimer--monomer equilibrium of the ErbB3 transmembrane domain in DPC micelles. Biochim Biophys Acta. 2011 Aug;1808(8):2081-8. doi: 10.1016/j.bbamem.2011.04.017