Group of synthetic biology
Synthetic biology group, headed by Karen Sarkisyan, was formed in 2017 as a part of the Department of Biomolecular Chemistry. The main focus of research of the group is the development of new bioluminescence-based imaging technologies, with the focus on reporter tools for plants.
The group also works on protein design, molecular characterisation of new bioluminescent systems and identification of genes coding for biosynthesis of biologically active molecules.
The most up-to-date list of our publications is available from Google Scholar.
|Anastasia Balakireva, Ph.D.||r. email@example.com|
|Liliya Fakhranurova||r. f.|
|Arina Duf||t. q. - lab. as.|
Creation of plants with genetically encoded autoluminescence
In collaboration with Laboratory of molecular immunology,  Artificial Climate Station “BIOTRON”,  Laboratory of Chemistry of Metabolic Pathways,  Group of Plant Metabolic Engineering,  Group of molecular tags for optical nanoscopy,  Department of Biomolecular Chemistry
In Nature Biotechnology, scientists from IBCh RAS have announced the feasibility of creating plants that produce their own visible luminescence. It was revealed that bioluminescence found in some mushrooms is metabolically similar to the natural processes common among plants. By inserting DNA obtained from the mushroom Neonothopanus nambi, the scientists were able to create plants that glow much brighter than previously possible. Plants containing the mushroom DNA glow continuously throughout their lifecycle, from seedling to maturity. This biological light can be used for observing the inner workings of plants. In contrast to other commonly used forms of bioluminescence, such as from fireflies, unique chemical reagents are not necessary for sustaining mushroom bioluminescence.
- (2020). Plants with genetically encoded autoluminescence. Nat Biotechnol 38 (8), 944–946
Scientists uncovered a mechanism of fungal luminescence and created luminescent yeasts
In collaboration with Laboratory of Chemistry of Metabolic Pathways
Scientists from the Institute of Bioorganic Chemistry in Moscow and Krasnoyarsk Federal Research Center together with their Russian and foreign colleagues have fully described the mechanism of fungal luminescence. They found that fungi utilize only four key enzymes to produce light and that transfer of these enzymes into any other organisms makes them bioluminescent. To illustrate this, the authors have created a luminescent yeast strain visible to the naked eye. The theoretical and experimental parts of the study were supported by Russian Science Foundation. The results of the study are published in the journal Proceedings of the National Academy of Sciences.
Decoding of the mechanism of fungal luminescence become possible because of preceding research in this field. Back in the early 19th century, it was discovered that it was mycelium that made rotten trees glow. In 2009, Anderson G. Oliveira and Cassius V. Stevani, co-authors of the present paper, determined that a single biochemical mechanism is shared by all fungi emitting light. In 2015–2017, a team of Russian scientists led by Ilia Yampolsky made a series of key discoveries. In particular, the team determined the structure of luciferin, the molecule that emits light when oxidized.
- (2018). Genetically encodable bioluminescent system from fungi. Proc Natl Acad Sci U S A 115 (50), 12728–12732
A method of protein labeling in live cells based on fluorogen and fluorogen-binding protein
In collaboration with Laboratory of Chemistry of Metabolic Pathways,  Group of chemistry of heterocyclic compounds,  Laboratory of genetically encoded molecular tools
We developed a new method of target protein labeling called Protein-PAINT. This method is based on reversible binding of a protein domain with a fluorogenic dye that leads to a strong increase in fluorescence intensity. Using computer molecular docking we engineered three mutants of bacterial lipocalin Blc with different affinities to the fluorogen. It was shown that the fluorogen enters live cell quickly and stains target proteins fused with the Blc mutants. The new method ensures an order of magnitude higher photostability of the fluorescence signal in comparison with fluorescent proteins. Protein-PAINT also enables prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
- (2017). Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 8 (10), 7138–7142
Deep structure-functional analysis of amino acid substitutions on photophysical properties of green fluorescent proteins
In collaboration with Laboratory of genetically encoded molecular tools
A so called “fitness landscape” was for the first time experimentally probed at the whole protein level using GFP as a model. A unique approach developed in this work enabled to correlate a function (fluorescence) with amino acid sequence of several tens of thousands of random mutants, revealing a number of negative and positive epistatic interactions between substitutions. Characterization of the GFP fitness landscape allows for computer prediction of properties of new mutants of fluorescent proteins. It also has important implications for several fields including molecular evolution and protein design.
Using calculations of the possible electron transfer pathways from excited GFP chromophore to external molecules and further experimental verification of these hypotheses, we constructed mutants with blocked electron transfer pathway and correspondingly increased photostability. This strategy may represent a new approach toward enhancing photostability of fluorescent proteins.
Figure. (A) Scheme of GFP fitness landscape derived from analysis of 51000 mutants. The GFP sequence arranged in a circle, each column representing one amino acid site. In the first circle, the colour intensity of the squares indicates the brightness of a single mutation at the corresponding site relative to the wild type, shown in the centre. Sites with positive and negative epistatic interactions between pairs of mutations are connected by green and black lines, respectively. In circles further away from the centre, representing genotypes with multiple mutations, the fraction of the column coloured green (black) represents the fraction of genotypes corresponding to high (low) fluorescence among all assayed genotypes with a mutation at that site. (B) Electron transfer in GFP. Upper panel – scheme of calculated pathway of electron transfer from the chromophore to external acceptor molecule via tyrosine-145 as an intermediate electron acceptor. Bottom panel – photobleaching curves of EGFP and its mutants in the presence of oxidant in the medium, showing a dramatic enhancement of photostability due to blocking the electron transfer pathway.
- (2016). Local fitness landscape of the green fluorescent protein. Nature 533 (7603), 397–401
- (2016). Turning on and off Photoinduced Electron Transfer in Fluorescent Proteins by π-Stacking, Halide Binding, and Tyr145 Mutations. J Am Chem Soc 138 (14), 4807–4817
- (2017). Photoinduced chemistry in fluorescent proteins: Curse or blessing? Chem Rev 117 (2), 758–795