这个基础项目的主要目标是回答有关生命系统的结构和组织原理的基本问题。为寻找代谢反应的“核心”蛋白，工作中将软体动物纲细菌鸡毒支原体(Mycoplasma gallisepticum) 作为主要的模型研究对象。多年来我们致力于这种细菌的多组学研究，事实上，它是各种扰动模型中的最小细胞模型。
所获成果使我们可以将注意力集中在一系列能振荡的代谢反应上。糖酵解是活细胞中最重要和最广泛的途径，其反应具有振荡能力。在影响代谢反应的定性和定量组成的同时，改变振荡的频率和幅度，从而导致细胞的“化学心脏”的启动或停止。 查明此类反应是重建人造细胞的关键任务。
为了实施该项目，既可使用数学计算方法、建模，也可以使用实际操作细菌模型并利用细胞提取物或重组蛋白在脂质体中体外构建代谢途径，分析细胞中单独复合物存在的可能性- 糖酵解酶体 -研究这种结构中糖酵解酵素的性能机制。
除了基础作用外，该项目还具有应用作用：创建具有一组已知功能和指定属性的分子机器。
高可塑性、耐受性、快速有效地在群体水平而不是在细胞水平上产生对抗菌药物和毒素的耐药性的能力，尽管装置简单且支原体属细菌退化让人产生存在调节和适应这些微生物替代机制的想法。 由于缺乏刚性的细胞壁，支原体可能的适应性策略之一可能是通过改变细胞质的大小和/或密度、蛋白质复合物的重排来调节细胞体积。 为此，我们的科学团队使用不同的物理、生化和微观分析方法。 此外，作为替代研究对象，为了理解所研究的细胞调节替代机制的“普遍性”，我们使用了生物学家的经典模型——不同状态（杆状、丝状、原生质球状）的大肠杆菌（Escherichia coli）。
COVID-19疫情的后果表明，从体内消除病原体固然重要，分析感染新冠后出现的并发症机制也很重要。
研究单独的病毒蛋白对大型生物的影响使我们能够更详细地研究感染模式，同时找出涉及哪些代谢环节和结构成分。 这种方法将使我们能找出病毒发病机制中的新环节，从而使病毒可以被药物靶向。 此外，这项研究还将能够回答 SARS-CoV-2 病毒亚单位疫苗在多大程度上导致并发症发生的问题。
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Koksharova OA, Butenko IO, Govorun VM. beta-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study. Toxins (Basel) 2021 Apr 30;13(5):325. DOI: 10.3390/toxins13050325.
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Alekhina OM, Terenin IM, Dmitriev SE, Vassilenko KS. Functional cyclization of eukaryotic mRNAs. Int J Mol Sci. 2020, 21(5), 1677; https://doi.org/10.3390/ijms21051677
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Babenko VV, Podgorny OV, Manuvera VA, Kasianov AS, Manolov AI, Grafskaia EN, Shirokov DA, Kurdyumov AS, Vinogradov DV, Nikitina AS, Kovalchuk SI, Anikanov NA, Butenko IO, Pobeguts OV, Matyushkina DS, Rakitina DV, Kostryukova ES, Zgoda VG, Baskova IP, Trukhan VM, Gelfand MS, Govorun VM, Schiöth HB, Lazarev VN. Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches. BMC Genomics 2020 Apr 29;21(1):331. doi: 10.1186/s12864-020-6748-0. Erratum in: BMC Genomics. 2020 Jul 22;21(1):503.
Koksharova OA, Butenko IO, Govorun VM. Proteomic Insights into Starvation of Nitrogen-Replete Cells of Nostoc sp. PCC 7120 under beta-N-Methylamino-L-Alanine (BMAA) Treatment. Toxins (Basel) 2020,12(6), 372; https://doi.org/10.3390/toxins12060372.
Koksharova OA, Butenko IO, Govorun VM. The First Proteomic Study of Nostoc sp. PCC 7120 Exposed to Cyanotoxin BMAA under Nitrogen Starvation. Toxins (Basel) 2020 May 9;12(5):310. doi: 10.3390/toxins12050310.
Fedorov OV, Scherbinina SI, Levin VV, Dilman A D. Light-mediated dual phosphine-/copper-catalyzed atom-transfer radical addition reaction. J Org Chem. 2019, 84(17), 11068–11079.
Kamashev DE, Rakitina TV, Matyushkina DS, Evsyutina DV, Vanyushkina AA, Agapova YuK, Anisimova VE, Drobyshev AL, Butenko IO, Pobeguts OV, Fisunov GY. Proteome of HU-Lacking E. coli Studied by Means of 2D Gel Electrophoresis. Russian Journal of Bioorganic Chemistry 2019, 45: 366–373.
Gao F, Alekhina OM, Vassilenko KS, Simon AE. Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA. Nucleic Acids Research 2018, 46(22):11726-11742. DOI: 10.1093/nar/gky871.
Rubtsova M, Naraykina Yu, Vasilkova D, Meerson M, Zvereva M, Prassolov V, Lazarev V, Manuvera V, Kovalchuk S, Anikanov N, Butenko I, Pobeguts O, Govorun V, Dontsova O. Protein encoded in human telomerase RNA is involved in cell protective pathways. Nucleic Acids Research 2018, 46(17): 8966–8977.
Anufrieva KS, Shender VO, Arapidi GP, Pavlyukov MS, Shakhparonov MI, Shnaider PV, Butenko IO, Lagarkova MA, Govorun VM. Therapy-induced stress response is associated with downregulation of premRNA splicing in cancer cells. Genome Medicine 2018, 10: 49. https://doi.org/10.1186/s13073-018-0557-y.
Butenko I, Pobeguts O, Matyshkina D, Kovalchuk S, Anikanov N, Fisunov G, Govorun V. Data-independent proteome profile of Mycoplasma gallisepticum under normal conditions and heat stress. Data in Brief 2018, 16, 700-704.
Du Z, Alekhina OM, Vassilenko KS, Simon AE. Concerted action of two 3′ cap-independent translation enhancers increases the competitive strength of translated viral genomes. Nucleic Acids Research. 2017, 45(16), 9558-9572. DOI: 10.1093/nar/gkx643.
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Matyushkina DS, Butenko IO, Pobeguts OV, Fisunov GY, Govorun VM. Proteomic response of bacteria during the interaction with a host cell in a model of Mycoplasma gallisepticum. Russian Journal of Bioorganic Chemistry 2017, 43, 531–539.
Fisunov GY, Evsyutina DV, Garanina IA, Arzamasov AA, Butenko IO, Altukhov IA, Nikitina AS, Govorun VM. Ribosome profiling reveals an adaptation strategy of reduced bacterium to acute stress. Biochimie 2017, 132, 66-74.
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