St Petersburg State University, Department of Genetics and Biotechnology
RESEARCH, TEACHING, or OTHER INTERESTS
Biochemistry, Genetics and Molecular Biology
12
Scopus Publications
Scopus Publications
Evaluation of Selective Agent Requirements for Pea Callus Culture Expressing Foreign DNA Veronika Yu. Simonova, Elina A. Potsenkovskaia, Alexandra A. Vanina, Anna S. Kiseleva, Andrew G. Matveenko, Daria B. Pavlova, Kirill V. Smirnov, Elena P. Efremova, Anna V. Brynchikova, Varvara E. Tvorogova Ecological Genetics, 2026 BACKGROUND: Genetic modification of pea remains challenging, which can likely be attributed to its low regeneration efficiency. To obtain transgenic pea plants, shoot regeneration followed by rooting is usually applied. Another regeneration pathway, somatic embryogenesis, is not used for pea genome modification due to very low frequency of this process. If a gene stimulating somatic embryogenesis was identified, it could be used as a morphogenic regulator to enable regeneration of pea plants from genetically modified callus cells. The search for such genes relies on the development of a cultivation system, allowing production of a significant amount of callus tissue in which a potential morphogenic regulator is ectopically expressed.AIM: The aim of study was to evaluate the possibility of obtaining pea callus tissue expressing foreign DNA with or without usage of selective agents, specifically, kanamycin and hygromycin B.METHODS: In this study, we combined agrobacterial transformation protocol with a method of callus induction from pea shoot apex explants. To evaluate the effectiveness of this transformation system with different selective agents, we used two different reporters: RUBY and DsRed.RESULTS: Our results demonstrate that transformation of pea shoot apices using the developed system yields a significant percentage of calli containing tissue regions which express foreign DNA. Addition of the antibiotics as selective agents doesn’t increase frequency of calli expressing introduced DNA.CONCLUSION: Results obtained in this study suggest that searching for regeneration stimulators is feasible in Pisum sativum without usage of selective agents.
Peas in Rouge: Tyrosine Supplementation Enhances RUBY Reporter Visibility in Pisum sativum Veronika Simonova, Elina Potsenkovskaia, Nikolai Kozlov, Alexandra Vanina, Elena Efremova, Kirill Smirnov, Anastasia Artemiuk, Anna Kiseleva, Anna Brynchikova, Zakhar Konstantinov, Varvara Tvorogova Plants, 2025 Genome modification of legumes, peas in particular, is accompanied by significant challenges. Establishing a reliable reporter system to identify tissue that expresses foreign DNA may help to optimize and develop transformation protocols for these species. The RUBY system, based on the synthesis of red betalain from tyrosine, offers a convenient solution for monitoring the efficiency of transgene introduction. To evaluate the effectiveness of RUBY application in pea tissue culture, we combined agrobacterial transformation with an in vitro cultivation system, inducing callus development. Transformed explants demonstrated RUBY pigmentation, but it disappeared during cultivation. We hypothesized that this issue is caused by tyrosine depletion. To check this suggestion, we tested whether tyrosine supplementation could maintain RUBY coloring. In the later stages, pigmentation still could not be preserved. However, our modified conditions increased the percent of colored shoot apex explants during the early cultivation stages. Thus, it is likely that some explants transformed with the RUBY cassette do not synthesize a sufficient amount of betalain due to the deficit of endogenous tyrosine. In this case, adding exogenous tyrosine would enhance betalain production and improve the detectability of tissues containing the RUBY cassette. These data can be used for the optimization of RUBY application conditions for peas and other species.
Gene Expression Analysis of Yeast Strains with a Nonsense Mutation in the eRF3-Coding Gene Highlights Possible Mechanisms of Adaptation Evgeniia M. Maksiutenko, Yury A. Barbitoff, Lavrentii G. Danilov, Andrew G. Matveenko, Olga M. Zemlyanko, Elena P. Efremova, Svetlana E. Moskalenko, Galina A. Zhouravleva International Journal of Molecular Sciences, 2024 In yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 (Sup45) and eRF3 (Sup35), which are essential for viability. Previous studies have revealed that presence of nonsense mutations in these genes leads to amplification of mutant alleles (sup35-n and sup45-n), which appears to be necessary for the viability of such cells. However, the mechanism of this phenomenon remained unclear. In this study, we used RNA-Seq and proteome analysis to reveal the complete set of gene expression changes that occur during cellular adaptation to the introduction of the sup35-218 nonsense allele. Our analysis demonstrated significant changes in the transcription of genes that control the cell cycle: decreases in the expression of genes of the anaphase promoting complex APC/C (APC9, CDC23) and their activator CDC20, and increases in the expression of the transcription factor FKH1, the main cell cycle kinase CDC28, and cyclins that induce DNA biosynthesis. We propose a model according to which yeast adaptation to nonsense mutations in the translation termination factor genes occurs as a result of a delayed cell cycle progression beyond the G2-M stage, which leads to an extension of the S and G2 phases and an increase in the number of copies of the mutant sup35-n allele.
Application of Flow Cytometry for Viability Assay of Mutants for Translation Termination Factors in the Yeast Saccharomyces cerevisiae E. P. Efremova, O. M. Zemlyanko, G. A. Zhouravleva Microbiology Russian Federation, 2024 Abstract Nonsense mutations in the essential SUP45 and SUP35 genes encoding translation termination factors affect the viability of Saccharomyces cerevisiae cells. Flow cytometry revealed that the viability of the mutants was 3.5‒4 times lower compared to the wild-type strains. Moreover, the mutants were found to have higher sensitivity to ultrasonic treatment.
The WOX Genes from the Intermediate Clade: Influence on the Somatic Embryogenesis in Medicago truncatula Daria V. Yakovleva, Elena P. Efremova, Kirill V. Smirnov, Veronika Y. Simonova, Zakhar S. Konstantinov, Varvara E. Tvorogova, Ludmila A. Lutova Plants, 2024 Transcription factors from the WOX family are well-known regulators of cell proliferation and differentiation in plants. Herein, we focused on several WOX genes from the intermediate clade and checked their impact on somatic embryogenesis using the model legume object Medicago truncatula. As a result, we show that MtWOX9-1 overexpression not only stimulates somatic embryogenesis in the embryogenic M. truncatula line, as it was shown previously, but can also induce somatic embryogenesis in the non-embryogenic line. Other intermediate clade WOX, including the close paralog of MtWOX9-1, as well as WOX11 homologs, did not have any significant impact on somatic embryogenesis in our in vitro cultivation system. Together, our results give new information about the diversity of the WOX family proteins and their specific functions. These data can be used for the search of new regeneration stimulators.
MtWOX2 and MtWOX9-1 Effects on the Embryogenic Callus Transcriptome in Medicago truncatula Elizaveta Y. Krasnoperova, Varvara E. Tvorogova, Kirill V. Smirnov, Elena P. Efremova, Elina A. Potsenkovskaia, Anastasia M. Artemiuk, Zakhar S. Konstantinov, Veronika Y. Simonova, Anna V. Brynchikova, Daria V. Yakovleva, Daria B. Pavlova, Ludmila A. Lutova Plants, 2024 WOX family transcription factors are well-known regulators of plant development, controlling cell proliferation and differentiation in diverse organs and tissues. Several WOX genes have been shown to participate in regeneration processes which take place in plant cell cultures in vitro, but the effects of most of them on tissue culture development have not been discovered yet. In this study, we evaluated the effects of MtWOX2 gene overexpression on the embryogenic callus development and transcriptomic state in Medicago truncatula. According to our results, overexpression of MtWOX2 leads to an increase in callus weight. Furthermore, transcriptomic changes in MtWOX2 overexpressing calli are, to a large extent, opposite to the changes caused by overexpression of MtWOX9-1, a somatic embryogenesis stimulator. These results add new information about the mechanisms of interaction between different WOX genes and can be useful for the search of new regeneration regulators.
Functional Modules in the Meristems: “Tinkering” in Action Ksenia Kuznetsova, Elena Efremova, Irina Dodueva, Maria Lebedeva, Ludmila Lutova Plants, 2023 Background: A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems—structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). Conclusions: The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
MtCLE08, MtCLE16, and MtCLE18 Transcription Patterns and Their Possible Functions in the Embryogenic Calli of Medicago truncatula Andrei A. Kudriashov, Natalia S. Zlydneva, Elena P. Efremova, Varvara E. Tvorogova, Ludmila A. Lutova Plants, 2023 CLE peptides are well-known hormonal regulators of plant development, but their role in somatic embryogenesis remains undetermined. CLE genes are often regulated by WOX transcription factors and, in their turn, regulate the expression level of WOX genes. In this study, we used in vitro cultivation, as well as qPCR and transcriptomic analysis, to find CLE peptides which could regulate the MtWOX9-1 gene, stimulating somatic embryogenesis in Medicago truncatula. Three CLE peptides were found which could probably be such regulators, but none of them was found to influence MtWOX9-1 expression in the embryogenic calli. Nevertheless, overexpression of one of CLE genes under study, MtCLE16, decreased somatic embryogenesis intensity. Additionally, overexpression of MtCLE08 was found to suppress expression of MtWOX13a, a supposed antagonist of somatic embryo development. Our findings can be helpful for the search for new regeneration regulators which could be used for plant transformation.
The MtWOX genes in the regulation of Medicago truncatula somatic embryogenesis Elena P. Efremova, Varvara E. Tvorogova, Ludmila A. Lutova Ecological Genetics, 2023 Plant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form embryos in a process called somatic embryogenesis (SE). SE can occur naturally in some plant species and it is widely used for the plant’s genetic transformation and regeneration.
 This process is regulated by hormone treatment and many proteins, among which WUSCHEL-related homeobox (WOX) transcription factors are believed to play crucial roles. Our previous studies have shown thatMtWOX9-1stimulates SE inMedicago truncatula. The aim of the present research was to search for newMtWOXgenes regulating SE. In this study, using transcriptomic data and literature data, we had selected several genes with an increased expression level during SE or in the generative organs and examined the overexpression effect of these genes on the SE ability. It was found that explants of theM.truncatulaembryogenic line, transformed with the construct forMtWOX6-likeoverexpression, develop more somatic embryos compared to the control.
 Our findings could be a helpful point for searching and studying new morphogenic regulators controlling SE and could have a positive impact on plant biotechnology in improving the transformation and regeneration capacity for other legumes.
 This work was supported by the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 date 22.04.2022 on providing a grant in the form of subsidies from the Federal budget of Russian Federation. The grant was provided for state support for the creation and development of a World-class Scientific Center “Agrotechnologies for the Future”.
Stanislava I. Narbut, the author of the first radish genetic collection in Russia Ksenia A. Kuznetsova, Elena P. Efremova, Irina S. Buzovkina, Irina E. Dodueva, Ludmila A. Lutova Ecological Genetics, 2023 Stanislava Iosifovna Narbut (19092001) was an agronomist, a graduate of the Leningrad Agricultural Institute. She worked as a Senior Researcher at the Plant Genetics Laboratory of the Biological Research Institute of the Leningrad State University from 1949 to 1985. S.I. Narbut was a creator of radish inbred lines genetic collection at Leningrad State University. This article discusses the main milestones of S.I. Narbuts biography and presents a series of previously unpublished photographs and memoirs of her colleagues and students.
