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Suhorukova AV, Sobolev DS, Milovskaya IG, Fadeev VS, Goldenkova-Pavlova IV, Tyurin AA. A Molecular Orchestration of Plant Translation under Abiotic Stress. Cells 2023; 12:2445. [PMID: 37887289 PMCID: PMC10605726 DOI: 10.3390/cells12202445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.
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Deyneko IV, Mustafaev ON, Tyurin AА, Zhukova KV, Varzari A, Goldenkova-Pavlova IV. Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes. BMC Bioinformatics 2022; 23:488. [DOI: 10.1186/s12859-022-05023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/29/2022] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
RNA-seq has become a standard technology to quantify mRNA. The measured values usually vary by several orders of magnitude, and while the detection of differences at high values is statistically well grounded, the significance of the differences for rare mRNAs can be weakened by the presence of biological and technical noise.
Results
We have developed a method for cleaning RNA-seq data, which improves the detection of differentially expressed genes and specifically genes with low to moderate transcription. Using a data modeling approach, parameters of randomly distributed mRNA counts are identified and reads, most probably originating from technical noise, are removed. We demonstrate that the removal of this random component leads to the significant increase in the number of detected differentially expressed genes, more significant pvalues and no bias towards low-count genes.
Conclusion
Application of RNAdeNoise to our RNA-seq data on polysome profiling and several published RNA-seq datasets reveals its suitability for different organisms and sequencing technologies such as Illumina and BGI, shows improved detection of differentially expressed genes, and excludes the subjective setting of thresholds for minimal RNA counts. The program, RNA-seq data, resulted gene lists and examples of use are in the supplementary data and at https://github.com/Deyneko/RNAdeNoise.
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Suhorukova AV, Tyurin AA, Pavlenko OS, Mustafayev ON, Sinelnikov IG, Goldenkova-Pavlova IV. Development of dual reporter vector system for estimating translational activity of regulatory elements. BMC Plant Biol 2022; 22:356. [PMID: 35864445 PMCID: PMC9306140 DOI: 10.1186/s12870-022-03735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND For the needs of modern biotechnology, a quantitative approach to the control of regulatory elements at all stages of gene expression has long become indispensable. Such a control regime is impossible without a quantitative analysis of the role of each regulatory element or pattern used. Therefore, it seems important to modify and develop the accuracy, reproducibility, and availability of methods for quantifying the contribution of each regulatory code to the implementation of genetic information. RESULTS A new vector system for transient expression in plants is described; this system is intended for quantitative analysis of the contribution of regulatory elements to transcription and translation efficiencies. The proposed vector comprises two expression cassettes carrying reporter genes (of the Clostridium thermocellum thermostable lichenase and E. coli β-glucuronidase) under the control of different promoters. Herewith we also propose a new method for quantification of the effect of tested regulatory elements on expression, which relies on assessment of the enzyme activities of reporter proteins taking into account the transcription of their genes. CONCLUSIONS In our view, this approach makes it possible to precisely determine the amounts of reporter proteins and their transcripts at all stages of expression. The efficiency of the proposed system has been validated by the analysis of the roles of known translation enhancers at the stages of transcription and translation.
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Affiliation(s)
- Aleksandra V. Suhorukova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A. Tyurin
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga S. Pavlenko
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Orkhan N. Mustafayev
- Genetic resources institute, Azerbaijan National Academy of Sciences, Baku, Azerbaijan
| | - Igor G. Sinelnikov
- Laboratory of enzyme biotechnology, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Goldenkova-Pavlova
- Laboratory of functional genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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Tsypurskaya EV, Nikolaeva TN, Lapshin PV, Nechaeva TL, Yuorieva NO, Baranova EN, Derevyagina MK, Nazarenko LV, Goldenkova-Pavlova IV, Zagoskina NV. Response of Transgenic Potato Plants Expressing Heterologous Genes of ∆9- or ∆12-Acyl-lipid Desaturases to Phytophthora infestans Infection. Plants (Basel) 2022; 11:plants11030288. [PMID: 35161270 PMCID: PMC8840463 DOI: 10.3390/plants11030288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 05/29/2023]
Abstract
Late blight is one of the most economically important diseases affecting potato and causing a significant loss in yield. The development of transgenic potato plants with enhanced resistance to infection by Phytophthora infestans may represent a possible approach to solving this issue. A comparative study of the leaf response in control potato plants (S.tuberosum L. cultivar Skoroplodnyi), control transgenic plants expressing the reporter gene of thermostable lichenase (transgenic licBM3 line) and transgenic plants expressing cyanobacterial hybrid genes ∆9-acyl-lipid desaturase (transgenic desC lines) and ∆12-acyl-lipid desaturase (transgenic desA lines) to infection with P. infestans has been performed. The expression of desaturase genes in potato plants enhanced their tolerance to potato late blight agents as compared with the control. The lipid peroxidation level raised in the leaves of the control and transgenic desA plants on third day after inoculation with P. infestans zoospores and remained the same in the transgenic desC plants. The number of total phenolic compounds was increased as early as on the second day after infection in all studied variants and continued to remain the same, except for transgenic desC plants. Accumulation of flavonoids, the main components of the potato leaf phenolic complex, raised on the second day in all studied variants, remained unchanged on the third day in the control plants and decreased in most transgenic plants expressing desaturase genes. The results obtained in our study demonstrate that the expression of genes of Δ9- and Δ12-acyl-lipid desaturases in potato plants enhanced their resistance to P. infestans as compared with the control non-transgenic plants due to concomitant accumulation of phenolic compounds, including flavonoids, in the leaves. All these changes were more pronounced in transgenic desC plants, which indicates that the Δ9-acyllipid desaturase gene appears to be a potential inducer of the production of biological antioxidants in plant cells.
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Affiliation(s)
- Elena V. Tsypurskaya
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Tatiana N. Nikolaeva
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Petr V. Lapshin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Tatiana L. Nechaeva
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Natalya O. Yuorieva
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Ekaterina N. Baranova
- N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia
- All Russia Research Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, 127550 Moscow, Russia
| | | | - Lyudmila V. Nazarenko
- Department of Biology and Human Physiology, Institute of Natural Sciences and Sports Technologies, Moscow City Teachers’ Training University, 129226 Moscow, Russia;
| | - Irina V. Goldenkova-Pavlova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
| | - Natalia V. Zagoskina
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (T.N.N.); (P.V.L.); (T.L.N.); (N.O.Y.); (I.V.G.-P.)
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Tyurin AA, Suhorukova AV, Deineko IV, Pavlenko OS, Fridman VA, Goldenkova-Pavlova IV. A high throughput assay of lichenase activity with Congo red dye in plants. Plant Methods 2021; 17:102. [PMID: 34627294 PMCID: PMC8501550 DOI: 10.1186/s13007-021-00801-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/17/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Since the beginning of the use of reporter proteins for expression analysis, a variety of approaches have been developed and proposed; both qualitative and quantitative. The lack of simple methods for direct observation of gene expression in living organisms makes it necessary to continue to propose new methods. In this work, we consider a method for the quantitative analysis of the expression of thermostable lichenase from Clostridium thermocellum used as a sensitive reporter protein. RESULTS In this study, we report the design a high throughput fluorometric method for quantification of thermostable lichenase C. thermocellum using Congo red and further experimental verification of its relevance and efficiency in assessment of the functional role of regulatory sequences in the plant cell. CONCLUSIONS The specific interaction between the dye Congo red and [Formula: see text]-D-glucans formed the background for designing a high-throughput fluorometric assay for quantification of C. thermocellum thermostable lichenase as a reporter protein for plants. This assay (i) makes it possible to precisely measure the amount of reporter protein in a plant sample; (ii) has shown a high sensitivity for quantification of thermostable lichenase; (iii) is more time- and cost-efficient as compared with the Somogyi-Nelson assay; and (iv) is to the least degree dependent on the presence of the tested buffer components as compared with the Somogyi-Nelson assay.
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Affiliation(s)
- Alexander A. Tyurin
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra V. Suhorukova
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Igor V. Deineko
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga S. Pavlenko
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Viktoriia A. Fridman
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Irina V. Goldenkova-Pavlova
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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Tyurin AA, Suhorukova AV, Kabardaeva KV, Goldenkova-Pavlova IV. Transient Gene Expression is an Effective Experimental Tool for the Research into the Fine Mechanisms of Plant Gene Function: Advantages, Limitations, and Solutions. Plants (Basel) 2020; 9:E1187. [PMID: 32933006 PMCID: PMC7569937 DOI: 10.3390/plants9091187] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
A large data array on plant gene expression accumulated thanks to comparative omic studies directs the efforts of researchers to the specific or fine effects of the target gene functions and, as a consequence, elaboration of relatively simple and concurrently effective approaches allowing for the insight into the physiological role of gene products. Numerous studies have convincingly demonstrated the efficacy of transient expression strategy for characterization of the plant gene functions. The review goals are (i) to consider the advantages and limitations of different plant systems and methods of transient expression used to find out the role of gene products; (ii) to summarize the current data on the use of the transient expression approaches for the insight into fine mechanisms underlying the gene function; and (iii) to outline the accomplishments in efficient transient expression of plant genes. In general, the review discusses the main and critical steps in each of the methods of transient gene expression in plants; areas of their application; main results obtained using plant objects; their contribution to our knowledge about the fine mechanisms of the plant gene functions underlying plant growth and development; and clarification of the mechanisms regulating complex metabolic pathways.
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Affiliation(s)
| | | | | | - Irina V. Goldenkova-Pavlova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences (IPP RAS), Moscow 127276, Russia; (A.A.T.); (A.V.S.); (K.V.K.)
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Pavlenko OS, Gra OA, Mustafaev ON, Kabarbaeva KV, Sadovskaya NS, Tyurin AA, Fadeev VS, Goldenkova-Pavlova IV. Thermostable Lichenase from Clostridium thermocellum as a Host Protein in the Domain Insertion Approach. Biochemistry (Mosc) 2019; 84:931-940. [PMID: 31522675 DOI: 10.1134/s0006297919080091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
Abstract
Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.73 (P29716)) has been tested for the insertion of two model fluorescent proteins (EGFP and TagRFP) into two regions of this enzyme. Functional folding of the resulting proteins was confirmed by retention of lichenase activity and EGFP and TagRFP fluorescence. These results convincingly demonstrate that (i) the two experimentally selected lichenase loop regions may serve as the areas for domain insertion without disturbing enzyme folding in vivo; (ii) lichenase permits not only single but also tandem insertions of large protein domains. High specific activity, outstanding thermostability, and efficient in vitro refolding of thermostable lichenase make it an attractive new host protein for the insertional fusion of domains in the engineering of multifunctional proteins.
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Affiliation(s)
- O S Pavlenko
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
| | - O A Gra
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - O N Mustafaev
- Baku State University, Department of Biophysics and Molecular Biology, Baku, AZ1106, Azerbaijan.
| | - K V Kabarbaeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - N S Sadovskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - A A Tyurin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - V S Fadeev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - I V Goldenkova-Pavlova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
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Goldenkova-Pavlova IV, Pavlenko OS, Mustafaev ON, Deyneko IV, Kabardaeva KV, Tyurin AA. Computational and Experimental Tools to Monitor the Changes in Translation Efficiency of Plant mRNA on a Genome-Wide Scale: Advantages, Limitations, and Solutions. Int J Mol Sci 2018; 20:E33. [PMID: 30577638 PMCID: PMC6337405 DOI: 10.3390/ijms20010033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
The control of translation in the course of gene expression regulation plays a crucial role in plants' cellular events and, particularly, in responses to environmental factors. The paradox of the great variance between levels of mRNAs and their protein products in eukaryotic cells, including plants, requires thorough investigation of the regulatory mechanisms of translation. A wide and amazingly complex network of mechanisms decoding the plant genome into proteome challenges researchers to design new methods for genome-wide analysis of translational control, develop computational algorithms detecting regulatory mRNA contexts, and to establish rules underlying differential translation. The aims of this review are to (i) describe the experimental approaches for investigation of differential translation in plants on a genome-wide scale; (ii) summarize the current data on computational algorithms for detection of specific structure⁻function features and key determinants in plant mRNAs and their correlation with translation efficiency; (iii) highlight the methods for experimental verification of existed and theoretically predicted features within plant mRNAs important for their differential translation; and finally (iv) to discuss the perspectives of discovering the specific structural features of plant mRNA that mediate differential translation control by the combination of computational and experimental approaches.
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Affiliation(s)
- Irina V Goldenkova-Pavlova
- Group of Functional Genomics, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, Moscow 127276, Russia.
| | - Olga S Pavlenko
- Group of Functional Genomics, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, Moscow 127276, Russia.
| | - Orkhan N Mustafaev
- Department of Biophysics and Molecular Biology, Baku State University, Zahid Khalilov Str. 23, Baku AZ 1148, Azerbaijan.
| | - Igor V Deyneko
- Group of Functional Genomics, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, Moscow 127276, Russia.
| | - Ksenya V Kabardaeva
- Group of Functional Genomics, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, Moscow 127276, Russia.
| | - Alexander A Tyurin
- Group of Functional Genomics, Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya str. 35, Moscow 127276, Russia.
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Vasina DV, Mustafaev ON, Moiseenko KV, Sadovskaya NS, Glazunova OA, Tyurin АА, Fedorova TV, Pavlov AR, Tyazhelova TV, Goldenkova-Pavlova IV, Koroleva OV. The Trametes hirsuta 072 laccase multigene family: Genes identification and transcriptional analysis under copper ions induction. Biochimie 2015. [PMID: 26196690 DOI: 10.1016/j.biochi.2015.07.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Laccases, blue copper-containing oxidases, ≿ an play an important role in a variety of natural processes. The majority of fungal laccases are encoded by multigene families that express closely related proteins with distinct functions. Currently, only the properties of major gene products of the fungal laccase families have been described. Our study is focused on identification and characterization of laccase genes, which are transcribed in basidiomycete Trametes hirsuta 072, an efficient lignin degrader, in a liquid medium, both without and with induction of laccase transcription by copper ions. We carried out production of cDNA libraries from total fungal RNA, followed by suppression subtractive hybridization and mirror orientation selection procedures, and then used Next Generation Sequencing to identify low abundance and differentially expressed laccase transcripts. This approach resulted in description of five laccase genes of the fungal family, which, according to the phylogenetic analysis, belong to distinct clusters within the Trametes genus. Further analysis established similarity of physical, chemical, and catalytic properties between laccases inside each cluster. Structural modeling suggested importance of the sequence differences in the clusters for laccase substrate specificity and catalytic efficiency. The implications of the laccase variations for the fungal physiology are discussed.
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Affiliation(s)
- Daria V Vasina
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia.
| | - Orkhan N Mustafaev
- Institute of Plant Physiology, Russian Academy of Sciences, st. Botanicheskaya, 35, Moscow 127276, Russia
| | - Konstantin V Moiseenko
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
| | - Natalia S Sadovskaya
- Institute of Plant Physiology, Russian Academy of Sciences, st. Botanicheskaya, 35, Moscow 127276, Russia
| | - Olga A Glazunova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
| | - Аlexander А Tyurin
- Institute of Plant Physiology, Russian Academy of Sciences, st. Botanicheskaya, 35, Moscow 127276, Russia
| | - Tatiana V Fedorova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
| | - Andrey R Pavlov
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
| | - Tatiana V Tyazhelova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
| | - Irina V Goldenkova-Pavlova
- Institute of Plant Physiology, Russian Academy of Sciences, st. Botanicheskaya, 35, Moscow 127276, Russia
| | - Olga V Koroleva
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky prospekt, 33, build. 2, Moscow 119071, Russia
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Zagoskina NV, Priadekhina EV, Lapshin PV, Iur'eva NO, Goldenkova-Pavlova IV. [Morphophysiological and biochemical characteristics of potato plants with various expression rates of the Δ12 acyl-lipid desaturase gene]. Izv Akad Nauk Ser Biol 2014:142-149. [PMID: 25735165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This paper reports on morphophysiological and biochemical characteristics of control and potato plants (Solarium tuberosum L., Skoroplodnyi cultivar) transformed with the Δ12 acyl-lipid desaturase gene (desA) grown long-term in vitro. The transformed plants showed faster growth and faster ontogenesis as compared to controls, which was accompanied with changes in the accumulation of photosynthetic pigments (chlorophylls a and b, carotenoids) and phenolic compounds, including flavonoids in the leaves. These characteristics were pronounced to a high degree in Line II plants with high expression rates of the desA gene, whereas Line I plants (moderate expression rate) were similar to control plants in many parameters.
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Vasina DV, Loginov DS, Mustafaev ON, Goldenkova-Pavlova IV, Koroleva OV. [Range of Gene candidates involved in biosynthesis of laccase from basidiomycete Trametes hirsuta]. Genetika 2013; 49:1149-1154. [PMID: 25474891 DOI: 10.7868/s0016675813090129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A comparative analysis of transcripts from the basidiomycota T. hirsuta grown with and without an inducer of the laccase biosynthesis was carried out. Methods of subtraction hybridization and massive parallel sequencing were used for this purpose. Unique transcripts encoded by genes that have a relatively high level of expression and belong to different gene ontology categories were identified. Also, a large number of transcripts were found to encode for predicted proteins, as well as noncoding transcripts. The latter may represent regulatory RNA molecules. Transcripts that increase their abundance when the laccase synthesis is induced are selected as gene-candidates involved in the laccase biosynthetic pathway.
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Viacheslavova AO, Berdichevets IN, Tiurin AA, Shimshilashvili KR, Mustafaev O, Goldenkova-Pavlova IV. [Expression of heterologous genes in plant systems: new possibilities]. Genetika 2012; 48:1245-1259. [PMID: 23297480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The basic methods used in current practice for stable and transient expression of heterologous genes in plants are presented and compared. The key areas of research in the heterologous expression of genes in plants have been identified by analyzing literature and experimental data: modeling of metabolic pathways; creation of marker-free transgenic plants; the search for new regulatory elements and plant genes influencing the efficiency of expression of heterologous genes in plants; development of new methods for analyzing of transgenic plants and new approaches to the expression of heterologous genes in plants.
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Viacheslavova AO, Mustafaev ON, Tiurin AA, Shimshilashvili KR, Berdichevets IN, Shaiakhmetova DM, Goldenkov MA, Fadeev VS, Shelud'ko IV, Goldenkova-Pavlova IV. [Set of module vectors for stable or transient expression of heterologous genes in plants]. Genetika 2012; 48:1046-56. [PMID: 23113332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A set of module vectors for stable or transient gene expression in plants was constructed with regard to the majority of factors ensuring efficient heterologous gene expression in plants. The vectors are convenient to clone new regulatory elements and genes of interest via simple molecular cloning procedures. The vectors can be used to obtain transgenic plants with stable heterologous gene expression as well as to achieve transient expression because one vector includes the gene for the tomato bushy stunt virus p19 protein, which acts as a suppressor of posttranscriptional gene silencing.
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Radzhabov MO, Shamov IA, Gasaev DG, Shil'nikova IN, Shneĭder IV, Goldenkova-Pavlova IV. [The Dagestan gene pool: polymorphism of immunogenetic and biochemical markers in Kumyks]. Genetika 2011; 47:260-267. [PMID: 21516797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This study is a part of long-term investigations devoted to the analysis of the gene pool of Dagestan ethnic groups. The phenotype (in %), gene, and haplotype frequencies in Kumyk ethnic group are reported. A total of 39 alleles and six haplotypes of 14 loci (AB0, Rhesus, P, Levis, Kell, HP, GC, C'3, TF, 6PGD, GLO1, ESD, ACP, and PGM1) of immunobiochemical genetic marker systems were examined. Rare haplotypes of the Rhesus system were identified, including CDE in the Karabudakhkent population with the frequency of 0.030, and Cde and cdE in the Dorgeli population with the frequencies of 0.034 and 0.38, respectively. Similarly to the other ethnic populations of Dagestan examined, Kukyk populations carried rare, albeit typically "Caucasoid" gene ACP1(c) of the AcP1 locus. The frequency of this allele in the two populations was similar, constituting 0.031 for Karabudakhkent and 0.032 for Dorgeli. In Kumyks, allele frequencies of the AB0, Rhesus, P, Lewis, Kell, HP, GC, C'3, TF, 6PGD, GLO1, ESD, ACP, but not PGM1, systems were similar to the mean allele frequencies at these loci observed in the other ethnic groups from the Dagestan, Caucasus, and the whole European historical ethnographic province. At the same time, the allele frequency values obtained were different from those for the populations of Kazakhstan, Central Asia, Siberia, and the Ruswsian Far East. Thus, the results obtained for classical genetic markers indicate that Kumyks are genetically closer to the indigenous populations of Dagestan than to Turkic-speaking populations. Analysis of the fit of the observed phenotype frequencies to the Hardy-Weinberg expectations showed that compared to other indigenous populations of Dagestan examined, in Kumyks the genetic state of the population upon random allele association was close to equilibrium. Probably, this state was determined by practical absence of the consanguineous marriages upon preservation of intra-aul endogamy.
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Komakhin RA, Komakhina VV, Miliukova NA, Goldenkova-Pavlova IV, Fadina OA, Zhuchenko AA. [Transgenic tomato plants expressing recA and NLS-recA-licBM3 genes as a model for studying meiotic recombination]. Genetika 2010; 46:1635-1644. [PMID: 21434416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Homologous DNA recombination in eukaryotes is necessary to maintain genome stability and integrity and for correct chromosome segregation and formation of new haplotypes in meiosis. At the same time, genetic determination and nonrandomness of meiotic recombination restrict the introgression of genes and generation of unique genotypes. As one of the approaches to study and induce meiotic recombination in plants, it is recommended to use the recA gene of Escherichia coli. It is shown that the recA and NLS-recA-licBM3 genes have maternal inheritance and are expressed in the progeny of transgenic tomato plants. Plants expressing recA or NLS-recA-licBM3 and containing one T-DNA insertion do not differ in pollen fertility from original nontransgenic forms and can therefore be used for comparative studies of the effect of bacterial recombinases on meiotic recombination between linked genes.
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Radzhabov MO, Shamov IA, Gasaev DG, Goldenkova-Pavlova IV, Shil'nikova IN, Shneĭder IV. [Gene pool of Dagestan ethnic groups: polymorphism of classical gene markers in the Darghin ethnic group]. Genetika 2010; 46:1692-1699. [PMID: 21434423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The work is part of a study of the gene pool for Daghestan ethnic groups. In total, 38 alleles and eight genotypes were studied at 14 loci (AB0, Rhesus, P, Lewis, Kell, HP, GC, C'3, TF, 6-PGD, GLO1, ESD, ACP, and PGM1) of immunogenetic and biochemical polymorphic gene systems. A high frequency of allele d of the Rhesus system was observed in all populations examined (0.399-0.474). Among the rare haplotypes of the Rhesus system, we observed CDE in the Degva population, Cde in the Sergokala and Degva populations, and cdE in the Sergokala and Vanashimakhi populations. The typical Caucasian ACP1c allele of the ACP1 locus, which is rather uncommon, was observed at a relatively high frequency in three (Segokala, Vanashimakhi, and Gubden) of the four local populations under study. In the Lewis system, a high frequency of the Le(a+b+) phenotype, which is characteristic of early childhood, was detected in the adult populations of Sergokala and Degva. The rare PGM1v allele of the phosphoglucomutase 1 system (PGM 1) was additionally observed in the Sergokala population. Statistical analysis identified 19 cases where the observed phenotype frequencies significantly differed from the frequencies expected from the Hardy--Weinberg equilibrium.
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Golenkina SA, Gol'tsov AI, Kuznetsova IL, Grigorenko AP, Andreeva TV, Reshetov DA, Kunizheva SS, Shagam LI, Morozova II, Goldenkova-Pavlova IV, Shimshilashvili K, Viacheslavova AO, Faskhutdinova G, Gareeva AÉ, Zaĭnullina AG, Khusnutdinova ÉK, Puzyrev VP, Stepanov VA, Kolotvin AV, Samokhodskaia LM, Selezneva ND, Gavrilova SI, Rogaev EI. [Analysis of clusterin gene (CLU/APOJ) polymorphism in Alzheimer's disease patients and in normal cohorts from Russian populations]. Mol Biol (Mosk) 2010; 44:620-626. [PMID: 20873220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Three genes mutations in which cause familial forms of Alzheimer's disease are known to date:PSEN1, PSEN2 and APP; and APOE gene polymorphism is a strong risk factor for Alzheimer's disease. We have evaluated allele and genotype frequency distribution of rs11136000 polymorphism in clusterin (CLU) gene (or apolipoprotein J, APOJ) in populations of three Russian regions and i nAlzheimhner's diseasepatients. Genome-wideassociation studies in samples from several European populations have recently revealed highly significant association o fCLU gene with AD (p = 8.5 x 10(-10)). We found no differences in allele and genotype frequencies of rs11136000 between populations from Moscow, Ural and Siberia regions. The allele frequencies are close to those in European populations. The genetic association analysis in cohort of Alzheimer's disease patients and normal individuals (>500 individuals ineach group) revealed no significant association of the rs11136000 polymorphism in CLU with Alzheimer's disease in Russian populations. Although our resultsdo not confirm the role of CLU gene as a majorgenetic factor forcommon form of Alzheimer's disease, the data do not rule out the possibility of modest effect of CLU and interaction between CLU and APOE genotypes in etiology of Alzheimer's disease.
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Berdichevets IN, Shimshilashvili HR, Gerasymenko IM, Sindarovska YR, Sheludko YV, Goldenkova-Pavlova IV. Multiplex PCR assay for detection of recombinant genes encoding fatty acid desaturases fused with lichenase reporter protein in GM plants. Anal Bioanal Chem 2010; 397:2289-93. [PMID: 20461503 DOI: 10.1007/s00216-010-3770-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 04/16/2010] [Accepted: 04/21/2010] [Indexed: 10/19/2022]
Abstract
Thermostable lichenase encoded by licB gene of Clostridium thermocellum can be used as a reporter protein in plant, bacterial, yeast, and mammalian cells. It has important advantages of high sensitivity and specificity in qualitative and quantitative assays. Deletion variants of LicB (e.g., LicBM3) retain its enzymatic activity and thermostability and can be expressed in translational fusion with target proteins without compromising with their properties. Fusion with the lichenase reporter is especially convenient for the heterologous expression of proteins whose analysis is difficult or compromised by host enzyme activities, as it is in case of fatty acid desaturases occurring in all groups of organisms. Recombinant desaturase-lichenase genes can be used for creating genetically modified (GM) plants with improved chill tolerance. Development of an analytical method for detection of fused desaturase-lichenase transgenes is necessary both for production of GM plants and for their certification. Here, we report a multiplex polymerase chain reaction method for detection of desA and desC desaturase genes of cyanobacteria Synechocystis sp. PCC6803 and Synechococcus vulcanus, respectively, fused to licBM3 reporter in GM plants.
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Affiliation(s)
- Iryna N Berdichevets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, 119991 Moscow, Russia
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Amiri RM, Yur'eva NO, Shimshilashvili KR, Goldenkova-Pavlova IV, Pchelkin VP, Kuznitsova EI, Tsydendambaev VD, Trunova TI, Los DA, Jouzani GS, Nosov AM. Expression of acyl-lipid Delta12-desaturase gene in prokaryotic and eukaryotic cells and its effect on cold stress tolerance of potato. J Integr Plant Biol 2010; 52:289-97. [PMID: 20377689 DOI: 10.1111/j.1744-7909.2010.00890.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report the expression profile of acyl-lipid Delta12-desaturase (desA) gene from Synechocystis sp. PCC6803 and its effect on cell membrane lipid composition and cold tolerance in prokaryotic (Escherichia coli) and eukaryotic (Solanum tuberosum) cells. For this purpose, a hybrid of desA and reporter gene encoding thermostable lichenase (licBM3) was constructed and used to transform these cells. The expression of this hybrid gene was measured using qualitative (Petri dish test, electrophoregram and zymogram) and quantitative methods (spectrometry and gas liquid chromatography assays). The maximum level of linoleic acid in the bacterial cells containing hybrid gene was 1.9% of total fatty acids. Cold stress tolerance assays using plant damage index and growth parameters showed that cold tolerance was enhanced in primary transgenic lines because of increased unsaturated fatty acid concentration in their lipids. The greatest content of 18:2 and 18:3 fatty acids in primary transgenic plants was observed for lines 2 (73%) and 3 (41%). Finally, our results showed that desaturase could enhance tolerance to cold stress in potato, and desaturase and lichenase retain their functionality in the structure of the hybrid protein where the enzymatic activity of target gene product was higher than in the case of reporter lichenase gene absence in the construction.
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Affiliation(s)
- Reza Maali Amiri
- Department of Agronomy and Plant Breeding, University College of Agriculture and Natural Resources of the University of Tehran, Karaj 31587-77871, Iran
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Fedorova II, Gra OA, Karunas AS, Khuzina AK, Ramazanova NN, Iuldasheva AA, Biktasheva AR, Etkina EI, Nasedkina TV, Goldenkova-Pavlova IV, Khusnutdinova EK. [Association of xenobiotic-metabolizing gene polymorphisms with childhood atopic diseases in Russian patients from the Republic of Bashkortostan]. Mol Biol (Mosk) 2009; 43:1032-1039. [PMID: 20088379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Enzymes of biotransformation system involved in the metabolism of exogenous and endogenous compounds are effective mechanism of protection from negative environmental factors. Decreasing activity or insufficient synthesis of biotransformation system enzymes caused by genetic polymorphism form the risk of various complex diseases, including atopic. Using allele-specific hybridization on the biochip the frequencies of xenobiotic-metabolizing gene polymorphisms in Russian children with bronchial asthma, allergic rhinitisand healthy donors from the Republic of Bashkortostan have been determined. The analysis of polymorphisms in CYP1A1, GSTT1, GSTM1, NAT2, MTHFR, CYP2C9 and CYP2C19 genes didn't reveal any association with atopic diseases. The frequencies of CYP2D6*1934G/G genotype and CYP2D6*1934G allele were significantly higher among boys with rhinitis symptoms than in control group.
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Abdeev RM, Abdeeva IA, Bruskin SS, Musiychuk KA, Goldenkova-Pavlova IV, Piruzian ES. Bacterial thermostable beta-glucanases as a tool for plant functional genomics. Gene 2009; 436:81-9. [PMID: 19393166 DOI: 10.1016/j.gene.2009.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 01/28/2009] [Accepted: 01/28/2009] [Indexed: 11/24/2022]
Abstract
A new strategy for creating experimental models for functional genomics has been proposed. It is based on the expression in transgenic plants of genes from thermophilic bacteria encoding functional analogues of plant proteins with high specific activity and thermal stability. We have validated this strategy by comparing physiological, biochemical and molecular properties of control tobacco plants and transgenic plants expressing genes of beta-glucanases with different substrate specificity. We demonstrate that the expression of bacterial beta-1,3-1,4-glucanase gene exerts no significant influence on tobacco plant metabolism, while the expression of bacterial beta-1,3-glucanase affects plant metabolism only at early stages of growth and development. By contrast, the expression of bacterial beta-1,4-glucanase has a significant effect on transgenic tobacco plant metabolism, namely, it affects plant morphology, the thickness of the primary cell wall, phytohormonal status, and the relative sugar content. We propose a hypothesis of beta-glucanase action as an important factor of genetic regulation of metabolic processes in plants.
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Affiliation(s)
- Rustam M Abdeev
- Center for Theoretical Problems of Physico-Chemical Pharmacology RAS, Moscow, Russia
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Kozhekbaeva ZM, Gra OA, Fadeev VS, Goldenkova-Pavlova IV, Korsunskaia IM, Bruskin SA, Agafonova EE, Piruzian AL, Surzhikov SA, Nasedkina TV. [Association of NAT2 polymorphism with risks to develop psoriasis and various dermatological diseases in Moscow population]. Mol Biol (Mosk) 2009; 43:62-76. [PMID: 19334527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ruacetyltransferase 2 (NAT2) is one of key enzymes of the second phase of biotransformation that metabolize genotoxic compounds such as carcinogens and mutagens in different types of cells. There is a correlation between the decreasing activity of NAT2 gene product and the sensitivity to harmful environmental factors that increase the risk of occurrence of different multifactorial diseases, including dermatological ones like psoriasis. We developed the NAT2-biochip for 17 SNPs. The biochip was been tested on 279 clinical DNA samples from 180 patients with psoriasis and 99 healthy individuals, residents of Moscow. We found only six SNPs that were significant for European populations (282C > T, 341T > C, 481C > T, 590G > A, 803A > G and 857G > A). The analysis in psoriasis group did not show any genotype association. The increase in frequency of a slow acetylation phenotype in group of patients with type II psoriasis and in group of patients with normosthenic constitution, in comparison with control group (OR = 1.76,p = 0.177 and OR = 2.07,p = 0.050, respectively) has been revealed. The results for patients smoking one or more pack of cigarettes per day, and daily alcohol drinking in comparison with the control showed an increase in frequency for the genotype 341C/C, 481T/T, 803G/G (OR = 7.42, p = 0.008 and OR = 106.11, p = 0.003, respectively). We also found an increase of frequency of genotype 341T/T, 481C/C, 590A/-, 803A/A in patients with side reactions to medical products comparing with group of healthy donors (OR = 2.05, p = 0.099). Thus, the present data show that the certain NAT2 genotypes and some styles of life can be considered as risk factors of psoriasis development in this muscovite population.
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Kozhekbaeva ZM, Glotov AS, Gra OA, Goldenkova-Pavlova IV, Bruskin SA, Agafonova EE, Markarova EV, Abdeev RM, Korsunskaia IM, Piruzian AL, Barskiĭ VE, Zasedatelev AS, Nasedkin TV. [Identification of functionally significant mutations in NAT2 gene using biological microchips]. Mol Biol (Mosk) 2007; 41:725-733. [PMID: 17936995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The product of gene NAT2 (N-acetyltransferase 2) is involved in the biotransformation system and participates in detoxication of some arylamine derivatives (in particular 2-aminofluorene, 4-aminobiphenyl and 4-naphthylamine) which are strongly mutagenic and carcinogenic. It also renders toxicological and pharmacological influence on a metabolism of medical products metabolized by the enzyme. We developed a microchip for detection of 16 functionally significant mutations coding 36 alleles of gene NAT2. Combinations of these alleles allow us to reveal more than 660 genotypes, which can be divided into four groups according acetylation phenotype: "fast" (R/R), "intermediate" (R/S), "slow" (S/S) and group with average or slow acetylating (R/S or S/S) alleles. The groups "R/S or S/S" include alleles, formed by a combination of 7 mutations (191G/A, 282C/T, 341T/C, 481C/T, 590G/A, 803A/G, 857G/A), theirs cis-trans position can be revealed by restriction analysis. In 37 of 71 DNA samples we unequivocally defined NAT2-genotypes, and other 34 samples have been characterized by more than two genotypes. 16 samples out of 34 had acetylation phenotype of group "R/S or S/S", which is characterized by the following combination of mutations: 282C/T, 341T/C, 481C/T, 590G/A and 803A/G. Thus, the developed biochip is a convenient screening method for primary detection of the majority of polymorphic replacements in gene NAT2.
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Goldenkova-Pavlova IV, Mirakhorli N, Maali AR, Isaenko E, Kartel' NA, Iur'eva NO, Abdeeva IA. [Experimental models for creation of transgenic plants resistant to stress factors]. Tsitol Genet 2007; 41:44-9. [PMID: 17649623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Experimental models of the potato primary transgenic plants which express the hybrid gene cry3aM-licBM2 have been created. Modecular analysis and the biotests of the experimental models allow proposing a new system of cry genes expression in plants. The system is based on the expression of hybrid genes possessing the sequence of reporter lichenase gene and the use as a regulator element of a light-induced promoter providing preferential expression of the controled genes only in green plant tissues (leaves)--the target tissues for pests. The lichanase presence in hybrid proteins facilitates selection and analysis of the expression level of the hybris proteins in transgenic organisms. Basing on the lichenase properties in hybrid proteins it seems possible to use this reporter system for transgene monitoring in agrocoenosis as this system is rather simple and precise and does not need large material and time expenses.
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Abdeeva IA, Goldenkova-Pavlova IV, Mokriakova MV, Volkova LV, Bogush VG, Sidoruk KV, Iur'eva NO, Debabov VG, Piruzian ES. [Experimental models of transgenic plants promising for the modern technologies]. Tsitol Genet 2007; 41:55-61. [PMID: 17649625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Transgenic popato plants have been created which express recombinant proteins, analogues of spidroin 1, the protein of the cobweb skeleton thread. Expression of the hybrid spidroin 1 genes possessing some repeated sequences retains both in the model test-tube-growing plants and in the crops. Expression level of the synthetic spidroin 1 genes and the level of accumulation of their products in plants depend on the type of promoter, number of repeats, organ specificity and plant species but not on the duration of plant material storage. The results show that the strategy based on constuction and expression of hybrid proteins which include the reporter protein makes it easier to select and analyse expression of hybrid proteins in transgenic organisms.
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Maali R, Shimshilashvili KR, Pchelkin VP, Tsydendambaev VD, Nosov AM, Los' DA, Goldenkova-Pavlova IV. [Comparative expression in Escherichia coli of the native and hybrid genes for acyl-lipid delta(9) desaturase]. Genetika 2007; 43:176-82. [PMID: 17385315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Expression of the desC gene coding for acyl-lipid delta(9) desaturase of thermophilic cyanobacterium Synechocystis sp. PCC6803 was studied in Escherichia coli cells. In a hybrid gene constructed (desC-licBM3), a sequence of the native acyl-lipid delta(9) desaturase was fused in frame with the reporter gene coding for thermostable lichenase. Lichenase contained in the hybrid protein simplified selection and analysis of the expression of membrane desaturase in the heterologous host. Comparisons of the expression for the native and hybrid genes in bacterial cells showed that lichenase remained active and thermostable in the hybrid protein, while desaturase retains the capability of introducing a double bound in the corresponding position of fatty acids.
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Goldenkova-Pavlova IV, Piruzian AL, Abdeev RM, Khripach LV, Radzhabov MO, Piruzian LA. [Population analysis and determination of the ethnic background are necessary in the study of multifactorial diseases: a study using the Dagestan population as a model]. Genetika 2006; 42:1137-42. [PMID: 17025165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Psoriasis, a multifactorial disease with genetic predisposition, has been used as an example to study the role of the ethnic background in multifactorial diseases in the Dagestan population. The individual information card (IIC) is proposed as the main tool for correct collection and processing of information. The results of the study demonstrate that the Dagestan population is a convenient and adequate model population for studying multifactorial diseases, such as psoriasis, and may serve as an object for studying the role of heredity in the etiologies and pathogeneses of this and other multifactorial diseases.
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Goldenkova-Pavlova IV, Bruskin SA, Abdeev RM, Markarova EV, Bigvava SG, Radkevich LA, Kozhekbaeva ZM, Glotov AS, Gra OA, Zasedatelev AS, Nasedkina TV, Kurdanov KA, Piruzian ES. [Comparative analysis of N-acetylation polymorphism in humans as determined by phenotyping and genotyping]. Genetika 2006; 42:1143-50. [PMID: 17025166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The N-acetylation polymorphisms of volunteers from the Moscow population analyzed by phenotyping and genotyping have been compared. The ratios between the proportions of fast acetylators (FAs) and slow acetylators (SAs) estimated by phenotyping and genotyping do not differ significantly from each other (47 and 44%, respectively). The absolute acetylation rate widely varies in both FAs and SAs. The NAT2 genotype and allele frequencies in the population sample have been calculated. The most frequent alleles are NAT2*4 (a "fast" allele), NAT2*5, and NAT2*6 ("slow" alleles); the most frequent genotypes are NAT2*5/*5, NAT2*4/*6, and NAT2*4/*5. Comparative analysis of N-acetylation polymorphism estimated by phenotyping and genotyping in the same subjects has shown a complete concordance between the phenotype and genotype in only 62 out of 75 subjects (87%). Comparative characteristics and presumed applications of the two approaches (quantitative estimation of acetylation rate and qualitative determination of the acetylator genotype) to the identification of individual acetylation status are presented.
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