The possibility of using the CRISPR/Cas method of genomic editing has provided researchers with a powerful tool not only for targeted modification of genes that determine economically valuable traits in plants, but also for solving fundamental problems of their functioning. The most striking examples of the use of CRISPR/Cas9 to improve various plant species by knockouts of target genes or knockins of expression cassettes, including genes that change the biosynthesis of important plant metabolites, obtained by foreign research groups, are presented. We discuss our own results on the directed change in the functioning of genes encoding photosystem II carbonic anhydrases, as well as genes involved in plant responses to stress in theArabidopsis thalianamodel. Examples of the use of the genomic editing method to improve the characteristics of plant cell cultures as bioproducers of pharmaceutically valuable recombinant proteins are given. Methodological issues related to plant genome editing are considered — the problems of chimerism, obtaining homozygotes and biallelic knockout mutations, knockout of regulatory and structural genes, as well as repair features in the regions of integration of expression cassettes in knockins. The main directions for further development and improvement of the CRISPR/Cas genomic editing method aimed at optimizing the efficiency of delivery of target genetic constructs and editing tools to the nuclear and chloroplast genomes of plants using single-walled carbon nanotubes are summarized.
{"title":"Current state of research in the development of the genomic editing method: problems and prospects","authors":"E. Deineko","doi":"10.17816/ecogen568610","DOIUrl":"https://doi.org/10.17816/ecogen568610","url":null,"abstract":"The possibility of using the CRISPR/Cas method of genomic editing has provided researchers with a powerful tool not only for targeted modification of genes that determine economically valuable traits in plants, but also for solving fundamental problems of their functioning. The most striking examples of the use of CRISPR/Cas9 to improve various plant species by knockouts of target genes or knockins of expression cassettes, including genes that change the biosynthesis of important plant metabolites, obtained by foreign research groups, are presented. We discuss our own results on the directed change in the functioning of genes encoding photosystem II carbonic anhydrases, as well as genes involved in plant responses to stress in theArabidopsis thalianamodel. Examples of the use of the genomic editing method to improve the characteristics of plant cell cultures as bioproducers of pharmaceutically valuable recombinant proteins are given. Methodological issues related to plant genome editing are considered — the problems of chimerism, obtaining homozygotes and biallelic knockout mutations, knockout of regulatory and structural genes, as well as repair features in the regions of integration of expression cassettes in knockins. The main directions for further development and improvement of the CRISPR/Cas genomic editing method aimed at optimizing the efficiency of delivery of target genetic constructs and editing tools to the nuclear and chloroplast genomes of plants using single-walled carbon nanotubes are summarized.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"30 26","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. Tvorogova, E. A. Potsenkovskaia, Elena P. Efremova, Nikolai V. Kozlov, Veronika Y. Simonova, E. Y. Krasnoperova, Zakhar S. Konstantinov, Daria V. Yakovleva, Anastasiya M. Artemiuk, Lyudmila A. Lutova
Pea (Pisum sativum) is an important agricultural crop and a model object in various fields of plant research. At the same time, the genetic modification of pea is still a difficult task, which, apparently, is associated with its low ability to regenerate. There are a lot of different pea transformation protocols, however, for most of them, the transformation efficiency, i.e. the number of transgenic plants per explant, is extremely low. In addition, none of the protocols known to us has demonstrated itself to be universal, i.e. suitable for all varieties and lines of peas. We searched for studies on the transformation and regeneration of peas and systematized the data obtained. The resulting database made it possible to identify the most effective protocols for the transformation and regeneration ofP. sativum, as well as to analyze statistically the general features of the methods used, such as the source of the explant, the composition of the culture media, the duration of cultivation, and so on. We assume that our system for the analysis of publications devoted toin vitrocell cultures can also be used for similar data on other plant species. This research was supported by the Sirius University of Science and Technology project: PBB-RND-2243.
{"title":"The transformation and genome editing of Pisum sativum: protocols and their modifications","authors":"V. Tvorogova, E. A. Potsenkovskaia, Elena P. Efremova, Nikolai V. Kozlov, Veronika Y. Simonova, E. Y. Krasnoperova, Zakhar S. Konstantinov, Daria V. Yakovleva, Anastasiya M. Artemiuk, Lyudmila A. Lutova","doi":"10.17816/ecogen567891","DOIUrl":"https://doi.org/10.17816/ecogen567891","url":null,"abstract":"Pea (Pisum sativum) is an important agricultural crop and a model object in various fields of plant research. At the same time, the genetic modification of pea is still a difficult task, which, apparently, is associated with its low ability to regenerate. There are a lot of different pea transformation protocols, however, for most of them, the transformation efficiency, i.e. the number of transgenic plants per explant, is extremely low. In addition, none of the protocols known to us has demonstrated itself to be universal, i.e. suitable for all varieties and lines of peas. We searched for studies on the transformation and regeneration of peas and systematized the data obtained. The resulting database made it possible to identify the most effective protocols for the transformation and regeneration ofP. sativum, as well as to analyze statistically the general features of the methods used, such as the source of the explant, the composition of the culture media, the duration of cultivation, and so on. We assume that our system for the analysis of publications devoted toin vitrocell cultures can also be used for similar data on other plant species. \u0000This research was supported by the Sirius University of Science and Technology project: PBB-RND-2243.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"7 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Genetic colonization by agrobacteria is possible due to agrobacterial transformation, which implies interspecies transfer of genetic material (T-DNA). A transgenic tissue is formed on the whole non-transgenic plant during that process. However, it turned out that in nature there are plants containing T-DNA fragments in their genomes and they can inherit these T-DNAs sexually. Such T-DNA was called cellular, and such plants were called natural transgenic. Examples of such organisms are plants of the genus Vaccinium. In the genomes of two species of this genus we found cT-DNA, represented by a rolB/C-like gene [1]. Previously, analyzing the natural transgenes in another genus (Camellia L.) [2], we showed the importance of reconstructing the allelic states of transgenes for phylogenetic studies. In this study, we performed analysis of the spreading of the rolB/C-like gene for its use as a molecular marker within Vaccinium. We used molecular-genetic and bioinformatics methods for sequencing, assembly, and analysis of the rolB/C-like gene. We discovered 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer as containing the rolB/C-like gene. Most of studied samples are characterized by the presence of full-size genes. This made it possible to develop approaches for alleles phasing of the rolB/C-like gene and reconstruct a Vaccinium phylogenetic relationship. We subjected the studied species to phylogenetic analysis based on sequences of the rolB/C-like gene. The resulting phylogenetic tree of the genus Vaccinium divided the species into sections in accordance with the classical genus system based on morphological characters. At the same time, our tree did not confirm the taxa determined on the basis of ITS.
{"title":"Distribution of the rolB/C-like natural transgene in representatives of the genus Vaccinium L.","authors":"Roman R. Zhidkin, P. Zhurbenko, T. Matveeva","doi":"10.17816/ecogen567934","DOIUrl":"https://doi.org/10.17816/ecogen567934","url":null,"abstract":"Genetic colonization by agrobacteria is possible due to agrobacterial transformation, which implies interspecies transfer of genetic material (T-DNA). A transgenic tissue is formed on the whole non-transgenic plant during that process. However, it turned out that in nature there are plants containing T-DNA fragments in their genomes and they can inherit these T-DNAs sexually. Such T-DNA was called cellular, and such plants were called natural transgenic. \u0000Examples of such organisms are plants of the genus Vaccinium. In the genomes of two species of this genus we found cT-DNA, represented by a rolB/C-like gene [1]. \u0000Previously, analyzing the natural transgenes in another genus (Camellia L.) [2], we showed the importance of reconstructing the allelic states of transgenes for phylogenetic studies. In this study, we performed analysis of the spreading of the rolB/C-like gene for its use as a molecular marker within Vaccinium. \u0000We used molecular-genetic and bioinformatics methods for sequencing, assembly, and analysis of the rolB/C-like gene. We discovered 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer as containing the rolB/C-like gene. Most of studied samples are characterized by the presence of full-size genes. This made it possible to develop approaches for alleles phasing of the rolB/C-like gene and reconstruct a Vaccinium phylogenetic relationship. \u0000We subjected the studied species to phylogenetic analysis based on sequences of the rolB/C-like gene. The resulting phylogenetic tree of the genus Vaccinium divided the species into sections in accordance with the classical genus system based on morphological characters. At the same time, our tree did not confirm the taxa determined on the basis of ITS.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"64 16","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138605082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Eggplants, known scientifically asSolanum melongenaL., are renowned for their health benefits, largely attributed to phenolic acids. Chlorogenic acid stands out as one of the most prevalent phenolic acids in eggplants. The enzyme hydroxycinnamoyl CoA-quinate transferase (SmHQT) plays a pivotal role in the production and concentration of this acid in the fruit. However, until this study, the exact function and influence of SmHQT on the eggplant’s composition remained elusive [1–3]. This research aimed to explore SmHQT’s role by overexpressing it in the eggplant’s flesh using agroinfiltration, a technique that transiently introduces genes into plants. This method offers insights into potential changes in the plant’s chemical makeup. Advanced techniques like quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography (HPLC) revealed that the chlorogenic acid content in the genetically altered eggplants was over twice that of the unaltered ones. The study also investigated the cascading effects of this overexpression. The qRT-PCR results showed variations in the expression of genes linked to the chlorogenic acid pathway, hinting at SmHQT’s wider role in phenolic acid biosynthesis in eggplants. Comprehensive analyses of protein interactions and cis-regulating elements were undertaken to grasp SmHQT’s full impact. Phenolic acids, like chlorogenic acid, offer therapeutic benefits against conditions such as diabetes, cancer, and arthritis in humans. In plants, they enhance natural defenses against pests and diseases. While there have been attempts to boost the phenolic acid content in eggplants using genes from wild variants, this study’s approach proved more effective. Another notable achievement of this research was the introduction of an improved agroinfiltration protocol. This method is promising for future studies focused on transient gene expression in fruits, facilitating swift genetic modification prototyping. In essence, this research underscores the immense potential of bioengineering in augmenting the nutritional profiles of crops by enhancing their inherent phytochemicals.
{"title":"Bioengineering eggplants: a deep dive into SmHQT and phenolic acid biosynthesis","authors":"P. Kaushik, S. Meenakshi, K. Anil","doi":"10.17816/ecogen568585","DOIUrl":"https://doi.org/10.17816/ecogen568585","url":null,"abstract":"Eggplants, known scientifically asSolanum melongenaL., are renowned for their health benefits, largely attributed to phenolic acids. Chlorogenic acid stands out as one of the most prevalent phenolic acids in eggplants. The enzyme hydroxycinnamoyl CoA-quinate transferase (SmHQT) plays a pivotal role in the production and concentration of this acid in the fruit. However, until this study, the exact function and influence of SmHQT on the eggplant’s composition remained elusive [1–3]. \u0000This research aimed to explore SmHQT’s role by overexpressing it in the eggplant’s flesh using agroinfiltration, a technique that transiently introduces genes into plants. This method offers insights into potential changes in the plant’s chemical makeup. Advanced techniques like quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography (HPLC) revealed that the chlorogenic acid content in the genetically altered eggplants was over twice that of the unaltered ones. \u0000The study also investigated the cascading effects of this overexpression. The qRT-PCR results showed variations in the expression of genes linked to the chlorogenic acid pathway, hinting at SmHQT’s wider role in phenolic acid biosynthesis in eggplants. Comprehensive analyses of protein interactions and cis-regulating elements were undertaken to grasp SmHQT’s full impact. \u0000Phenolic acids, like chlorogenic acid, offer therapeutic benefits against conditions such as diabetes, cancer, and arthritis in humans. In plants, they enhance natural defenses against pests and diseases. While there have been attempts to boost the phenolic acid content in eggplants using genes from wild variants, this study’s approach proved more effective. \u0000Another notable achievement of this research was the introduction of an improved agroinfiltration protocol. This method is promising for future studies focused on transient gene expression in fruits, facilitating swift genetic modification prototyping. In essence, this research underscores the immense potential of bioengineering in augmenting the nutritional profiles of crops by enhancing their inherent phytochemicals.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"2 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Elkonin, Grigoryi A. Gerashchenkov, Natalie V. Borisenko, O. A. Kenzhegulov, S. Sarsenova, V. M. Panin, N. A. Rozhnova
The use of genome editing technologies opens wide opportunities for the targeted mutagenesis in important agricultural crops. In the context of global warming, sorghum, an important drought- and heat-tolerant crop is of particular importance. However, compared to other cereals, sorghum grain has a lower nutritional value, due to the resistance of its storage proteins (kafirins) to proteolytic digestion. A decrease in the synthesis of kafirins as a result of mutations or the expression of the RNAi genetic constructs modifies the ultrastructure of protein bodies and improves their digestibility by proteases. To obtain mutants with improved protein digestibility, we created four binary vectors for site-directed mutagenesis of the k1C5 and gKAF1 genes encoding α- and γ-kafirin, respectively. Each of these vectors contained the cas9 endonuclease gene and a guide RNA targeted the nucleotide sequences encoding the kafirin signal polypeptides. By means of agrobacterial transformation, the created vectors were introduced into the genome of the grain sorghum cv. Avans. 14 transgenic plants were regenerated. Sequencing of 5 regenerants obtained using a vector for the k1C5 mutagenesis revealed 3 plants with mutations. The offspring of these mutants had a higher digestibility of grain proteins in vitro (86–92%) compared to the initial cv. Avans (63–67%). Notably, the T1 plants lacked the cas9 gene and the bar marker gene, which indicates the production of mutants with the edited k1C5 gene sequence, which lack the genetic construct that induced this mutation. Two mutants with mutations in the gKAF1 sequence were obtained. Thus, using the CRISPR/Cas technology, we have obtained mutants with improved digestibility of kafirins, which can be used in practical sorghum breeding.
{"title":"SITE-directed mutagenesis for producing grain sorgum mutants with improved kafirine digestibility","authors":"L. Elkonin, Grigoryi A. Gerashchenkov, Natalie V. Borisenko, O. A. Kenzhegulov, S. Sarsenova, V. M. Panin, N. A. Rozhnova","doi":"10.17816/ecogen567897","DOIUrl":"https://doi.org/10.17816/ecogen567897","url":null,"abstract":"The use of genome editing technologies opens wide opportunities for the targeted mutagenesis in important agricultural crops. In the context of global warming, sorghum, an important drought- and heat-tolerant crop is of particular importance. However, compared to other cereals, sorghum grain has a lower nutritional value, due to the resistance of its storage proteins (kafirins) to proteolytic digestion. A decrease in the synthesis of kafirins as a result of mutations or the expression of the RNAi genetic constructs modifies the ultrastructure of protein bodies and improves their digestibility by proteases. To obtain mutants with improved protein digestibility, we created four binary vectors for site-directed mutagenesis of the k1C5 and gKAF1 genes encoding α- and γ-kafirin, respectively. Each of these vectors contained the cas9 endonuclease gene and a guide RNA targeted the nucleotide sequences encoding the kafirin signal polypeptides. By means of agrobacterial transformation, the created vectors were introduced into the genome of the grain sorghum cv. Avans. 14 transgenic plants were regenerated. Sequencing of 5 regenerants obtained using a vector for the k1C5 mutagenesis revealed 3 plants with mutations. The offspring of these mutants had a higher digestibility of grain proteins in vitro (86–92%) compared to the initial cv. Avans (63–67%). Notably, the T1 plants lacked the cas9 gene and the bar marker gene, which indicates the production of mutants with the edited k1C5 gene sequence, which lack the genetic construct that induced this mutation. Two mutants with mutations in the gKAF1 sequence were obtained. Thus, using the CRISPR/Cas technology, we have obtained mutants with improved digestibility of kafirins, which can be used in practical sorghum breeding.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"24 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cultivated peanut is an allotetraploid species that received the A and B genomes from Arachis duranensis and A. ipaensis. Homologs of the agrobacterial cucumopine synthase gene were previously found in both genomes as a result of horizontal transfer [1]. These sequences are found both in ancestral species and in cultivated peanuts. In addition to them, natural GMOs are A. monticola and A. stenosperma. How widespread natural GMOs are within the genus Arachis is currently unknown. The aim of our study was to search for natural GMOs within the genus Arachis and to analyze the polymorphism of natural transgenes out the studied species. METHODS: Gene sequencing for various Arachis species was determined using the bwa [2], GATK [3] and samtools [4] packages based on NGS data aggregated in the SRA NCBI database. RESULTS: We have found homologues of the cucumopine synthase gene in the genomes of A. appressipila, A. batizocoi, A. cardenasii, A. correntina, A. diogoi, A. duranensis, A. glandulifera, A. helodes, A. hoehnei, A. ipaensis, A. macedoi, A. magna, A. monticola, A. paraguariensis, A. pintoi, A. pusilla, A. rigonii, A. stenophylla, A. stenosperma, A. trinitensis, A. valida, A. villosa, and also characterized the intraspecific variability of the gene in cultivated peanuts. In 16 of the 22 species studied, the gene is full-length. The report will consider the possibility of using the cucumopine synthase gene in peanut phylogenetic studies. CONCLUSION: The list of species of natural GMOs within the genus Arachis today includes 23 species.
{"title":"Natural GMOs inside the genus Arachis L.","authors":"Olesja D. Bogomaz, V. D. Bemova, T. Matveeva","doi":"10.17816/ecogen568618","DOIUrl":"https://doi.org/10.17816/ecogen568618","url":null,"abstract":"Cultivated peanut is an allotetraploid species that received the A and B genomes from Arachis duranensis and A. ipaensis. Homologs of the agrobacterial cucumopine synthase gene were previously found in both genomes as a result of horizontal transfer [1]. These sequences are found both in ancestral species and in cultivated peanuts. In addition to them, natural GMOs are A. monticola and A. stenosperma. How widespread natural GMOs are within the genus Arachis is currently unknown. The aim of our study was to search for natural GMOs within the genus Arachis and to analyze the polymorphism of natural transgenes out the studied species. \u0000METHODS: Gene sequencing for various Arachis species was determined using the bwa [2], GATK [3] and samtools [4] packages based on NGS data aggregated in the SRA NCBI database. \u0000RESULTS: We have found homologues of the cucumopine synthase gene in the genomes of A. appressipila, A. batizocoi, A. cardenasii, A. correntina, A. diogoi, A. duranensis, A. glandulifera, A. helodes, A. hoehnei, A. ipaensis, A. macedoi, A. magna, A. monticola, A. paraguariensis, A. pintoi, A. pusilla, A. rigonii, A. stenophylla, A. stenosperma, A. trinitensis, A. valida, A. villosa, and also characterized the intraspecific variability of the gene in cultivated peanuts. In 16 of the 22 species studied, the gene is full-length. The report will consider the possibility of using the cucumopine synthase gene in peanut phylogenetic studies. \u0000CONCLUSION: The list of species of natural GMOs within the genus Arachis today includes 23 species.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"22 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microalgae contain a wide range of useful substances: antioxidants, lipids, proteins, carbohydrates and secondary metabolites which could be used in nutraceuticals and dietary supplements. Green microalgaeChlorellacontaining highest amount of chlorophylls of any known plant, 60% protein, 18 amino acids, 20 vitamins and minerals [1]. Microalgae are exceptionally rich source of pharmacologically active metabolites with antineoplastic, antitumor, antibacterial, antifungal and antiviral properties and, also capable of wastewater treatment, and biomass production. The genetic information can improve the scenario of metabolic engineering in microalgae. Green algaeC. reinhardtii, a reference organism for understanding the basic algal genetics and metabolism is usually used to work out various genetic strategies, including omics resources and mutant libraries, for the enhancement of beneficial properties of microalgae. The synergy of microalgal multi-omics datasets (genomic, transcriptomic and proteomic) offer a rapid and predictable strategic path for the strain improvement [2]. The algal nuclear or chloroplast engineering (transformation and CRISPR/CAS editing) has been carried out using synthetic biology approach for the production of recombinant proteins having therapeutic properties. More than 100 recombinant proteins have been expressed in microalgae, mainly inC. reinhardtii, including: the vaccines, antibodies, immunotoxins and therapeutic proteins (human erythropoietin, fibronectin, interferon B1, proinsulin, endothelial growth factor and others [3]. Thus, the wide taxonomic and biochemical diversity among the microalgae when using modern biotechnologies, makes them suitable resource of abundant biomolecules with industrial and biomedical importance.
{"title":"Microalgae as production systems of bioactive compounds. Bioengineering approaches","authors":"Elena M. Chekunova, Pavel A. Virolainen","doi":"10.17816/ecogen568627","DOIUrl":"https://doi.org/10.17816/ecogen568627","url":null,"abstract":"Microalgae contain a wide range of useful substances: antioxidants, lipids, proteins, carbohydrates and secondary metabolites which could be used in nutraceuticals and dietary supplements. Green microalgaeChlorellacontaining highest amount of chlorophylls of any known plant, 60% protein, 18 amino acids, 20 vitamins and minerals [1]. Microalgae are exceptionally rich source of pharmacologically active metabolites with antineoplastic, antitumor, antibacterial, antifungal and antiviral properties and, also capable of wastewater treatment, and biomass production. \u0000The genetic information can improve the scenario of metabolic engineering in microalgae. Green algaeC. reinhardtii, a reference organism for understanding the basic algal genetics and metabolism is usually used to work out various genetic strategies, including omics resources and mutant libraries, for the enhancement of beneficial properties of microalgae. The synergy of microalgal multi-omics datasets (genomic, transcriptomic and proteomic) offer a rapid and predictable strategic path for the strain improvement [2]. The algal nuclear or chloroplast engineering (transformation and CRISPR/CAS editing) has been carried out using synthetic biology approach for the production of recombinant proteins having therapeutic properties. More than 100 recombinant proteins have been expressed in microalgae, mainly inC. reinhardtii, including: the vaccines, antibodies, immunotoxins and therapeutic proteins (human erythropoietin, fibronectin, interferon B1, proinsulin, endothelial growth factor and others [3]. Thus, the wide taxonomic and biochemical diversity among the microalgae when using modern biotechnologies, makes them suitable resource of abundant biomolecules with industrial and biomedical importance.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"5 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138602829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ke Chen, P. Zhurbenko, Lavrentii G. Danilov, T. Matveeva, Léon Otten
Horizontal gene transfer (HGT) plays an important role in plant evolution and plant development. Agrobacterium-mediated gene transfer leads to the formation of crown galls or hairy roots, due to expression of transferred T-DNA genes. Spontaneous regeneration of transformed cells can produce natural transformants carrying cellular T-DNA (cT-DNA) sequences of bacterial origin. HGT from Agrobacterium to dicots is remarkably widespread. The production of naturally genome modified plants could play a role in plant evolution and environment. Among these natural GMOs (nGMOs) there are the tea plants. Camellia sinensis var. sinensis cv. Shuchazao contains a single 5.5 kb cT-DNA fragment organized as imperfect inverted repeat with three inactive genes. 142 Camellia accessions, belonging to 10 of 11 species of the section Thea, were studied for the presence of cT-DNA alleles. All of them contain the cT-DNA insert, indicating that they are resulted from the single transformed event. Allele phasing showed that 82 accessions were heterozygous for T-DNA alleles, 60 others were homozygous. A phylogenetic analysis of all found alleles showed existence of two separate groups of them, further divided into subgroups. The alleles of the different Camellia species were distributed mosaically over groups, and different species showed very similar T-DNA alleles. This indicates that the taxonomy of Thea requires revision. The nucleotide divergence of the imperfect cT-DNA repeats indicates that the age of cT-DNA insertion is about 15 mya, which is earlier then emergence of section Thea [1]. We present a working model for the origin and evolution of nGMO plants derived from allogamous transformants.
{"title":"Natural transformants of Camellia section Thea","authors":"Ke Chen, P. Zhurbenko, Lavrentii G. Danilov, T. Matveeva, Léon Otten","doi":"10.17816/ecogen568588","DOIUrl":"https://doi.org/10.17816/ecogen568588","url":null,"abstract":"Horizontal gene transfer (HGT) plays an important role in plant evolution and plant development. Agrobacterium-mediated gene transfer leads to the formation of crown galls or hairy roots, due to expression of transferred T-DNA genes. Spontaneous regeneration of transformed cells can produce natural transformants carrying cellular T-DNA (cT-DNA) sequences of bacterial origin. HGT from Agrobacterium to dicots is remarkably widespread. The production of naturally genome modified plants could play a role in plant evolution and environment. \u0000Among these natural GMOs (nGMOs) there are the tea plants. Camellia sinensis var. sinensis cv. Shuchazao contains a single 5.5 kb cT-DNA fragment organized as imperfect inverted repeat with three inactive genes. 142 Camellia accessions, belonging to 10 of 11 species of the section Thea, were studied for the presence of cT-DNA alleles. All of them contain the cT-DNA insert, indicating that they are resulted from the single transformed event. Allele phasing showed that 82 accessions were heterozygous for T-DNA alleles, 60 others were homozygous. A phylogenetic analysis of all found alleles showed existence of two separate groups of them, further divided into subgroups. The alleles of the different Camellia species were distributed mosaically over groups, and different species showed very similar T-DNA alleles. This indicates that the taxonomy of Thea requires revision. The nucleotide divergence of the imperfect cT-DNA repeats indicates that the age of cT-DNA insertion is about 15 mya, which is earlier then emergence of section Thea [1]. We present a working model for the origin and evolution of nGMO plants derived from allogamous transformants.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"17 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Firuza Yusufovna Nasyrova, Samariddin S. Barotov, Farzona A. Abdukholiqova
The policy of the Republic of Tajikistan in the field of biosafety, regarding the issue of handling and use of living genetically modified organisms (LMOs or GMOs) is aimed at compliance with international legal acts, agreements and obligations to ratified Conventions. Tajikistan ratified the Convention on Biological Diversity in 1997 and the Cartagena Protocol on Biological Safety in 2004. After ratifying the protocol, the country has prepared three National Reports in accordance with the requirements of international agreements. Earlier in Tajikistan, the Law of the Republic of Tajikistan “On Biological Safety” (2005) was adopted. “The Law regulates the development, testing, production, import, export and release on the market and into the environment of GMOs, is aimed at reducing the risk of adverse effects of GMO on human health, biological diversity, ecological balance and the state of the environment”. Currently, this Law has been renamed into the Law “On Genetically Modified Organisms” and is under discussion, approval and adoption by the Parliament of the Republic of Tajikistan. Among the urgent problems that the Republic of Tajikistan is currently facing, considering the prospects for the coming years, is the problem of food security, including issues related to ensuring food safety. Taking into account the importance of conducting research in the field of biological and food safety, scientifically based risk assessment of biological agents (including GMOs) and toxins, chemical contaminants in food products and crops by the Decree of the Presidium of the Academy of Sciences of the Republic of Tajikistan No. 108 dated 30.11.2015 the Laboratory of Biological Safety was established at the Institute of Botany, Plant Physiology and Genetics of Tajikistan National Academy of Science, the main tasks of which are the development and application of modern methods of analysis for the detection of biological agents and toxins, chemical contaminants in food products and crops, and analysis of GMO products. It should be noted that at present there is no official information related to the production, use, distribution, sale, import and export of GMOs, as well as the registration of incoming GMO food products in Tajikistan. An analysis of the market for agricultural products in the capital city of Dushanbe showed that a number of GMO food products and genetically modified seed material are still imported from abroad in the form of technical and humanitarian assistance as well as international trade. In this regard, food safety activities should include risk assessment based on scientific evidence. Its emphasis should be on both process control and end product safety so that potentially unsafe foods can be identified early. GMO food can be considered safe if the risks associated with it are at an acceptable and acceptable level. It should be noted that an effective system for monitoring food products, including products containing GMOs, their complia
{"title":"GMOs policy and research in Tajikistan","authors":"Firuza Yusufovna Nasyrova, Samariddin S. Barotov, Farzona A. Abdukholiqova","doi":"10.17816/ecogen568495","DOIUrl":"https://doi.org/10.17816/ecogen568495","url":null,"abstract":"The policy of the Republic of Tajikistan in the field of biosafety, regarding the issue of handling and use of living genetically modified organisms (LMOs or GMOs) is aimed at compliance with international legal acts, agreements and obligations to ratified Conventions. Tajikistan ratified the Convention on Biological Diversity in 1997 and the Cartagena Protocol on Biological Safety in 2004. After ratifying the protocol, the country has prepared three National Reports in accordance with the requirements of international agreements. Earlier in Tajikistan, the Law of the Republic of Tajikistan “On Biological Safety” (2005) was adopted. “The Law regulates the development, testing, production, import, export and release on the market and into the environment of GMOs, is aimed at reducing the risk of adverse effects of GMO on human health, biological diversity, ecological balance and the state of the environment”. Currently, this Law has been renamed into the Law “On Genetically Modified Organisms” and is under discussion, approval and adoption by the Parliament of the Republic of Tajikistan. \u0000Among the urgent problems that the Republic of Tajikistan is currently facing, considering the prospects for the coming years, is the problem of food security, including issues related to ensuring food safety. Taking into account the importance of conducting research in the field of biological and food safety, scientifically based risk assessment of biological agents (including GMOs) and toxins, chemical contaminants in food products and crops by the Decree of the Presidium of the Academy of Sciences of the Republic of Tajikistan No. 108 dated 30.11.2015 the Laboratory of Biological Safety was established at the Institute of Botany, Plant Physiology and Genetics of Tajikistan National Academy of Science, the main tasks of which are the development and application of modern methods of analysis for the detection of biological agents and toxins, chemical contaminants in food products and crops, and analysis of GMO products. \u0000It should be noted that at present there is no official information related to the production, use, distribution, sale, import and export of GMOs, as well as the registration of incoming GMO food products in Tajikistan. An analysis of the market for agricultural products in the capital city of Dushanbe showed that a number of GMO food products and genetically modified seed material are still imported from abroad in the form of technical and humanitarian assistance as well as international trade. In this regard, food safety activities should include risk assessment based on scientific evidence. Its emphasis should be on both process control and end product safety so that potentially unsafe foods can be identified early. GMO food can be considered safe if the risks associated with it are at an acceptable and acceptable level. It should be noted that an effective system for monitoring food products, including products containing GMOs, their complia","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. Lebedeva, D. A. Dobychkina, Lilia A. Kochetkova, Lyudmila A. Lutova
CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides are known as systemic regulators of legume-rhizobium symbiosis that negatively control the number of nitrogen-fixing nodules. These regulatory peptides are produced in the root in response to inoculation with rhizobia, and are transported through the xylem to the shoot, where they are recognized by their receptor, CLV1-like (CLAVATA1-like) kinase, active in leaf phloem cells. After that, a shoot-derived signaling pathway is activated that inhibits subsequent nodule development in the root. Previously, we found that in Medicago truncatula, the expression of the MtCLE35 gene is activated in response to rhizobia and nitrate treatment, and its overexpression systemically inhibits nodulation. However, little is known about the downstream target genes regulated by a MtCLE35 signaling pathway in the root. Moreover, it is not completely clear which stage of symbiosis development is affected by MtCLE35-activated pathway. In order to identify genes regulated by the MtCLE35-induced signaling pathway, we performed a transcriptomic analysis of the roots overexpressing the MtCLE35 gene. Totally, 1122 genes were found to be differentially expressed between MtCLE35-overexpressing and control roots after rhizobial inoculation, among them 185 genes were upregulated and 937 genes were downregulated. Among downregulated genes, many known regulators of legume-rhizobia symbiosis were found. In addition to this, we analyze early steps of interaction between M. truncatula overexpressing the MtCLE35 gene and Sinorhizobium meliloti labeled with fluorescent reporter. We did not observe penetration of S. meliloti into host plant roots with MtCLE35 overexpression. Our data suggest that overexpression of the MtCLE35 gene inhibits nodulation at the very early stages of symbiosis development.
{"title":"Overexpression of the MtCLE35 gene in transgenic Medicago truncatula plants inhibits nodulation at early stages of symbiosis development","authors":"M. Lebedeva, D. A. Dobychkina, Lilia A. Kochetkova, Lyudmila A. Lutova","doi":"10.17816/ecogen568451","DOIUrl":"https://doi.org/10.17816/ecogen568451","url":null,"abstract":"CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION-related) peptides are known as systemic regulators of legume-rhizobium symbiosis that negatively control the number of nitrogen-fixing nodules. These regulatory peptides are produced in the root in response to inoculation with rhizobia, and are transported through the xylem to the shoot, where they are recognized by their receptor, CLV1-like (CLAVATA1-like) kinase, active in leaf phloem cells. After that, a shoot-derived signaling pathway is activated that inhibits subsequent nodule development in the root. Previously, we found that in Medicago truncatula, the expression of the MtCLE35 gene is activated in response to rhizobia and nitrate treatment, and its overexpression systemically inhibits nodulation. However, little is known about the downstream target genes regulated by a MtCLE35 signaling pathway in the root. Moreover, it is not completely clear which stage of symbiosis development is affected by MtCLE35-activated pathway. In order to identify genes regulated by the MtCLE35-induced signaling pathway, we performed a transcriptomic analysis of the roots overexpressing the MtCLE35 gene. Totally, 1122 genes were found to be differentially expressed between MtCLE35-overexpressing and control roots after rhizobial inoculation, among them 185 genes were upregulated and 937 genes were downregulated. Among downregulated genes, many known regulators of legume-rhizobia symbiosis were found. In addition to this, we analyze early steps of interaction between M. truncatula overexpressing the MtCLE35 gene and Sinorhizobium meliloti labeled with fluorescent reporter. We did not observe penetration of S. meliloti into host plant roots with MtCLE35 overexpression. Our data suggest that overexpression of the MtCLE35 gene inhibits nodulation at the very early stages of symbiosis development.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"2 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138603156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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