A. Weisberg, Edward W. Davis II, Javier F. Tabima, M. Putnam, M. Miller, Michael S. Belcher, N. Grünwald, W. Ream, E. Lai, Chih-Horng Kuo, J. Loper, Jeff H. Chang
Agrobacterium tumefaciens is unique in that it can facilitate the interkingdom transfer of DNA and genetically modify its plant host. While Agrobacterium has been coopted for use in the genetic modification of plants, it is also a major pathogen, causing crown gall disease in the nursery, orchard, and vineyard industries. Pathogenicity in Agrobacterium is the result of two components. First is the Ti plasmid, which carries virulence genes and the transferred T-DNA region. The second component is the chromosome of Agrobacterium, which comprises diverse bacterial lineages and multiple species-level groups. The Ti plasmid can be transferred from strain to strain, diversifying the pathogen and complicating efforts to understand its epidemiology. This system provides an opportunity to study transmission of plasmids and their impact on disease persistence and spread. However, the movement of plasmids, and diversity of chromosomal lineages, means that conventional methods of using whole genome SNPs to track outbreaks are not sufficient, and new techniques must be developed. Additionally, Ti plasmids, like Agrobacterium, are genetically diverse and represent multiple plasmid types. Using a framework of 200 sequenced Agrobacterium genomes isolated from around the world, and a previously developed model of Ti plasmid types, we modelled their epidemiology. Key to this study was that we first separately analyzed plasmids and strain. Combining results revealed links between nurseries, potential horizontal transfer of the plasmid between strains within nurseries, global spread of plasmids, and long-term persistence of plasmids in the agricultural system. Agricultural practices have the potential to promote the diversification of pathogens and the emergence of new pathogen lineages.
{"title":"Evolution and epidemiology of global populations of nursery-associated Agrobacterium","authors":"A. Weisberg, Edward W. Davis II, Javier F. Tabima, M. Putnam, M. Miller, Michael S. Belcher, N. Grünwald, W. Ream, E. Lai, Chih-Horng Kuo, J. Loper, Jeff H. Chang","doi":"10.17816/ecogen112374","DOIUrl":"https://doi.org/10.17816/ecogen112374","url":null,"abstract":"Agrobacterium tumefaciens is unique in that it can facilitate the interkingdom transfer of DNA and genetically modify its plant host. While Agrobacterium has been coopted for use in the genetic modification of plants, it is also a major pathogen, causing crown gall disease in the nursery, orchard, and vineyard industries. Pathogenicity in Agrobacterium is the result of two components. First is the Ti plasmid, which carries virulence genes and the transferred T-DNA region. The second component is the chromosome of Agrobacterium, which comprises diverse bacterial lineages and multiple species-level groups. The Ti plasmid can be transferred from strain to strain, diversifying the pathogen and complicating efforts to understand its epidemiology. This system provides an opportunity to study transmission of plasmids and their impact on disease persistence and spread. However, the movement of plasmids, and diversity of chromosomal lineages, means that conventional methods of using whole genome SNPs to track outbreaks are not sufficient, and new techniques must be developed. Additionally, Ti plasmids, like Agrobacterium, are genetically diverse and represent multiple plasmid types. Using a framework of 200 sequenced Agrobacterium genomes isolated from around the world, and a previously developed model of Ti plasmid types, we modelled their epidemiology. Key to this study was that we first separately analyzed plasmids and strain. Combining results revealed links between nurseries, potential horizontal transfer of the plasmid between strains within nurseries, global spread of plasmids, and long-term persistence of plasmids in the agricultural system. Agricultural practices have the potential to promote the diversification of pathogens and the emergence of new pathogen lineages.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"75 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72797689","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}
Plant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE). SE can occur naturally in various plant species and it is widely used for clonal propagation, transformation and regeneration of different crops. This process is regulated by hormone treatment and many proteins, among which WUSCHEL-related homeobox (WOX) transcription factors are believed to play crucial roles. The WOX family is involved in the regulation of a wide range of key developmental programs in different plant organs and tissues. CLE peptides are well-known hormonal regulators of plant development. WOX and CLE genes can be related to each other through feedback regulatory loops. Our previous studies have shown that MtWOX9-1 stimulates SE in Medicago truncatula [1] and overexpression of the MtWOX9-1 gene increases the expression level of the MtCLE08, MtCLE16, MtCLE18 genes in SE. In this study, we examine the overexpression effect of MtCLE08, 16, and 18 on the expression level of MtWOX9-1 gene and a number of other MtWOX genes, which were shown to change expression in SE according to the transcriptomic data. No significant impact of MtCLE overexpression on any MtWOX gene under study was found. Our findings could be a helpful point for searching and studying new morphogenetic regulators controlling SE and could have a positive impact on plant biotechnology in improving the transformation and regeneration capacity for other legumes. The research was supported by grant from the Russian Foundation for Basic Research No. 20-016-00124.
{"title":"The MtWOX and MtCLE genes in the regulation of Medicago truncatula somatic embryogenesis","authors":"Elena P. Efremova, V. Tvorogova, L. Lutova","doi":"10.17816/ecogen112308","DOIUrl":"https://doi.org/10.17816/ecogen112308","url":null,"abstract":"Plant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE). SE can occur naturally in various plant species and it is widely used for clonal propagation, transformation and regeneration of different crops. This process is regulated by hormone treatment and many proteins, among which WUSCHEL-related homeobox (WOX) transcription factors are believed to play crucial roles. The WOX family is involved in the regulation of a wide range of key developmental programs in different plant organs and tissues. CLE peptides are well-known hormonal regulators of plant development. WOX and CLE genes can be related to each other through feedback regulatory loops. \u0000Our previous studies have shown that MtWOX9-1 stimulates SE in Medicago truncatula [1] and overexpression of the MtWOX9-1 gene increases the expression level of the MtCLE08, MtCLE16, MtCLE18 genes in SE. In this study, we examine the overexpression effect of MtCLE08, 16, and 18 on the expression level of MtWOX9-1 gene and a number of other MtWOX genes, which were shown to change expression in SE according to the transcriptomic data. No significant impact of MtCLE overexpression on any MtWOX gene under study was found. \u0000Our findings could be a helpful point for searching and studying new morphogenetic regulators controlling SE and could have a positive impact on plant biotechnology in improving the transformation and regeneration capacity for other legumes. \u0000The research was supported by grant from the Russian Foundation for Basic Research No. 20-016-00124.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81047468","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}
A. V. Chirinskaite, Aleksandra S. Fotina, E. V. Markova, P. Vishnyakova, A. Poltavets, J. Sopova, E. Leonova
Preeclampsia is a multisystem pregnancy disorder that occurs after 20 weeks of gestation, leading to e.g. preterm labor. It is characterized by hypertension, proteinuria, edema, and multiple organ dysfunction. Up to 8% of pregnancies are complicated by preeclampsia, which is one of the most serious causes of maternal and perinatal mortality [1]. For research of pregnancy disorders and development of therapy for it, a mouse model can be used due of the fact that pregnancy development in mice, especially at early stages, is somewhat similar to human and is well-studied, in particular, in terms of molecular biology [2]. One of the possible options for creating mouse models of preeclampsia is considered to be a mutation in the COMT gene encoding сatechol-O-methyltransferase [3]. This enzyme plays an important role in the catecholamines conversion and it also catalyzes the O-methylation of hydroxyestradiol producing methoxyestradiol. COMT gene knockout results in a phenotype similar to preeclampsia with elevated blood pressure and proteinuria [3]. The previous model was obtained through classic transgenesis methods with Neomycin cassette insertion in the COMT locus potentially influencing the results of the experiments. The development of the genome editing systems and its active utilization at Saint Petersburg State University made it possible to obtain a COMT-KO mouse line using CRISPR/Cas9 technology which had not been done in Russia before. This model will allow to effectively study the development of preeclampsia and ways to prevent and treat it. This work was supported by a Saint Petersburg State University grant for the development of scientific research (ID 92561695).
子痫前期是一种多系统妊娠疾病，发生在妊娠20周后，可导致早产等。其特点是高血压、蛋白尿、水肿和多器官功能障碍。高达8%的妊娠合并先兆子痫，这是孕产妇和围产期死亡的最严重原因之一[1]。对于妊娠障碍的研究和治疗方法的开发，可以使用小鼠模型，因为小鼠的妊娠发育，特别是在早期阶段，与人类有一定的相似之处，并且在分子生物学方面得到了很好的研究[2]。创建子痫前期小鼠模型的一种可能选择被认为是编码乙酰胆碱- o -甲基转移酶的COMT基因突变[3]。该酶在儿茶酚胺转化中起重要作用，并催化羟雌二醇的o -甲基化生成甲氧基雌二醇。COMT基因敲除导致的表型类似于先兆子痫，伴有血压升高和蛋白尿[3]。先前的模型是通过经典的转基因方法获得的，在COMT位点插入新霉素盒可能会影响实验结果。基因组编辑系统的发展及其在圣彼得堡国立大学的积极利用，使得使用CRISPR/Cas9技术获得COMT-KO小鼠品系成为可能，这在俄罗斯以前从未做过。这个模型将允许有效地研究先兆子痫的发展和预防和治疗方法。这项工作得到了圣彼得堡国立大学科学研究发展补助金(ID 92561695)的支持。
{"title":"Design of COMT-Knockout mouse as a preeclampsia mode","authors":"A. V. Chirinskaite, Aleksandra S. Fotina, E. V. Markova, P. Vishnyakova, A. Poltavets, J. Sopova, E. Leonova","doi":"10.17816/ecogen112358","DOIUrl":"https://doi.org/10.17816/ecogen112358","url":null,"abstract":"Preeclampsia is a multisystem pregnancy disorder that occurs after 20 weeks of gestation, leading to e.g. preterm labor. It is characterized by hypertension, proteinuria, edema, and multiple organ dysfunction. Up to 8% of pregnancies are complicated by preeclampsia, which is one of the most serious causes of maternal and perinatal mortality [1]. For research of pregnancy disorders and development of therapy for it, a mouse model can be used due of the fact that pregnancy development in mice, especially at early stages, is somewhat similar to human and is well-studied, in particular, in terms of molecular biology [2]. One of the possible options for creating mouse models of preeclampsia is considered to be a mutation in the COMT gene encoding сatechol-O-methyltransferase [3]. This enzyme plays an important role in the catecholamines conversion and it also catalyzes the O-methylation of hydroxyestradiol producing methoxyestradiol. COMT gene knockout results in a phenotype similar to preeclampsia with elevated blood pressure and proteinuria [3]. The previous model was obtained through classic transgenesis methods with Neomycin cassette insertion in the COMT locus potentially influencing the results of the experiments. The development of the genome editing systems and its active utilization at Saint Petersburg State University made it possible to obtain a COMT-KO mouse line using CRISPR/Cas9 technology which had not been done in Russia before. This model will allow to effectively study the development of preeclampsia and ways to prevent and treat it. \u0000This work was supported by a Saint Petersburg State University grant for the development of scientific research (ID 92561695).","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"151 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76457031","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}
Amyloids are fibrous protein structures often found in patients with severe diseases, such as Alzheimers, Parkinsons diseases etc. A number of studies have shown that the production of heterologous amyloidogenic proteins in Saccharomyces cerevisiae strains results in formation of amyloid aggregates with properties similar to those found in mammals. Amyloid aggregates formed in yeasts usually do not have their own phenotypic manifestation. To assess amyloidogenic potential of individual proteins a yeast test-system was developed under supervision of Prof. Y.O. Chernoff. The system is based on usage of genetically modified S. cerevisiae cells auxotrophic for certain growth factors, allowing effective phenotypic selection to search for amyloidogenic proteins within proteomes of various organisms [1]. Using this test-system, our laboratory evaluated amyloid potential of a spectrum of human proteins, the amyloidogenicity of which was previously predicted by bioinformatics algorithms. The proteins that have shown amyloidogenic potential in yeast-based model are being currently tested in vitro and in vivo. Some mutant Escherichia coli strains can be applied for studying propensity of heterologous proteins to form amyloids in vitro. Thus, application of genetically modified microorganisms makes it possible to identify new human amyloidogenic proteins and to improve predictive ability of bioinformatics algorithms. The research is supported by RSF grant №20-14-00148 and by St. Petersburg State University (project No. 93025998). Authors acknowledge SPbSU Resource Centers Chromas, Molecular and Cell Technologies and Biobank.
{"title":"Application of genetically modified microorganisms for potential human amyloids search","authors":"Marina V. Ryabinina, Andrew A. Zelinsky, A. Rubel","doi":"10.17816/ecogen112346","DOIUrl":"https://doi.org/10.17816/ecogen112346","url":null,"abstract":"Amyloids are fibrous protein structures often found in patients with severe diseases, such as Alzheimers, Parkinsons diseases etc. A number of studies have shown that the production of heterologous amyloidogenic proteins in Saccharomyces cerevisiae strains results in formation of amyloid aggregates with properties similar to those found in mammals. \u0000Amyloid aggregates formed in yeasts usually do not have their own phenotypic manifestation. To assess amyloidogenic potential of individual proteins a yeast test-system was developed under supervision of Prof. Y.O. Chernoff. The system is based on usage of genetically modified S. cerevisiae cells auxotrophic for certain growth factors, allowing effective phenotypic selection to search for amyloidogenic proteins within proteomes of various organisms [1]. Using this test-system, our laboratory evaluated amyloid potential of a spectrum of human proteins, the amyloidogenicity of which was previously predicted by bioinformatics algorithms. The proteins that have shown amyloidogenic potential in yeast-based model are being currently tested in vitro and in vivo. Some mutant Escherichia coli strains can be applied for studying propensity of heterologous proteins to form amyloids in vitro. Thus, application of genetically modified microorganisms makes it possible to identify new human amyloidogenic proteins and to improve predictive ability of bioinformatics algorithms. \u0000The research is supported by RSF grant №20-14-00148 and by St. Petersburg State University (project No. 93025998). Authors acknowledge SPbSU Resource Centers Chromas, Molecular and Cell Technologies and Biobank.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77660268","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}
E. Ilina, A. S. Kiryushkin, V. A. Puchkova, K. Demchenko
Genetic transformation of most dicotyledonous plants by Rhizobium rhizogenes (also known as Agrobacterium rhizogenes) results in production of composite plants plants consisting of wild-type shoot and transgenic root system. Composite plants are the suitable model for investigation of hormonal mechanisms related to development of the root system as regulatory links between the root system and the shoot maintains in such plants. In most plants initiation of lateral root primordia occurs above the elongation zone [1]. However, in cucurbits and some other species, including important cereal crop buckwheat (Fagopyrum esculentum Moench), lateral root primordia initiation and development occurs in the apical meristem of the parental root [2, 3]. The phytohormone auxin is a key regulator of lateral root development. Fusions of auxin-responsive promoters and reporter genes can be used to study the role of auxin in the development of root system of non-model plants such as cucumber (Cucumis sativus L.) and buckwheat [4]. The agrobacterium mediated transformation technique of cucurbits [5] has been adapted for buckwheat. R. rhizogenes strain R1000 was used in all transformations. Set of binary vectors based on pKGW-RR-MGW or pKGW-MGW was developed to study auxin response maxima (DR5::mNeonGreen) or auxin transport (fusions of genes encoding auxin efflux proteins PIN and mNeonGreen). Pattern of auxin response maxima was similar in both species and included quiescent center and initial cells, columella, xylem cell files and lateral root primordia on all stages of development. Members of CsPIN1 (CsPINb and CsSoPIN1) group contributed unequally in generation of auxin maximum required for lateral root primordium initiation. The research was supported by the RFBR grant 20-016-00233-a.
{"title":"Composite plants of cucumber and buckwheat as a tool to study auxin distribution and transport in the root system","authors":"E. Ilina, A. S. Kiryushkin, V. A. Puchkova, K. Demchenko","doi":"10.17816/ecogen112369","DOIUrl":"https://doi.org/10.17816/ecogen112369","url":null,"abstract":"Genetic transformation of most dicotyledonous plants by Rhizobium rhizogenes (also known as Agrobacterium rhizogenes) results in production of composite plants plants consisting of wild-type shoot and transgenic root system. Composite plants are the suitable model for investigation of hormonal mechanisms related to development of the root system as regulatory links between the root system and the shoot maintains in such plants. \u0000In most plants initiation of lateral root primordia occurs above the elongation zone [1]. However, in cucurbits and some other species, including important cereal crop buckwheat (Fagopyrum esculentum Moench), lateral root primordia initiation and development occurs in the apical meristem of the parental root [2, 3]. \u0000The phytohormone auxin is a key regulator of lateral root development. Fusions of auxin-responsive promoters and reporter genes can be used to study the role of auxin in the development of root system of non-model plants such as cucumber (Cucumis sativus L.) and buckwheat [4]. \u0000The agrobacterium mediated transformation technique of cucurbits [5] has been adapted for buckwheat. R. rhizogenes strain R1000 was used in all transformations. Set of binary vectors based on pKGW-RR-MGW or pKGW-MGW was developed to study auxin response maxima (DR5::mNeonGreen) or auxin transport (fusions of genes encoding auxin efflux proteins PIN and mNeonGreen). \u0000Pattern of auxin response maxima was similar in both species and included quiescent center and initial cells, columella, xylem cell files and lateral root primordia on all stages of development. Members of CsPIN1 (CsPINb and CsSoPIN1) group contributed unequally in generation of auxin maximum required for lateral root primordium initiation. \u0000The research was supported by the RFBR grant 20-016-00233-a.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86461265","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}
K. Kulichikhin, Andrew A. Zelinsky, Natalia A. Gorsheneva, Marina V. Ryabinina, Alexey V. Grizel, V. V. Azarov, A. Rubel
Amyloid protein aggregation is a key factor in the development of a variety of serious diseases in humans, commonly named as amyloidoses (Alzheimers and Parkinsons diseases, type II diabetes, etc.), and a determinant of protein-based inheritance in lower eukaryotes. In yeast, translation termination factor Sup35 is one of the most extensively studied amyloidogenic proteins. Aggregation of Sup35 (induction of [PSI+] prion) decreases its functional activity and leads to the suppression of nonsense-mutation as stop-codons become recognized as meaningful more frequently. This phenomenon is the basis of phenotypic detection of Sup35 aggregation in yeast strains possessing nonsense mutation ade1-14 in ADE1 gene. Yeast is convenient model for genetic, biochemical and molecular biology studies. Yeast genome can be easily edited and plasmids can be used for induction of gene expression. Yeast is suitable for analysis of mammalian genes and proteins and thus can be applied for the analysis of amyloidogenic properties of proteins associated with human diseases. Phenotyping detection of [PSI+] prion can be modified for the analysis of amyloid aggregation of mammalian proteins in yeast. We use genetically modified yeasts Saccharomyces cerevisiae adopted for amyloid biology research. The mutations leading to auxotrophy toward certain amino acids (leucine, lysine, tryptophane, histidine) and nucleobases (adenine, uracil) were implemented into yeast genome allowing phenotyping detection of [PSI+] and the usage of plasmids for the investigation of mammalian protein in yeast. Application of yeast-based experimental system for studies of different aspects of human amyloidoses is discussed. This study was supported by Saint Petersburg State University (project 93025998).
{"title":"Genetically modified yeasts in studies of human amyloidosis","authors":"K. Kulichikhin, Andrew A. Zelinsky, Natalia A. Gorsheneva, Marina V. Ryabinina, Alexey V. Grizel, V. V. Azarov, A. Rubel","doi":"10.17816/ecogen112321","DOIUrl":"https://doi.org/10.17816/ecogen112321","url":null,"abstract":"Amyloid protein aggregation is a key factor in the development of a variety of serious diseases in humans, commonly named as amyloidoses (Alzheimers and Parkinsons diseases, type II diabetes, etc.), and a determinant of protein-based inheritance in lower eukaryotes. In yeast, translation termination factor Sup35 is one of the most extensively studied amyloidogenic proteins. Aggregation of Sup35 (induction of [PSI+] prion) decreases its functional activity and leads to the suppression of nonsense-mutation as stop-codons become recognized as meaningful more frequently. This phenomenon is the basis of phenotypic detection of Sup35 aggregation in yeast strains possessing nonsense mutation ade1-14 in ADE1 gene. \u0000Yeast is convenient model for genetic, biochemical and molecular biology studies. Yeast genome can be easily edited and plasmids can be used for induction of gene expression. Yeast is suitable for analysis of mammalian genes and proteins and thus can be applied for the analysis of amyloidogenic properties of proteins associated with human diseases. Phenotyping detection of [PSI+] prion can be modified for the analysis of amyloid aggregation of mammalian proteins in yeast. \u0000We use genetically modified yeasts Saccharomyces cerevisiae adopted for amyloid biology research. The mutations leading to auxotrophy toward certain amino acids (leucine, lysine, tryptophane, histidine) and nucleobases (adenine, uracil) were implemented into yeast genome allowing phenotyping detection of [PSI+] and the usage of plasmids for the investigation of mammalian protein in yeast. \u0000Application of yeast-based experimental system for studies of different aspects of human amyloidoses is discussed. \u0000This study was supported by Saint Petersburg State University (project 93025998).","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"115 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80481017","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}
The process of horizontal gene transfer causes the appearance of natural genetically modified organisms. At the moment, it is known that over 7% of dicotyledonous plant species are naturally transgenic, i.e. nGMO [1]. These plants contain the genes of agrobacteria, which are integrated in the nuclear genome during infection. In some species of naturally transgenic plants, agrobacterial genes have been preserved for millions of years of evolution. Among these genes, genes encoding octopine/vitopine synthase (ocs/vis) can be distinguished [2]. The study of homologues of octopin/vitopin synthase genes in naturally transgenic plants: their structures and diversity, products of encoded enzymes will allow us to establish the functions and evolutionary role of homologues in nGMO. Currently, bioinformatic and genetic engineering methods are used to solve these problems. ocsvis-like were found in 7 species: Albizia julibrissin Durazz., Cenostigma pyramidale (Tul.) Gagnon G.P.Lewis, Paulownia fortunei (Seem.) Hemsl., Pterocarya stenoptera C.DC., Rehmannia glutinosa Steud., Santalum album L., Viscum album L. In total twenty one ocs/vis sequences are known in 17 nGMO species. Twenty sequences are intact. This may indicate the functional significance of these genes for nGMO. Phylogenetic analysis of currently known ocs/vis-like genes of Agrobacterium, Rhizobium and natural GMOs suggests that diversity of studied genes is wider, than it was estimated based on agrobacterial sequences. On the phylogenetic tree constructed by the neighbor-joining method, 6 clusters for ocs/vis can be distinguished. Three clusters contain nGMOs and agrobacteria, showing the relationship of the T-DNA sequences of nGMO with those of currently known strains of of Agrobacterium/Rhizobium. Three clusters contain only nGMOs. One of them consists of species that belong to the Cannabaceae family. Other clusters are heterogeneous. No significant ecological similarities were found among the studied species. The obtained results can be used to study the diversity of ancient and modern strains of agrobacteria, their host specificity and the possible role of their genes in plant evolution. The work was supported by the RSF, grant 21-14-00050 and Research Resource Center for molecular and cellular technologies of Saint Petersburg State University.
{"title":"Homologues of octopine/vitopine synthase genes in natural GMOs","authors":"Anton D. Shaposhnikov, T. Matveeva","doi":"10.17816/ecogen112343","DOIUrl":"https://doi.org/10.17816/ecogen112343","url":null,"abstract":"The process of horizontal gene transfer causes the appearance of natural genetically modified organisms. At the moment, it is known that over 7% of dicotyledonous plant species are naturally transgenic, i.e. nGMO [1]. These plants contain the genes of agrobacteria, which are integrated in the nuclear genome during infection. In some species of naturally transgenic plants, agrobacterial genes have been preserved for millions of years of evolution. Among these genes, genes encoding octopine/vitopine synthase (ocs/vis) can be distinguished [2]. \u0000The study of homologues of octopin/vitopin synthase genes in naturally transgenic plants: their structures and diversity, products of encoded enzymes will allow us to establish the functions and evolutionary role of homologues in nGMO. Currently, bioinformatic and genetic engineering methods are used to solve these problems. \u0000ocsvis-like were found in 7 species: Albizia julibrissin Durazz., Cenostigma pyramidale (Tul.) Gagnon G.P.Lewis, Paulownia fortunei (Seem.) Hemsl., Pterocarya stenoptera C.DC., Rehmannia glutinosa Steud., Santalum album L., Viscum album L. In total twenty one ocs/vis sequences are known in 17 nGMO species. Twenty sequences are intact. This may indicate the functional significance of these genes for nGMO. \u0000Phylogenetic analysis of currently known ocs/vis-like genes of Agrobacterium, Rhizobium and natural GMOs suggests that diversity of studied genes is wider, than it was estimated based on agrobacterial sequences. On the phylogenetic tree constructed by the neighbor-joining method, 6 clusters for ocs/vis can be distinguished. Three clusters contain nGMOs and agrobacteria, showing the relationship of the T-DNA sequences of nGMO with those of currently known strains of of Agrobacterium/Rhizobium. Three clusters contain only nGMOs. One of them consists of species that belong to the Cannabaceae family. Other clusters are heterogeneous. No significant ecological similarities were found among the studied species. \u0000The obtained results can be used to study the diversity of ancient and modern strains of agrobacteria, their host specificity and the possible role of their genes in plant evolution. \u0000The work was supported by the RSF, grant 21-14-00050 and Research Resource Center for molecular and cellular technologies of Saint Petersburg State University.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73078230","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}
Pavel Yu. Lipatov, F. D. Bogomaz, Konstantin D. Gosudarev, Sofya A. Kondrashova, Maxim V. Kuchevsky, Nikita L. Malyuga, Egor V. Myagkiy, Marta V. Sergeenkova, Valeria R. Tverdokhlebova, Anna D. Shtina, T. Matveeva, G. Khafizova
Naturally transgenic plants represent the result of Agrobacterium-mediated gene transfer. T-DNA of soil bacteria Agrobacterium integrated into plants genome is called cellular T-DNA (cT-DNA) [1]. Today, more than 50 species of naturally transgenic plants, or natural GMO (nGMO) are known [2, 3]. The function of cT-DNA in plants remains unknown. It is assumed that the fixation of transgenes could give plants different selective advantages depending on which genes had been integrated into the plant [4]. In order to clarify this issue, it is necessary to study more naturally transgenic plants. Until recently, the list of nGM plants contained less than 2 dozen species, but a search through genomic and transriptomic sequencing data made it possible to more than double this list [2]. In this work, we used the same approach, looking for cT-DNA genes in whole genome sequencing data that have appeared in the NCBI WGS since 2021. We found 14 new species of naturally transgenic plants, among which the most extended cT-DNAs were found in Triadica sebifera, Lonicera japonica, and Lonicera maackii. The cT-DNAs in these species are organized as imperfect inverted repeats. In the genomes of the species Paulownia fortunei, Apocynum venetum, Elaeagnus angustifolia, Erythroxylum havanense, E. densum, E. daphnites, E. cataractarum, Ceriops decandra, Camellia oleifera, Silene uniflora, short cT-DNAs containing only opine synthesis genes were found. We also estimated the approximate age of the cT-DNAs. The first described examples date back to the Late Paleogene, and the process continues to the present. Thus, we can conclude that natural GMOs are a widespread phenomenon, many aspects of which remain unclear, requiring additional research on the topic. The article was made with support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 dated 22.04.2022 on providing a grant in the form of subsidies from the federal budget of the Russian Federation. The grant was provided for state support for the creation and development of a world-class scientific center, Agrotechnologies for the Future.
{"title":"New cellular T-DNAs in naturally transgenic plants","authors":"Pavel Yu. Lipatov, F. D. Bogomaz, Konstantin D. Gosudarev, Sofya A. Kondrashova, Maxim V. Kuchevsky, Nikita L. Malyuga, Egor V. Myagkiy, Marta V. Sergeenkova, Valeria R. Tverdokhlebova, Anna D. Shtina, T. Matveeva, G. Khafizova","doi":"10.17816/ecogen112352","DOIUrl":"https://doi.org/10.17816/ecogen112352","url":null,"abstract":"Naturally transgenic plants represent the result of Agrobacterium-mediated gene transfer. T-DNA of soil bacteria Agrobacterium integrated into plants genome is called cellular T-DNA (cT-DNA) [1]. Today, more than 50 species of naturally transgenic plants, or natural GMO (nGMO) are known [2, 3]. The function of cT-DNA in plants remains unknown. It is assumed that the fixation of transgenes could give plants different selective advantages depending on which genes had been integrated into the plant [4]. In order to clarify this issue, it is necessary to study more naturally transgenic plants. Until recently, the list of nGM plants contained less than 2 dozen species, but a search through genomic and transriptomic sequencing data made it possible to more than double this list [2]. In this work, we used the same approach, looking for cT-DNA genes in whole genome sequencing data that have appeared in the NCBI WGS since 2021. We found 14 new species of naturally transgenic plants, among which the most extended cT-DNAs were found in Triadica sebifera, Lonicera japonica, and Lonicera maackii. The cT-DNAs in these species are organized as imperfect inverted repeats. In the genomes of the species Paulownia fortunei, Apocynum venetum, Elaeagnus angustifolia, Erythroxylum havanense, E. densum, E. daphnites, E. cataractarum, Ceriops decandra, Camellia oleifera, Silene uniflora, short cT-DNAs containing only opine synthesis genes were found. We also estimated the approximate age of the cT-DNAs. The first described examples date back to the Late Paleogene, and the process continues to the present. Thus, we can conclude that natural GMOs are a widespread phenomenon, many aspects of which remain unclear, requiring additional research on the topic. \u0000The article was made with support of the Ministry of Science and Higher Education of the Russian Federation in accordance with agreement No. 075-15-2022-322 dated 22.04.2022 on providing a grant in the form of subsidies from the federal budget of the Russian Federation. The grant was provided for state support for the creation and development of a world-class scientific center, Agrotechnologies for the Future.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"39 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74864150","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}
Veronika Y. Simonova, Nikolai V. Kozlov, E. A. Potsenkovskaia, V. Tvorogova, L. Lutova
Pisum sativum L. (pea) is one of the most important agricultural crops, because its seeds have high protein content, and, due to its ability have symbiotic relationships with nitrogen-fixing bacteria, these plants need less fertilizers. Nevertheless, we are faced with the need to improve old and create new methods for obtaining novel varieties of peas and other agricultural plants. The formation of regenerated pea plants is difficult to achieve in the in vitro culture. Accordingly, transformation of this species is a laborious process. In this regard, the search for morphogenic regulators of somatic embryogenesis (SE) in pea is an urgent problem. A number of publications reported on the genes regulating the SE process in a model plant from the legume family, Medicago truncatula [1]. In our study, we search for the in vitro cultivation system in peas, suitable to test the effect of putative SE regulators in this species. We tested several pea transformation techniques using different explant variants: embryonic axes from mature and immature seeds, as well as shoot apexes. Out of the tested options, the transformation of mature seeds turned out to be optimal. We also designed a set of DNA constructs in silico, which are suitable for the search of morphogenic regulators in peas.
{"title":"Development of a testing system for regeneration regulators in Pisum sativum L.","authors":"Veronika Y. Simonova, Nikolai V. Kozlov, E. A. Potsenkovskaia, V. Tvorogova, L. Lutova","doi":"10.17816/ecogen112419","DOIUrl":"https://doi.org/10.17816/ecogen112419","url":null,"abstract":"Pisum sativum L. (pea) is one of the most important agricultural crops, because its seeds have high protein content, and, due to its ability have symbiotic relationships with nitrogen-fixing bacteria, these plants need less fertilizers. Nevertheless, we are faced with the need to improve old and create new methods for obtaining novel varieties of peas and other agricultural plants. The formation of regenerated pea plants is difficult to achieve in the in vitro culture. Accordingly, transformation of this species is a laborious process. In this regard, the search for morphogenic regulators of somatic embryogenesis (SE) in pea is an urgent problem. A number of publications reported on the genes regulating the SE process in a model plant from the legume family, Medicago truncatula [1]. In our study, we search for the in vitro cultivation system in peas, suitable to test the effect of putative SE regulators in this species. We tested several pea transformation techniques using different explant variants: embryonic axes from mature and immature seeds, as well as shoot apexes. Out of the tested options, the transformation of mature seeds turned out to be optimal. We also designed a set of DNA constructs in silico, which are suitable for the search of morphogenic regulators in peas.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84428524","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}
The paper covers major threats associated with wide-range introduction and cultivation of transgenic plants due to germplasm mixing with that of indigenous species of natural plant communities and risks of transgenic plants adverse impact on the environment. Among them are: influencing non-target species, invasive power, possibility of GMPs escaping into the environment by horizontal gene transfer as well as harmful effect on the soil biota. Currently, herbicide- and pest-resistant genetically modified plants (GMP) became an integral part of contemporary agrotechnologies in many economies [1]. However, most countries lack national strategy providing science-based substantiated procedure of creating, distribution and safe production of GMP. Rapid development of agricultural biotechnology and GMP production offered many economical benefits but also caused concern due to their potential environmental impact. To date, truly negative effects of GMP production, revealed in the course of growing, are known: harmful effect of entomocide Cry-proteins (Bt endotoxins) on non-target biota, target phytophage resistance to insecticidal plants, phytophage species succession to replace the species eliminated in the agrocoenosis. Vertical transfer of GMP transgenes (repollination between transgenic plants and wild species or isogenic varieties), as well as slow decomposition of transgenic plants remains all these factors can have remote environmental consequences [2, 3]. Wind-dispersed pollen of insecticidal GMP contaminates soil and open water reservoirs by toxins, thus posing potential hazards for aquatic organisms and geobionts (including rhizospheric organisms). Thus, uncontrolled GMP production and introduction, creates a real threat of losing biodiversity and genetic diversity of indigenous plants due to biological contamination. Therefore, GMP cultivation and monitoring in the fields is of exceptional importance and must be regulated by a science-based national strategy. This strategy would allow to exclude agroecological and environmental genetic risks, to keep the genetic diversity of natural plant communities.
{"title":"Transgenic plants — a threat to local flora?","authors":"Yu.S. Cheryatova, E. Y. Yembaturova","doi":"10.17816/ecogen112372","DOIUrl":"https://doi.org/10.17816/ecogen112372","url":null,"abstract":"The paper covers major threats associated with wide-range introduction and cultivation of transgenic plants due to germplasm mixing with that of indigenous species of natural plant communities and risks of transgenic plants adverse impact on the environment. Among them are: influencing non-target species, invasive power, possibility of GMPs escaping into the environment by horizontal gene transfer as well as harmful effect on the soil biota. \u0000Currently, herbicide- and pest-resistant genetically modified plants (GMP) became an integral part of contemporary agrotechnologies in many economies [1]. However, most countries lack national strategy providing science-based substantiated procedure of creating, distribution and safe production of GMP. Rapid development of agricultural biotechnology and GMP production offered many economical benefits but also caused concern due to their potential environmental impact. To date, truly negative effects of GMP production, revealed in the course of growing, are known: harmful effect of entomocide Cry-proteins (Bt endotoxins) on non-target biota, target phytophage resistance to insecticidal plants, phytophage species succession to replace the species eliminated in the agrocoenosis. Vertical transfer of GMP transgenes (repollination between transgenic plants and wild species or isogenic varieties), as well as slow decomposition of transgenic plants remains all these factors can have remote environmental consequences [2, 3]. Wind-dispersed pollen of insecticidal GMP contaminates soil and open water reservoirs by toxins, thus posing potential hazards for aquatic organisms and geobionts (including rhizospheric organisms). \u0000Thus, uncontrolled GMP production and introduction, creates a real threat of losing biodiversity and genetic diversity of indigenous plants due to biological contamination. Therefore, GMP cultivation and monitoring in the fields is of exceptional importance and must be regulated by a science-based national strategy. This strategy would allow to exclude agroecological and environmental genetic risks, to keep the genetic diversity of natural plant communities.","PeriodicalId":11431,"journal":{"name":"Ecological genetics","volume":"93 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72849198","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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