1
|
Bogomaz OD, Bemova VD, Mirgorodskii NA, Matveeva TV. Evolutionary Fate of the Opine Synthesis Genes in the Arachis L. Genomes. BIOLOGY 2024; 13:601. [PMID: 39194539 DOI: 10.3390/biology13080601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024]
Abstract
Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of "Agrobacterium". In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts.
Collapse
Affiliation(s)
- Olesja D Bogomaz
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | - Victoria D Bemova
- Department of Oil and Fibre Crops, N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg 190031, Russia
| | - Nikita A Mirgorodskii
- Field of Study Plant Genetics and Biotechnology, University "Sirius" Krasnodar Region, Federal Territory, Sirius 354340, Russia
| | - Tatiana V Matveeva
- Department of Genetic and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia
| |
Collapse
|
2
|
Khafizova GV, Sierro N, Ivanov NV, Sokornova SV, Polev DE, Matveeva TV. Nicotiana noctiflora Hook. Genome Contains Two Cellular T-DNAs with Functional Genes. PLANTS (BASEL, SWITZERLAND) 2023; 12:3787. [PMID: 38005684 PMCID: PMC10674353 DOI: 10.3390/plants12223787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/01/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023]
Abstract
Agrobacterium (Rhizobium)-mediated transformation leads to the formation of crown galls or hairy roots on infected plants. These effects develop due to the activity of T-DNA genes, gathered on a big plasmid, acquired from agrobacteria during horizontal gene transfer. However, a lot of plant species are known to contain such sequences, called cellular T-DNAs (cT-DNAs), and maintain normal phenotypes. Some of the genes remain intact, which leads to the conclusion of their functional role in plants. In this study, we present a comprehensive analysis of the cT-DNAs in the Nicotiana noctiflora Hook. genome, including gene expression and opine identification. Deep sequencing of the Nicotiana noctiflora genome revealed the presence of two different cT-DNAs, NnT-DNA1 and NnT-DNA2, which contain the intact genes iaaM, iaaH, acs, orf13, orf13a, and orf14. According to the expression analysis results, all these genes are most active in roots in comparison with other organs, which is consistent with data on cT-DNA gene expression in other plant species. We also used genetic engineering approaches and HPTLC and HPLC-MS methods to investigate the product of the acs gene (agrocinopine synthase), which turned out to be similar to agrocinopine A. Overall, this study expands our knowledge of cT-DNAs in plants and brings us closer to understanding their possible functions. Further research of cT-DNAs in different species and their functional implications could contribute to advancements in plant genetics and potentially unveil novel traits with practical applications in agriculture and other fields.
Collapse
Affiliation(s)
- Galina V. Khafizova
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia; (G.V.K.)
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland; (N.S.); (N.V.I.)
| | - Nikolai V. Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland; (N.S.); (N.V.I.)
| | - Sofie V. Sokornova
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia; (G.V.K.)
| | - Dmitrii E. Polev
- St. Petersburg Pasteur Institute, Saint Petersburg 197101, Russia
| | - Tatiana V. Matveeva
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia; (G.V.K.)
| |
Collapse
|
3
|
Chen K, Liu H, Blevins T, Hao J, Otten L. Extensive natural Agrobacterium-induced transformation in the genus Camellia. PLANTA 2023; 258:81. [PMID: 37715842 DOI: 10.1007/s00425-023-04234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023]
Abstract
MAIN CONCLUSION The genus Camellia underwent extensive natural transformation by Agrobacterium. Over a period of 15 million years, at least 12 different inserts accumulated in 72 investigated Camellia species. Like a wide variety of other wild and cultivated plants, Camellia species carry cellular T-DNA sequences (cT-DNAs) in their nuclear genomes, resulting from natural Agrobacterium-mediated transformation. Short and long DNA sequencing reads of 435 accessions belonging to 72 Camellia species (representing 12 out of 14 sections) were investigated for the occurrence of cT-DNA insertions. In all, 12 different cT-DNAs were recovered, either completely or partially, called CaTA to CaTL. Divergence analysis of internal cT-DNA repeats revealed that the insertion events span a period from 0.075 to 15 Mio years ago, and yielded an average transformation frequency of one event per 1.25 Mio years. The two oldest inserts, CaTA and CaTD, have been modified by spontaneous deletions and inversions, and by insertion of various plant sequences. In those cases where enough accessions were available (C. japonica, C. oleifera, C. chekiangoleosa, C. sasanqua and C. pitardii), the younger cT-DNA inserts showed a patchy distribution among different accessions of each species, indicating that they are not genetically fixed. It could be shown that Camellia breeding has led to intersectional transfer of cT-DNAs. Altogether, the cT-DNAs cover 374 kb, and carry 47 open reading frames (ORFs). Two Camellia cT-DNA genes, CaTH-orf358 and CaTK-orf8, represent new types of T-DNA genes. With its large number of cT-DNA sequences, the genus Camellia constitutes an interesting model for the study of natural Agrobacterium transformants.
Collapse
Affiliation(s)
- Ke Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Hai Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Todd Blevins
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Rue du Général Zimmer 12, 67084, Strasbourg, France
| | - Jie Hao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Léon Otten
- Institut de Biologie Moléculaire des Plantes du C.N.R.S., Rue du Général Zimmer 12, 67084, Strasbourg, France
| |
Collapse
|
4
|
Zhidkin R, Zhurbenko P, Bogomaz O, Gorodilova E, Katsapov I, Antropov D, Matveeva T. Biodiversity of rolB/C-like Natural Transgene in the Genus Vaccinium L. and Its Application for Phylogenetic Studies. Int J Mol Sci 2023; 24:ijms24086932. [PMID: 37108096 PMCID: PMC10138537 DOI: 10.3390/ijms24086932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
A variety of plant species found in nature contain agrobacterial T-DNAs in their genomes which they transmit in a series of sexual generations. Such T-DNAs are called cellular T-DNAs (cT-DNAs). cT-DNAs have been discovered in dozens of plant genera, and are suggested to be used in phylogenetic studies, since they are well-defined and unrelated to other plant sequences. Their integration into a particular chromosomal site indicates a founder event and a clear start of a new clade. cT-DNA inserts do not disseminate in the genome after insertion. They can be large and old enough to generate a range of variants, thereby allowing the construction of detailed trees. Unusual cT-DNAs (containing the rolB/C-like gene) were found in our previous study in the genome data of two Vaccinium L. species. Here, we present a deeper study of these sequences in Vaccinium L. Molecular-genetic and bioinformatics methods were applied for sequencing, assembly, and analysis of the rolB/C-like gene. The rolB/C-like gene was discovered in 26 new Vaccinium species and Agapetes serpens (Wight) Sleumer. Most samples were found to contain full-size genes. It allowed us to develop approaches for the phasing of cT-DNA alleles and reconstruct a Vaccinium phylogenetic relationship. Intra- and interspecific polymorphism found in cT-DNA makes it possible to use it for phylogenetic and phylogeographic studies of the Vaccinium genus.
Collapse
Affiliation(s)
- Roman Zhidkin
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Peter Zhurbenko
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia
- Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg 197022, Russia
| | - Olesya Bogomaz
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | | | - Ivan Katsapov
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Dmitry Antropov
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia
| | - Tatiana Matveeva
- Department of Genetic and Breeding, St. Petersburg State University, Saint Petersburg 199034, Russia
| |
Collapse
|
5
|
Zhang W, Zuo Z, Zhu Y, Feng Y, Wang Y, Zhao H, Zhao N, Zhang H, He S, Liu Q, Xu R, Zhai H, Gao S. Fast track to obtain heritable transgenic sweet potato inspired by its evolutionary history as a naturally transgenic plant. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:671-673. [PMID: 36533872 PMCID: PMC10037143 DOI: 10.1111/pbi.13986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Wen Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhidan Zuo
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yixuan Zhu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yuanxu Feng
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yong Wang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haoqiang Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Ran Xu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical CropsHainan UniversityHaikouChina
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & BiotechnologyChina Agricultural UniversityBeijingChina
| |
Collapse
|
6
|
Chen K, Zhurbenko P, Danilov L, Matveeva T, Otten L. Conservation of an Agrobacterium cT-DNA insert in Camellia section Thea reveals the ancient origin of tea plants from a genetically modified ancestor. FRONTIERS IN PLANT SCIENCE 2022; 13:997762. [PMID: 36561442 PMCID: PMC9763466 DOI: 10.3389/fpls.2022.997762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/16/2022] [Indexed: 05/13/2023]
Abstract
Introduction Many higher plants contain cellular T-DNA (cT-DNA) sequences from Agrobacterium and have been called "natural genetically modified organisms" (nGMOs). Among these natural transformants, the tea plant Camellia sinensis var. sinensis cv. Shuchazao contains a single 5.5 kb T-DNA fragment (CaTA) with three inactive T-DNA genes, with a 1 kb inverted repeat at the ends. Camellia plants are allogamous, so that each individual may contain two different CaTA alleles. Methods 142 Camellia accessions, belonging to 10 of 11 species of the section Thea, were investigated for the presence of CaTA alleles. Results discussion All accessions were found to contain the CaTA insert, showing that section Thea derives from a single transformed ancestor. Allele phasing showed that 82 accessions each contained two different CaTA alleles, 60 others had a unique allele. A phylogenetic tree of these 225 alleles showed two separate groups, A and B, further divided into subgroups. Indel distribution corresponded in most cases with these groups. The alleles of the different Camellia species were distributed over groups A and B, and different species showed very similar CaTA alleles. This indicates that the species boundaries for section Thea may not be precise and require revision. The nucleotide divergence of the indirect CaTA repeats indicates that the cT-DNA insertion took place about 15 Mio years ago, before the emergence of section Thea. The CaTA structure of a C. fangchengensis accession has an exceptional structure. We present a working model for the origin and evolution of nGMO plants derived from allogamous transformants.
Collapse
Affiliation(s)
- Ke Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Peter Zhurbenko
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint Petersburg, Russia
- Komarov Botanical Institute of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Lavrentii Danilov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Tatiana Matveeva
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint Petersburg, Russia
| | - Léon Otten
- Institute of Plant Molecular Biology, Centre National de Recherche Scientifique (C.N.R.S.), Strasbourg, France
| |
Collapse
|
7
|
Khafizova GV, Matveeva TV. Agrobacterium-mediated transformation of <i>Nicotiana glauca</i> and <i>Nicotiana sylvestris</i>. Vavilovskii Zhurnal Genet Selektsii 2022; 26:697-703. [DOI: 10.18699/vjgb-22-84] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- G. V. Khafizova
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | | |
Collapse
|
8
|
Matveeva T, Otten L. Opine biosynthesis in naturally transgenic plants: Genes and products. PHYTOCHEMISTRY 2021; 189:112813. [PMID: 34192603 DOI: 10.1016/j.phytochem.2021.112813] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/03/2021] [Accepted: 05/07/2021] [Indexed: 06/13/2023]
Abstract
The plant pathogen Agrobacterium transfers DNA into plant cells by a specific transfer mechanism. Expression of this transferred DNA or T-DNA leads to crown gall tumors or abnormal, hairy roots and the synthesis of specific compounds, called opines. Opines are produced from common plant metabolites like sugars, amino acids and α-keto acids, which are combined into different low molecular weight structures by T-DNA-encoded opine synthase enzymes. Opines can be converted back by Agrobacterium into the original metabolites and used for agrobacterial growth. Recently it has been discovered that about 7% of Angiosperms carry T-DNA-like sequences. These result from ancient Agrobacterium transformation events, followed by spontaneous regeneration of transformed cells into natural genetically transformed organisms (nGMOs). Nearly all nGMOs identified up to date carry opine synthesis genes, several of these are intact and potentially encode opine synthesis. So far, only tobacco and cuscuta have been demonstrated to contain opines. Whereas opines from crown gall and hairy root tissues have been studied for over 60 years, those from the nGMOs remain to be explored.
Collapse
Affiliation(s)
- Tatiana Matveeva
- St. Petersburg State University, University Emb., 7/9, Saint Petersburg, Russia.
| | - Léon Otten
- Institute of Plant Molecular Biology, C.N.R.S, 67084, Strasbourg, France.
| |
Collapse
|