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Zhang W, Zhang H, Zhao G, Wang N, Guo L, Hou X. Molecular mechanism of somatic embryogenesis in paeonia ostii 'Fengdan' based on transcriptome analysis combined histomorphological observation and metabolite determination. BMC Genomics 2023; 24:665. [PMID: 37924006 PMCID: PMC10625268 DOI: 10.1186/s12864-023-09730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Tree peony (Paeonia sect. Moutan DC.) is a famous flower native to China with high ornamental, medicinal, and oil value. However, the low regeneration rate of callus is one of the main constraints for the establishment of a genetic transformation system in tree peony. By histomorphological observation, transcriptomic analysis and metabolite determination, we investigated the molecular mechanism of somatic embryogenesis after the establishment of a culture system and the induction of somatic embryo(SE) formation. RESULTS We found that SE formation was successfully induced when cotyledons were used as explants. A total of 3185 differentially expressed genes were screened by comparative transcriptomic analysis of embryogenic callus (EC), SE, and non-embryogenic callus (NEC). Compared to NEC, the auxin synthesis-related genes GH3.6 and PCO2 were up-regulated, whereas cytokinin dehydrogenase (CKX6) and CYP450 family genes were down-regulated in somatic embryogenesis. In SE, the auxin content was significantly higher than the cytokinin content. The methyltransferase-related gene S-adenosylmethionine synthase (SAMS) and the flavonoid biosynthesis-related gene (ANS and F3'5'H) were down-regulated in somatic embryogenesis. The determination of flavonoids showed that rhoifolin and hyperoside had the highest content in SE. The results of transcriptome analysis were consistent with the relative expression of 8 candidate genes by quantitative polymerase chain reaction analysis. CONCLUSION The results revealed that auxin and cytokinin may play a key role in 'Fengdan' somatic embryogenesis. The genes related to somatic embryogenesis were revealed, which has partly elucidated the molecular mechanism of somatic embryogenesis in 'Fengdan'.
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Affiliation(s)
- Wanqing Zhang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Hongxiao Zhang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Guodong Zhao
- National Peony Gene Bank, 471011, Luoyang, Henan, China
| | - Na Wang
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Lili Guo
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China
| | - Xiaogai Hou
- Agricultural college, Henan University of Science and Technology, 471023, Luoyang, Henan, China.
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Caeiro A, Jarak I, Correia S, Canhoto J, Carvalho R. Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo ( Solanum betaceum Cav.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2869. [PMID: 37571022 PMCID: PMC10420837 DOI: 10.3390/plants12152869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023]
Abstract
Tamarillo is a solanaceous tree that has been extensively studied in terms of in vitro clonal propagation, namely somatic embryogenesis. In this work, a protocol of indirect somatic embryogenesis was applied to obtain embryogenic and non-embryogenic callus from leaf segments. Nuclear magnetic resonance spectroscopy was used to analyze the primary metabolome of these distinct calli to elucidate possible differentiation mechanisms from the common genetic background callus. Standard multivariate analysis methods were then applied, and were complemented by univariate statistical methods to identify differentially expressed primary metabolites and related metabolic pathways. The results showed carbohydrate and lipid metabolism to be the most relevant in all the calli assayed, with most discriminant metabolites being fructose, glucose and to a lesser extent choline. The glycolytic rate was higher in embryogenic calli, which shows, overall, a higher rate of sugar catabolism and a different profile of phospholipids with a choline/ethanolamine analysis. In general, our results show that a distinct primary metabolome between embryogenic and non-embryogenic calli occurs and that intracellular levels of fructose and sucrose and the glucose to sucrose ratio seem to be good candidates as biochemical biomarkers of embryogenic competence.
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Affiliation(s)
- André Caeiro
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
| | - Ivana Jarak
- Laboratory of Drug Development and Technologies, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal;
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo, Allen 208, 4200-393 Porto, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
- InnovPlanProtect CoLab, 7350-478 Elvas, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, Laboratory Associate TERRA, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal; (A.C.); (S.C.)
| | - Rui Carvalho
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, 3000-456 Coimbra, Portugal
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Cordeiro D, Camelo A, Pedrosa AC, Brandão I, Canhoto J, Espírito Santo C, Correia S. An Efficient Method to Prepare Barcoded cDNA Libraries from Plant Callus for Long-Read Sequencing. Methods Protoc 2023; 6:mps6020031. [PMID: 36961051 PMCID: PMC10037601 DOI: 10.3390/mps6020031] [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: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Long-read sequencing methods allow a comprehensive analysis of transcriptomes in identifying full-length transcripts. This revolutionary method represents a considerable breakthrough for non-model species since it allows enhanced gene annotation and gene expression studies when compared to former sequencing methods. However, woody plant tissues are challenging to the successful preparation of cDNA libraries, thus, impairing further cutting-edge sequencing analyses. Here, a detailed protocol for preparing cDNA libraries suitable for high throughput RNA sequencing using Oxford Nanopore Technologies® is described. This method was used to prepare eight barcoded cDNA libraries from two Solanum betaceum cell lines: one with compact morphology and embryogenic competency (EC) and another with friable and non-embryogenic (NEC). The libraries were successfully sequenced, and data quality assessment showed high mean quality scores. Using this method, long-read sequencing will allow a comprehensive analysis of plant transcriptomes.
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Affiliation(s)
- Daniela Cordeiro
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Alexandra Camelo
- Centro de Apoio Tecnológico Agro-Alimentar (CATAA) de Castelo Branco, 6000-459 Castelo Branco, Portugal
| | - Ana Carolina Pedrosa
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Inês Brandão
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Centro de Apoio Tecnológico Agro-Alimentar (CATAA) de Castelo Branco, 6000-459 Castelo Branco, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Christophe Espírito Santo
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- Centro de Apoio Tecnológico Agro-Alimentar (CATAA) de Castelo Branco, 6000-459 Castelo Branco, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLab, Estrada de Gil Vaz, 7350-478 Elvas, Portugal
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Cordeiro D, Alves A, Ferraz R, Casimiro B, Canhoto J, Correia S. An Efficient Agrobacterium-Mediated Genetic Transformation Method for Solanum betaceum Cav. Embryogenic Callus. PLANTS (BASEL, SWITZERLAND) 2023; 12:1202. [PMID: 36904062 PMCID: PMC10005457 DOI: 10.3390/plants12051202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Somatic embryogenesis in Solanum betaceum (tamarillo) has proven to be an effective model system for studying morphogenesis, since optimized plant regeneration protocols are available, and embryogenic competent cell lines can be induced from different explants. Nevertheless, an efficient genetic transformation system for embryogenic callus (EC) has not yet been implemented for this species. Here, an optimized faster protocol of genetic transformation using Agrobacterium tumefaciens is described for EC. The sensitivity of EC to three antibiotics was determined, and kanamycin proved to be the best selective agent for tamarillo callus. Two Agrobacterium strains, EHA105 and LBA4404, both harboring the p35SGUSINT plasmid, carrying the reporter gene for β-glucuronidase (gus) and the marker gene neomycin phosphotransferase (nptII), were used to test the efficiency of the process. To increase the success of the genetic transformation, a cold-shock treatment, coconut water, polyvinylpyrrolidone and an appropriate selection schedule based on antibiotic resistance were employed. The genetic transformation was evaluated by GUS assay and PCR-based techniques, and a 100% efficiency rate was confirmed in the kanamycin-resistant EC clumps. Genetic transformation with the EHA105 strain resulted in higher values for gus insertion in the genome. The protocol presented provides a useful tool for functional gene analysis and biotechnology approaches.
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Affiliation(s)
- Daniela Cordeiro
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Ana Alves
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | - Ricardo Ferraz
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Bruno Casimiro
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLab, Estrada de Gil Vaz, 7350-478 Elvas, Portugal
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Casimiro B, Mota I, Veríssimo P, Canhoto J, Correia S. Enhancing the Production of Hydrolytic Enzymes in Elicited Tamarillo ( Solanum betaceum Cav.) Cell Suspension Cultures. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010190. [PMID: 36616319 PMCID: PMC9824068 DOI: 10.3390/plants12010190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 05/07/2023]
Abstract
Plant cell suspension cultures are widely used as a tool for analyzing cellular and molecular processes, metabolite synthesis, and differentiation, bypassing the structural complexity of plants. Within the range of approaches used to increase the production of metabolites by plant cells, one of the most recurrent is applying elicitors capable of stimulating metabolic pathways related to defense mechanisms. Previous proteomics analysis of tamarillo cell lines and cell suspension cultures have been used to further characterize and optimize the growth and stress-related metabolite production under in vitro controlled conditions. The main objective of this work was to develop a novel plant-based bioreactor system to produce hydrolytic enzymes using an elicitation approach. Based on effective protocols for tamarillo micropropagation and plant cell suspension culture establishment from induced callus lines, cell growth has been optimized, and enzymatic activity profiles under in vitro controlled conditions characterized. By testing different sucrose concentrations and the effects of two types of biotic elicitors, it was found that 3% (w/v) sucrose concentration in the liquid medium enhanced the production of hydrolytic enzymes. Moreover, casein hydrolysate at 0.5 and 1.5 g/L promoted protein production, whereas yeast extract (0.5 g/L) enhanced glycosidase activity. Meanwhile, chitosan (0.05 and 0.1 g/L) enhanced glycosidases, alkaline phosphates, and protease activities.
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Affiliation(s)
- Bruno Casimiro
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, Calçada Martim de Freitas, University of Coimbra, 3000-456 Coimbra, Portugal
- Correspondence: (B.C.); (S.C.)
| | - Inês Mota
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, Calçada Martim de Freitas, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Paula Veríssimo
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, Calçada Martim de Freitas, University of Coimbra, 3000-456 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, Calçada Martim de Freitas, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, Calçada Martim de Freitas, University of Coimbra, 3000-456 Coimbra, Portugal
- InnovPlantProtect CoLab, Estrada de Gil Vaz, 7351-901 Elvas, Portugal
- Correspondence: (B.C.); (S.C.)
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Ferraz R, Coimbra S, Correia S, Canhoto J. RNA methyltransferases in plants: Breakthroughs in function and evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:449-460. [PMID: 36502609 DOI: 10.1016/j.plaphy.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/28/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Each day it is becoming increasingly difficult not to notice the completely new, fast growing, extremely intricate and challenging world of epitranscriptomics as the understanding of RNA methylation is expanding at a hasty rate. Writers (methyltransferases), erasers (demethylases) and readers (RNA-binding proteins) are responsible for adding, removing and recognising methyl groups on RNA, respectively. Several methyltransferases identified in plants are now being investigated and recent studies have shown a connection between RNA-methyltransferases (RNA-MTases) and stress and development processes. However, compared to their animal and bacteria counterparts, the understanding of RNA methyltransferases is still incipient, particularly those located in organelles. Comparative and systematic analyses allowed the tracing of the evolution of these enzymes suggesting the existence of several methyltransferases yet to be characterised. This review outlines the functions of plant nuclear and organellar RNA-MTases in plant development and stress responses and the comparative and evolutionary discoveries made on RNA-MTases across kingdoms.
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Affiliation(s)
- Ricardo Ferraz
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sílvia Coimbra
- University of Porto, Faculty of Sciences, Portugal; LAQV Requimte, Sustainable Chemistry, University of Porto, Porto, Portugal.
| | - Sandra Correia
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
| | - Jorge Canhoto
- Centre for Functional Ecology, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra 3000-456, Portugal.
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