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Hasanpour K, Aalami A, Seraj RGM, Hosseini R, Naeimi S, Esmaeilzadeh-Salestani K. Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis. Sci Rep 2023; 13:9499. [PMID: 37308505 DOI: 10.1038/s41598-023-36133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
Aegilops tauschii, as a donor of D genome to the bread wheat with a valuable source of resistance to different biotic and abiotic stresses, is used to improve the quality of wheat cultivars. Every genotype has a specific genetic content, the investigation of which can lead to the identification of useful genes such as stress tolerance genes, including drought. Therefore, 23 genotypes of Ae. tauschii were selected to evaluate their morphological and physiological traits under greenhouse conditions. Among them, a superior tolerant genotype (KC-2226) was chosen for transcriptomic analysis. Our result showed that 5007 and 3489 genes were deferentially up- and downregulated, respectively. Upregulated genes were involved in photosynthesis, glycolysis/gluconeogenesis, and amino acid biosynthesis whereas downregulated genes were often engaged in DNA synthesis, replication, repair and topological changes. The result of protein-protein interaction network analysis showed that AT1G76550 (1.46), AT1G20950 (1.42), IAR4 (1.19), and PYD2 (1.16) among upregulated genes and THY-1 (44), PCNA1 (41) and TOPII (22) among down-regulated genes had the highest interactions with other genes. In conclusion, Ae. tauschii employs elevated transcription of specific genes involved in photosynthesis, glycolysis and gluconeogenesis and amino acid biosynthesis pathways rather than genes active in DNA synthesis and repair to provide the energy needed for the plant to survive under stress conditions.
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Affiliation(s)
- Keyvan Hasanpour
- Department of Agricultural Biotechnology, University of Guilan, University Campus 2, Rasht, Iran
| | - Ali Aalami
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ramin Hosseini
- Department of Biotechnology, Faculty of Agriculture and Natural Resource, Imam Khomeini International University, Qazvin, Iran
| | - Shahram Naeimi
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, 19858-13111, Iran
| | - Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
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Affiliation(s)
- María E. Elguero
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Clara B. Nudel
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro D. Nusblat
- Facultad de Farmacia y Bioquímica, Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, Buenos Aires, Argentina
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Calow J, Behrens AJ, Mader S, Bockau U, Struwe WB, Harvey DJ, Cormann KU, Nowaczyk MM, Loser K, Schinor D, Hartmann MWW, Crispin M. Antibody production using a ciliate generates unusual antibody glycoforms displaying enhanced cell-killing activity. MAbs 2016; 8:1498-1511. [PMID: 27594301 PMCID: PMC5098438 DOI: 10.1080/19420862.2016.1228504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibody glycosylation is a key parameter in the optimization of antibody therapeutics. Here, we describe the production of the anti-cancer monoclonal antibody rituximab in the unicellular ciliate, Tetrahymena thermophila. The resulting antibody demonstrated enhanced antibody-dependent cell-mediated cytotoxicity, which we attribute to unusual N-linked glycosylation. Detailed chromatographic and mass spectrometric analysis revealed afucosylated, oligomannose-type glycans, which, as a whole, displayed isomeric structures that deviate from the typical human counterparts, but whose branches were equivalent to fragments of metabolic intermediates observed in human glycoproteins. From the analysis of deposited crystal structures, we predict that the ciliate glycans adopt protein-carbohydrate interactions with the Fc domain that closely mimic those of native complex-type glycans. In addition, terminal glucose structures were identified that match biosynthetic precursors of human glycosylation. Our results suggest that ciliate-based expression systems offer a route to large-scale production of monoclonal antibodies exhibiting glycosylation that imparts enhanced cell killing activity.
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Affiliation(s)
| | - Anna-Janina Behrens
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | | | | | - Weston B Struwe
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | - David J Harvey
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
| | - Kai U Cormann
- c Plant Biochemistry, Ruhr University Bochum , Bochum , Germany
| | - Marc M Nowaczyk
- c Plant Biochemistry, Ruhr University Bochum , Bochum , Germany
| | - Karin Loser
- d Department of Dermatology , University of Münster , Münster , Germany
| | - Daniel Schinor
- e Wessling GmbH, Pharmaanalytik Münster , Münster , Germany
| | | | - Max Crispin
- b Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford , Oxford , UK
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Rattanachuen W, Jönsson M, Swedberg G, Sirawaraporn W. Probing the roles of non-homologous insertions in the N-terminal domain of Plasmodium falciparum hydroxymethylpterin pyrophosphokinase–dihydropteroate synthase. Mol Biochem Parasitol 2009; 168:135-42. [DOI: 10.1016/j.molbiopara.2009.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/29/2009] [Accepted: 07/09/2009] [Indexed: 11/19/2022]
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Weide T, Bockau U, Rave A, Herrmann L, Hartmann MWW. A recombinase system facilitates cloning of expression cassettes in the ciliate Tetrahymena thermophila. BMC Microbiol 2007; 7:12. [PMID: 17328820 PMCID: PMC1839094 DOI: 10.1186/1471-2180-7-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 03/01/2007] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Tetrahymena thermophila is one of the best characterized unicellular eukaryotes and its genome is sequenced in its entirety. However, the AT-richness of the genome and an unusual codon usage cause problems in cloning and expression of the ciliate DNA. To overcome these technical hiatuses we developed a Cre-dependent recombinase system. RESULTS We created novel donor and acceptor vectors that facilitate the transfer of expression cassettes from the donor into novel acceptor plasmid. Expression vectors were used that encode the 19 kDa C-terminus of the MSP1 protein of Plasmodium falciparum and a blasticidin S (bsdR) resistance gene, respectively. The functional expression of these genes was demonstrated by western blot analysis with MSP1 specific antibodies and by a blasticidin growing assay. CONCLUSION The Cre dependent recombinase system in combination with the modular structure of the donor vectors ease cloning and expression of foreign genes in the ciliate system, providing a powerful tool for protistology research in future.
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Affiliation(s)
- Thomas Weide
- Universitaetskliniken Muenster (UKM), Abteilung für Molekulare Nephrologie, Domagkstr. 3a, D-48149 Muenster, Germany
| | - Ulrike Bockau
- Cilian AG, Johann-Krane-Weg 42, D-48149 Muenster, Germany
- Institut für allgemeine Zoologie und Genetik, Universitaet Muenster, Schloßplatz 5, D-48149 Muenster, Germany
| | - Angelika Rave
- Cilian AG, Johann-Krane-Weg 42, D-48149 Muenster, Germany
| | - Lutz Herrmann
- Cilian AG, Johann-Krane-Weg 42, D-48149 Muenster, Germany
- Provendis GmbH, Eppinghofer Str. 50, 48468 Muelheim an der Ruhr, Germany
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Toyomasu T, Tsukahara M, Kaneko A, Niida R, Mitsuhashi W, Dairi T, Kato N, Sassa T. Fusicoccins are biosynthesized by an unusual chimera diterpene synthase in fungi. Proc Natl Acad Sci U S A 2007; 104:3084-8. [PMID: 17360612 PMCID: PMC1805559 DOI: 10.1073/pnas.0608426104] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2006] [Indexed: 11/18/2022] Open
Abstract
Fusicoccins are a class of diterpene glucosides produced by the plant-pathogenic fungus Phomopsis amygdali. As modulators of 14-3-3 proteins, fusicoccins function as potent activators of plasma membrane H(+)-ATPase in plants and also exhibit unique biological activity in animal cells. Despite their well studied biological activities, no genes encoding fusicoccin biosynthetic enzymes have been identified. Cyclic diterpenes are commonly synthesized via cyclization of a C(20) precursor, geranylgeranyl diphosphate (GGDP), which is produced through condensation of the universal C(5) isoprene units dimethylallyl diphosphate and isopentenyl diphosphate by prenyltransferases. We found that (+)-fusicocca-2,10 (14)-diene, a tricyclic hydrocarbon precursor for fusicoccins, is biosynthesized from the C(5) isoprene units by an unusual multifunctional enzyme, P. amygdali fusicoccadiene synthase (PaFS), which shows both prenyltransferase and terpene cyclase activities. The functional analysis of truncated mutants and site-directed mutagenesis demonstrated that PaFS consists of two domains: a terpene cyclase domain at the N terminus and a prenyltransferase domain at the C terminus. These findings suggest that fusicoccadiene can be produced efficiently in the fungus by using the C(5) precursors, irrespective of GGDP availability. In fact, heterologous expression of PaFS alone resulted in the accumulation of fusicocca-2,10 (14)-diene in Escherichia coli cells, whereas no product was detected in E. coli cells expressing Gibberella fujikuroi ent-kaurene synthase, another fungal diterpene cyclase that also uses GGDP as a substrate but does not contain a prenyltransferase domain. Genome walking suggested that fusicoccin biosynthetic enzymes are encoded as a gene cluster near the PaFS gene.
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Affiliation(s)
- Tomonobu Toyomasu
- Department of Bioresource Engineering, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan.
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