1
|
Carrera-Castaño G, Mira S, Fañanás-Pueyo I, Sánchez-Montesino R, Contreras Á, Weiste C, Dröge-Laser W, Gómez L, Oñate-Sánchez L. Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1. THE NEW PHYTOLOGIST 2024; 242:2026-2042. [PMID: 38494681 DOI: 10.1111/nph.19681] [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: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Seed dormancy governs germination timing, with both evolutionary and applied consequences. Despite extensive studies on the hormonal and genetic control of these processes, molecular mechanisms directly linking dormancy and germination remain poorly understood. By screening a collection of lines overexpressing Arabidopsis transcription factors, we identified ERF50 as a key gene to control dormancy and germination. To study its regulation, we measured seed-related physiological parameters in loss-of-function mutants and carried out transactivation, protein interaction and ChIP-PCR analyses. We found direct ERF50-mediated repression of DOG1 and activation of EXPA2 transcription, which results in enhanced seed germination. Although ERF50 expression is increased by DOG1 in dormant seeds, ERF50 germination-promoting activity is blocked by RGL2. The physiological, genetic and molecular evidence gathered here supports that ERF50 controls germination timing by regulating DOG1 levels to leverage its role as enhancer of seed germination, via RGL2 antagonism on EXPA2 expression. Our results highlight the central role of ERF50 as a feedback regulator to couple and fine-tune seed dormancy and germination.
Collapse
Affiliation(s)
- Gerardo Carrera-Castaño
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Sara Mira
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Iris Fañanás-Pueyo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Rocío Sánchez-Montesino
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Ángela Contreras
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg, 97082, Germany
| | - Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Faculty of Biology, Biocenter, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Würzburg, 97082, Germany
| | - Luis Gómez
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, 28040, Madrid, Spain
- Centro para la Conservación de la Biodiversidad y el Desarrollo Sostenible, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, 28040, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| |
Collapse
|
2
|
Punia A, Kumari M, Chouhan M, Saini V, Joshi R, Kumar A, Kumar R. Proteomic and metabolomic insights into seed germination of Ferula assa-foetida. J Proteomics 2024; 300:105176. [PMID: 38604334 DOI: 10.1016/j.jprot.2024.105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/01/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SIGNIFICANCE: Seed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as "asafoetida," is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.
Collapse
Affiliation(s)
- Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Monika Chouhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal Saini
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ashok Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur 176061, HP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
3
|
Shinozaki D, Takayama E, Kawakami N, Yoshimoto K. Autophagy maintains endosperm quality during seed storage to preserve germination ability in Arabidopsis. Proc Natl Acad Sci U S A 2024; 121:e2321612121. [PMID: 38530890 PMCID: PMC10998590 DOI: 10.1073/pnas.2321612121] [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: 12/13/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
To preserve germination ability, plant seeds must be protected from environmental stresses during the storage period. Here, we demonstrate that autophagy, an intracellular degradation system, maintains seed germination ability in Arabidopsis thaliana. The germination ability of long-term (>5 years) stored dry seeds of autophagy-defective (atg) mutant and wild-type (WT) plants was compared. Long-term stored (old) seeds of atg mutants showed lower germination ability than WT seeds, although short-term stored (new) seeds of atg mutants did not show such a phenotype. After removal of the seed coat and endosperm from old atg mutant seeds, the embryos developed into seedlings. Autophagic flux was maintained in endosperm cells during the storage period, and autophagy defect resulted in the accumulation of oxidized proteins and accelerated endosperm cell death. Consistent with these findings, the transcripts of genes, ENDO-β-MANNANASE 7 and EXPANSIN 2, which are responsible for degradation/remodeling of the endosperm cell wall during germination, were reduced in old atg mutant seeds. We conclude that autophagy maintains endosperm quality during seed storage by suppressing aging-dependent oxidative damage and cell death, which allows the endosperm to perform optimal functions during germination, i.e., cell wall degradation/remodeling, even after long-term storage.
Collapse
Grants
- 16H07255 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19H05713 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20H03281 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- S1411023 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23H02506 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21J11995 MEXT | Japan Society for the Promotion of Science (JSPS)
Collapse
Affiliation(s)
- Daiki Shinozaki
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Erina Takayama
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki214-8571, Kanagawa, Japan
| |
Collapse
|
4
|
Contreras E, Martín-Fernández L, Manaa A, Vicente-Carbajosa J, Iglesias-Fernández R. Identification of Reference Genes for Precise Expression Analysis during Germination in Chenopodium quinoa Seeds under Salt Stress. Int J Mol Sci 2023; 24:15878. [PMID: 37958860 PMCID: PMC10650251 DOI: 10.3390/ijms242115878] [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: 09/20/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chenopodium quinoa Willd. (quinoa), a member of the Amaranthaceae family, is an allotetraploid annual plant, endemic to South America. The plant of C. quinoa presents significant ecological plasticity with exceptional adaptability to several environmental stresses, including salinity. The resilience of quinoa to several abiotic stresses, as well as its nutritional attributes, have led to significant shifts in quinoa cultivation worldwide over the past century. This work first defines germination sensu stricto in quinoa where the breakage of the pericarp and the testa is followed by endosperm rupture (ER). Transcriptomic changes in early seed germination stages lead to unstable expression levels in commonly used reference genes that are typically stable in vegetative tissues. Noteworthy, no suitable reference genes have been previously identified specifically for quinoa seed germination under salt stress conditions. This work aims to identify these genes as a prerequisite step for normalizing qPCR data. To this end, germinating seeds from UDEC2 and UDEC4 accessions, with different tolerance to salt, have been analyzed under conditions of absence (0 mM NaCl) and in the presence (250 mM NaCl) of sodium chloride. Based on the relevant literature, six candidate reference genes, Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Monensin sensitivity1 (MON1), Polypyrimidine tract-binding protein (PTB), Actin-7 (ACT7), Ubiquitin-conjugating enzyme (UBC), and 18S ribosomal RNA (18S), were selected and assessed for stability using the RefFinder Tool encompassing the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt in the evaluation. The data presented support the suitability of CqACT7 and CqUBC as reference genes for normalizing gene expression during seed germination under salinity stress. These recommended reference genes can be valuable tools for consistent qPCR studies on quinoa seeds.
Collapse
Affiliation(s)
- Estefanía Contreras
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Lucía Martín-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
| | - Arafet Manaa
- Laboratory of Extremophile Plants, Centre of Biotechnology de Borj Cedria, B.P. 901, Hammam-Lif 2050, Tunisia;
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (E.C.); (J.V.-C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (UPM), 28040 Madrid, Spain
| |
Collapse
|
5
|
Varshney V, Hazra A, Rao V, Ghosh S, Kamble NU, Achary RK, Gautam S, Majee M. The Arabidopsis F-box protein SKP1-INTERACTING PARTNER 31 modulates seed maturation and seed vigor by targeting JASMONATE ZIM DOMAIN proteins independently of jasmonic acid-isoleucine. THE PLANT CELL 2023; 35:3712-3738. [PMID: 37462265 PMCID: PMC10533341 DOI: 10.1093/plcell/koad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/21/2023] [Indexed: 09/29/2023]
Abstract
F-box proteins have diverse functions in eukaryotic organisms, including plants, mainly targeting proteins for 26S proteasomal degradation. Here, we demonstrate the role of the F-box protein SKP1-INTERACTING PARTNER 31 (SKIP31) from Arabidopsis (Arabidopsis thaliana) in regulating late seed maturation events, seed vigor, and viability through biochemical and genetic studies using skip31 mutants and different transgenic lines. We show that SKIP31 is predominantly expressed in seeds and that SKIP31 interacts with JASMONATE ZIM DOMAIN (JAZ) proteins, key repressors in jasmonate (JA) signaling, directing their ubiquitination for proteasomal degradation independently of coronatine/jasmonic acid-isoleucine (JA-Ile), in contrast to CORONATINE INSENSITIVE 1, which sends JAZs for degradation in a coronatine/JA-Ile dependent manner. Moreover, JAZ proteins interact with the transcription factor ABSCISIC ACID-INSENSITIVE 5 (ABI5) and repress its transcriptional activity, which in turn directly or indirectly represses the expression of downstream genes involved in the accumulation of LATE EMBRYOGENESIS ABUNDANT proteins, protective metabolites, storage compounds, and abscisic acid biosynthesis. However, SKIP31 targets JAZ proteins, deregulates ABI5 activity, and positively regulates seed maturation and consequently seed vigor. Furthermore, ABI5 positively influences SKIP31 expression, while JAZ proteins repress ABI5-mediated transactivation of SKIP31 and exert feedback regulation. Taken together, our findings reveal the role of the SKIP31-JAZ-ABI5 module in seed maturation and consequently, establishment of seed vigor.
Collapse
Affiliation(s)
- Vishal Varshney
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Abhijit Hazra
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Venkateswara Rao
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Shraboni Ghosh
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Nitin Uttam Kamble
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Rakesh Kumar Achary
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Shikha Gautam
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| | - Manoj Majee
- MM's Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi 110067, India
| |
Collapse
|
6
|
Temmerman A, De Keyser A, Boyer FD, Struk S, Goormachtig S. Histone Deacetylases Regulate MORE AXILLARY BRANCHED 2-Dependent Germination of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2023; 64:1008-1020. [PMID: 37279553 DOI: 10.1093/pcp/pcad047] [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: 01/29/2023] [Revised: 04/21/2023] [Accepted: 05/29/2023] [Indexed: 06/08/2023]
Abstract
Under specific conditions, the germination of Arabidopsis thaliana is dependent on the activation of the KARRIKIN INSENSITIVE 2 (KAI2) signaling pathway by the KAI2-dependent perception of karrikin or the artificial strigolactone analogue, rac-GR24. To regulate the induction of germination, the KAI2 signaling pathway relies on MORE AXILLARY BRANCHED 2- (MAX2-)dependent ubiquitination and proteasomal degradation of the repressor protein SUPPRESSOR OF MAX2 1 (SMAX1). It is not yet known how the degradation of SMAX1 proteins eventually results in the regulation of seed germination, but it has been hypothesized that SMAX1-LIKE generally functions as transcriptional repressors through the recruitment of co-repressors TOPLESS (TPL) and TPL-related, which in turn interact with histone deacetylases. In this article, we show the involvement of histone deacetylases HDA6, HDA9, HDA19 and HDT1 in MAX2-dependent germination of Arabidopsis, and more specifically, that HDA6 is required for the induction of DWARF14-LIKE2 expression in response to rac-GR24 treatment.
Collapse
Affiliation(s)
- Arne Temmerman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Gent 9052, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, Gent 9052, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Gent 9052, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, Gent 9052, Belgium
| | - François-Didier Boyer
- Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, UPR2301, Université Paris-Sud, Université Paris-Saclay, Aveue de la Terrasse 1, Gif-sur-Yvette 91198, France
| | - Sylwia Struk
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Gent 9052, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, Gent 9052, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Gent 9052, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 71, Gent 9052, Belgium
| |
Collapse
|
7
|
Bokhale M, Mwaba I, Allie F. The selection and validation of reference genes for quantitative real-time PCR studies in near-isogenic susceptible and resistant tomato lines, infected with the geminivirus tomato curly stunt virus. PLoS One 2023; 18:e0284456. [PMID: 37498814 PMCID: PMC10374155 DOI: 10.1371/journal.pone.0284456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/03/2023] [Indexed: 07/29/2023] Open
Abstract
Quantitative real-time PCR (qPCR) is a sensitive and commonly used technique for gene expression profiling and provides insight into biological systems. Successful qPCR requires the use of appropriate reference genes for the normalization of data. In the present study, we aimed to identify and assess the best-suited reference genes in near-isogenic resistant (R) and susceptible (S) tomato lines infected with begomovirus Tomato curly stunt virus (ToCSV). Ten candidate reference genes namely, Actin7 (ACT), β-6 Tubulin (TUB), Ubiquitin 3 (UBI), Clathrin adaptor complexes medium subunit (CAC), Phytoene desaturase (PDS), Expressed protein (EXP), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Adenine phosphoribosyl transferase-like protein (APT1), TAP42-interacting protein (TIP41) and Elongation factor 1-alpha (EF1α) were selected and evaluated for their expression stability in resistant and susceptible tomato leaves using the analytical tools geNorm, NormFinder, BestKeeper, and RefFinder. After ranking the reference genes from most to least stable, the results suggested that a combination of ACT, EXP, and EF1α in the S lines and a combination of TIP41, APT1, and ACT in the R line is appropriate for qPCR normalization. Furthermore, to validate the identified reference genes, iron superoxide dismutase (SOD), heat shock protein 70 (HSP70) and Glutathione-S-transferase (GST) were selected as targets for normalization. The relative expression of the target genes varied when normalized against the most stable reference genes in comparison to the least stable genes. These results highlight the importance of careful selection of reference genes for accurate normalization in qPCR studies.
Collapse
Affiliation(s)
- Mamokete Bokhale
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Imanu Mwaba
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Farhahna Allie
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| |
Collapse
|
8
|
Li G, Sun X, Zhu X, Wu B, Hong H, Xin Z, Xin X, Peng J, Jiang S. Selection and Validation of Reference Genes in Virus-Infected Sweet Potato Plants. Genes (Basel) 2023; 14:1477. [PMID: 37510381 PMCID: PMC10379385 DOI: 10.3390/genes14071477] [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: 06/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Quantitative real-time PCR (qRT-PCR) in sweet potatoes requires accurate data normalization; however, there are insufficient studies on appropriate reference genes for gene expression analysis. We examined variations in the expression of eight candidate reference genes in the leaf and root tissues of sweet potatoes (eight nonvirus-infected or eight virus-infected samples). Parallel analyses with geNorm, NormFinder, and Best-Keeper show that different viral infections and origin tissues affect the expression levels of these genes. Based on the results of the evaluation of the three software, the adenosine diphosphate-ribosylation factor is suitable for nonvirus or virus-infected sweet potato leaves. Cyclophilin and ubiquitin extension proteins are suitable for nonvirus-infected sweet potato leaves. Phospholipase D1 alpha is suitable for virus-infected sweet potato leaves. Actin is suitable for roots of nonvirus-infected sweet potatoes. Glyceraldehyde-3-phosphate dehydrogenase is suitable for virus-infected sweet potato roots. The research provides appropriate reference genes for further analysis in leaf and root samples of viruses in sweet potatoes.
Collapse
Affiliation(s)
- Guangyan Li
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaohui Sun
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaoping Zhu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Bin Wu
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hao Hong
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhimei Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiangqi Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shanshan Jiang
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| |
Collapse
|
9
|
Shivnauth V, Pretheepkumar S, Marchetta EJR, Rossi CAM, Amani K, Castroverde CDM. Structural diversity and stress regulation of the plant immunity-associated CALMODULIN-BINDING PROTEIN 60 (CBP60) family of transcription factors in Solanum lycopersicum (tomato). Funct Integr Genomics 2023; 23:236. [PMID: 37439880 DOI: 10.1007/s10142-023-01172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/23/2023] [Accepted: 07/08/2023] [Indexed: 07/14/2023]
Abstract
Cellular signaling generates calcium (Ca2+) ions, which are ubiquitous secondary messengers decoded by calcium-dependent protein kinases, calcineurins, calreticulin, calmodulins (CAMs), and CAM-binding proteins. Previous studies in the model plant Arabidopsis thaliana have shown the critical roles of the CAM-BINDING PROTEIN 60 (CBP60) protein family in plant growth, stress responses, and immunity. Certain CBP60 factors can regulate plant immune responses, like pattern-triggered immunity, effector-triggered immunity, and synthesis of major plant immune-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). Although homologous CBP60 sequences have been identified in the plant kingdom, their function and regulation in most species remain unclear. In this paper, we specifically characterized 11 members of the CBP60 family in the agriculturally important crop tomato (Solanum lycopersicum). Protein sequence analyses revealed that three CBP60 homologs have the closest amino acid identity to Arabidopsis CBP60g and SARD1, master transcription factors involved in plant immunity. Strikingly, AlphaFold deep learning-assisted prediction of protein structures highlighted close structural similarity between these tomato and Arabidopsis CBP60 homologs. Conserved domain analyses revealed that they possess CAM-binding domains and DNA-binding domains, reflecting their potential involvement in linking Ca2+ signaling and transcriptional regulation in tomato plants. In terms of their gene expression profiles under biotic (Pseudomonas syringae pv. tomato DC3000 pathogen infection) and/or abiotic stress (warming temperatures), five tomato CBP60 genes were pathogen-responsive and temperature-sensitive, reminiscent of Arabidopsis CBP60g and SARD1. Overall, we present a genome-wide identification of the CBP60 gene/protein family in tomato plants, and we provide evidence on their regulation and potential function as Ca2+-sensing transcriptional regulators.
Collapse
Affiliation(s)
- Vanessa Shivnauth
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Sonya Pretheepkumar
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Eric J R Marchetta
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Christina A M Rossi
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | - Keaun Amani
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, N2L 3C5, Canada
| | | |
Collapse
|
10
|
Ferreira MJ, Silva J, Pinto SC, Coimbra S. I Choose You: Selecting Accurate Reference Genes for qPCR Expression Analysis in Reproductive Tissues in Arabidopsis thaliana. Biomolecules 2023; 13:biom13030463. [PMID: 36979397 PMCID: PMC10046263 DOI: 10.3390/biom13030463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is a widely used method to analyse the gene expression pattern in the reproductive tissues along with detecting gene levels in mutant backgrounds. This technique requires stable reference genes to normalise the expression level of target genes. Nonetheless, a considerable number of publications continue to present qPCR results normalised to a single reference gene and, to our knowledge, no comparative evaluation of multiple reference genes has been carried out in specific reproductive tissues of Arabidopsis thaliana. Herein, we assessed the expression stability levels of ten candidate reference genes (UBC9, ACT7, GAPC-2, RCE1, PP2AA3, TUA2, SAC52, YLS8, SAMDC and HIS3.3) in two conditional sets: one across flower development and the other using inflorescences from different genotypes. The stability analysis was performed using the RefFinder tool, which combines four statistical algorithms (geNorm, NormFinder, BestKeeper and the comparative ΔCt method). Our results showed that RCE1, SAC52 and TUA2 had the most stable expression in different flower developmental stages while YLS8, HIS3.3 and ACT7 were the top-ranking reference genes for normalisation in mutant studies. Furthermore, we validated our results by analysing the expression pattern of genes involved in reproduction and examining the expression of these genes in published mutant backgrounds. Overall, we provided a pool of appropriate reference genes for expression studies in reproductive tissues of A. thaliana, which will facilitate further gene expression studies in this context. More importantly, we presented a framework that will promote a consistent and accurate analysis of gene expression in any scientific field. Simultaneously, we highlighted the relevance of clearly defining and describing the experimental conditions associated with qPCR to improve scientific reproducibility.
Collapse
Affiliation(s)
- Maria João Ferreira
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Jessy Silva
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- School of Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Sara Cristina Pinto
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sílvia Coimbra
- LAQV/REQUIMTE, Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- Correspondence:
| |
Collapse
|
11
|
Sahoo PK, Parida S, Parida S, Parida P, Paul A. Stability evaluation and validation of appropriate reference genes for real-time PCR expression analysis of immune genes in the rohu (Labeo rohita) skin following argulosis. Sci Rep 2023; 13:2660. [PMID: 36792637 PMCID: PMC9932016 DOI: 10.1038/s41598-023-29325-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Argulosis is one of the most unrestrained economically significant freshwater fish ectoparasitic diseases. Proper selection or normalization of the best reference gene governs the accuracy of results of gene expression studies using real-time PCR. Earlier studies in rohu carp (Labeo rohita) have used reference genes without proper validation. Here, seven candidate reference genes viz., acidic ribosomal protein (ARP0), glyceraldehyde 3-phosphate dehydrogenase, RNA polymerase II (RPo), elongation factor1α (EF1α), α- tubulin (AT), ribosomal protein L 10, and β-actin were evaluated using four algorithms (geNorm, BestKeeper, NormFinder and ∆Ct) followed by a comprehensive gene expression analysis using skin tissue of rohu at varied time points of experimental Argulus siamensis infection. ARP0 and EF1α were found to be the most stable whereas RPo and AT were considered as least stable genes based on basal expression level and variation in expression levels. Validation of candidate reference genes was undertaken by looking into the expression of six immune-related genes using the two most stable and two least stable genes as housekeeping genes in Argulus-infected rohu skin at different time points of infection. An increased expression of immune genes indicated the role of inflammation and the immune modulation process at the site of attachment of parasites in governing infection.
Collapse
Affiliation(s)
- Pramoda Kumar Sahoo
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, 751002, India.
| | - Sonali Parida
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, 751002, India
| | - Subhadarshini Parida
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, 751002, India
| | - Priyashree Parida
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, 751002, India
| | - Anirban Paul
- National Referral Laboratory for Freshwater Fish Diseases, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture (CIFA), Kausalyaganga, Bhubaneswar, 751002, India
| |
Collapse
|
12
|
van Ekelenburg YS, Hornslien KS, Van Hautegem T, Fendrych M, Van Isterdael G, Bjerkan KN, Miller JR, Nowack MK, Grini PE. Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm. PLANT PHYSIOLOGY 2023; 191:986-1001. [PMID: 36437711 PMCID: PMC9922421 DOI: 10.1093/plphys/kiac520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Paul E Grini
- Authors for correspondence: E-mail: (P.E.G.), (K.S.H.)
| |
Collapse
|
13
|
Shohat H, Cheriker H, Cohen A, Weiss D. Tomato ABA-IMPORTING TRANSPORTER 1.1 inhibits seed germination under high salinity conditions. PLANT PHYSIOLOGY 2023; 191:1404-1415. [PMID: 36449559 PMCID: PMC9922386 DOI: 10.1093/plphys/kiac545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 05/27/2023]
Abstract
The plant hormone abscisic acid (ABA) plays a central role in the regulation of seed maturation and dormancy. ABA also restrains germination under abiotic-stress conditions. Here, we show in tomato (Solanum lycopersicum) that the ABA importer ABA-IMPORTING TRANSPORTER 1.1 (AIT1.1/NPF4.6) has a role in radicle emergence under salinity conditions. AIT1.1 expression was upregulated following seed imbibition, and CRISPR/Cas9-derived ait1.1 mutants exhibited faster radicle emergence, increased germination and partial resistance to ABA. AIT1.1 was highly expressed in the endosperm, but not in the embryo, and ait1.1 isolated embryos did not show resistance to ABA. On the other hand, loss of AIT1.1 activity promoted the expression of endosperm-weakening-related genes, and seed-coat scarification eliminated the promoting effect of ait1.1 on radicle emergence. Therefore, we propose that imbibition-induced AIT1.1 expression in the micropylar endosperm mediates ABA-uptake into micropylar cells to restrain endosperm weakening. While salinity conditions strongly inhibited wild-type M82 seed germination, high salinity had a much weaker effect on ait1.1 germination. We suggest that AIT1.1 evolved to inhibit germination under unfavorable conditions, such as salinity. Unlike other ABA mutants, ait1.1 exhibited normal seed longevity, and therefore, the ait1.1 allele may be exploited to improve seed germination in crops.
Collapse
Affiliation(s)
- Hagai Shohat
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - Hadar Cheriker
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - Amir Cohen
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| | - David Weiss
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 76100, Israel
| |
Collapse
|
14
|
Chong SN, Ravindran P, Kumar PP. Regulation of primary seed dormancy by MAJOR LATEX PROTEIN-LIKE PROTEIN329 in Arabidopsis is dependent on DNA-BINDING ONE ZINC FINGER6. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6838-6852. [PMID: 35969447 DOI: 10.1093/jxb/erac337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Seeds exhibit primary dormancy to prevent germination under unfavourable conditions. Previous studies have shown that the gibberellin signalling intermediate RGA-LIKE2 (RGL2) forms a transcription factor complex with DNA-BINDING ONE ZINC FINGER6 (DOF6) in regulating seed dormancy in Arabidopsis. Using an RNA-sequencing approach, we identified MAJOR LATEX PROTEIN-LIKE PROTEIN329 (MLP329) as a downstream target of DOF6. MLP329 was found to be a positive regulator of primary seed dormancy, because freshly harvested unstratified mlp329 mutant seeds showed early germination, while unstratified transgenic seeds overexpressing MLP329 showed poor germination. MLP329 expression level was reduced in wild-type seeds upon dry storage and cold stratification. MLP329 expression level was enhanced by DOF6; however, DOF6-dependent MLP329 expression was suppressed in the presence of RGL2. MLP329 expression was enhanced in seeds treated with ABA and auxin IAA. Moreover, the mlp329 mutant seeds exhibited enhanced expression of the GA biosynthetic gene GA1 and suppression of the ABA biosynthetic gene ZEP compared to the overexpression lines. The observed suppression of DOF6-dependent MLP329 expression by RGL2 reveals a possible negative feedback mechanism to modulate seed dormancy. MLP329 also probably enhances the endogenous ABA/GA ratio to positively regulate primary seed dormancy.
Collapse
Affiliation(s)
- Sher Ney Chong
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| | - Pratibha Ravindran
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| |
Collapse
|
15
|
Yazdanpanah F, Willems LAJ, He H, Hilhorst HWM, Bentsink L. A Role for Allantoate Amidohydrolase (AtAAH) in the Germination of Arabidopsis thaliana Seeds. PLANT & CELL PHYSIOLOGY 2022; 63:1298-1308. [PMID: 35861030 PMCID: PMC9474941 DOI: 10.1093/pcp/pcac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 06/10/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Seed dormancy is a very complex trait controlled by interactions between genetic and environmental factors. Nitrate is inversely correlated with seed dormancy in Arabidopsis. This is explained by the fact that seed dry storage (after-ripening) reduces the need for nitrogen for germination. When nitrate is absorbed by plants, it is first reduced to nitrite and then to ammonium for incorporation into amino acids, nucleic acids and chlorophyll. Previously, we showed that ALLANTOATE AMIDOHYDROLASE (AtAAH) transcripts are up-regulated in imbibed dormant seeds compared with after-ripened seeds. AAH is an enzyme in the uric acid catabolic pathway which catalyzes the hydrolysis of allantoate to yield CO2, NH3 and S-ureidoglycine. This pathway is the final stage of purine catabolism, and functions in plants and some bacteria to provide nitrogen, particularly when other nitrogen sources are depleted. Ataah mutant seeds are more dormant and accumulate high levels of allantoate, allantoin and urea, whereas energy-related metabolites and several amino acids are lower upon seed imbibition in comparison with Columbia-0. AtAAH expression could be detected during the early stages of seed development, with a transient increase around 8 d after pollination. AtAAH expression is the highest in mature pollen. The application of exogenous potassium nitrate can partly complement the higher dormancy phenotype of the Ataah mutant seeds, whereas other nitrogen sources cannot. Our results indicate that potassium nitrate does not specifically overcome the alleviated dormancy levels in Ataah mutant seeds, but promotes germination in general. Possible pathways by which AtAAH affects seed germination are discussed.
Collapse
Affiliation(s)
| | - Leo A J Willems
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | | | - Henk W M Hilhorst
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, Wageningen 6708 PB, The Netherlands
| | | |
Collapse
|
16
|
Song S, Willems LAJ, Jiao A, Zhao T, Eric Schranz M, Bentsink L. The membrane associated NAC transcription factors ANAC060 and ANAC040 are functionally redundant in the inhibition of seed dormancy in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5514-5528. [PMID: 35604925 PMCID: PMC9467645 DOI: 10.1093/jxb/erac232] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
The NAC family of transcription factors is involved in plant development and various biotic and abiotic stresses. The Arabidopsis thaliana ANAC genes ANAC060, ANAC040, and ANAC089 are highly homologous based on protein and nucleotide sequence similarity. These three genes are predicted to be membrane bound transcription factors (MTFs) containing a conserved NAC domain, but divergent C-terminal regions. The anac060 mutant shows increased dormancy when compared with the wild type. Mutations in ANAC040 lead to higher seed germination under salt stress, and a premature stop codon in ANAC089 Cvi allele results in seeds exhibiting insensitivity to high concentrations of fructose. Thus, these three homologous MTFs confer distinct functions, although all related to germination. To investigate whether the differences in function are caused by a differential spatial or temporal regulation, or by differences in the coding sequence (CDS), we performed swapping experiments in which the promoter and CDS of the three MTFs were exchanged. Seed dormancy and salt and fructose sensitivity analyses of transgenic swapping lines in mutant backgrounds showed that there is functional redundancy between ANAC060 and ANAC040, but not between ANAC060 and ANAC089.
Collapse
Affiliation(s)
- Shuang Song
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, PB Wageningen, The Netherlands
| | - Leo A J Willems
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, PB Wageningen, The Netherlands
| | - Ao Jiao
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, PB Wageningen, The Netherlands
| | - Tao Zhao
- Present address: State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, PB Wageningen, The Netherlands
| | | |
Collapse
|
17
|
Wang Y, Durairaj J, Suárez Duran HG, van Velzen R, Flokova K, Liao C, Chojnacka A, MacFarlane S, Schranz ME, Medema MH, van Dijk ADJ, Dong L, Bouwmeester HJ. The tomato cytochrome P450 CYP712G1 catalyses the double oxidation of orobanchol en route to the rhizosphere signalling strigolactone, solanacol. THE NEW PHYTOLOGIST 2022; 235:1884-1899. [PMID: 35612785 PMCID: PMC9542622 DOI: 10.1111/nph.18272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Strigolactones (SLs) are rhizosphere signalling molecules and phytohormones. The biosynthetic pathway of SLs in tomato has been partially elucidated, but the structural diversity in tomato SLs predicts that additional biosynthetic steps are required. Here, root RNA-seq data and co-expression analysis were used for SL biosynthetic gene discovery. This strategy resulted in a candidate gene list containing several cytochrome P450s. Heterologous expression in Nicotiana benthamiana and yeast showed that one of these, CYP712G1, can catalyse the double oxidation of orobanchol, resulting in the formation of three didehydro-orobanchol (DDH) isomers. Virus-induced gene silencing and heterologous expression in yeast showed that one of these DDH isomers is converted to solanacol, one of the most abundant SLs in tomato root exudate. Protein modelling and substrate docking analysis suggest that hydroxy-orbanchol is the likely intermediate in the conversion from orobanchol to the DDH isomers. Phylogenetic analysis demonstrated the occurrence of CYP712G1 homologues in the Eudicots only, which fits with the reports on DDH isomers in that clade. Protein modelling and orobanchol docking of the putative tobacco CYP712G1 homologue suggest that it can convert orobanchol to similar DDH isomers as tomato.
Collapse
Affiliation(s)
- Yanting Wang
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Janani Durairaj
- Bioinformatics GroupWageningen University6708PBWageningenthe Netherlands
| | | | - Robin van Velzen
- Biosystematics GroupWageningen University6708PBWageningenthe Netherlands
| | - Kristyna Flokova
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Che‐Yang Liao
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht University3584 CHUtrechtthe Netherlands
| | - Aleksandra Chojnacka
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Stuart MacFarlane
- Cell and Molecular Sciencesthe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - M. Eric Schranz
- Biosystematics GroupWageningen University6708PBWageningenthe Netherlands
| | - Marnix H. Medema
- Bioinformatics GroupWageningen University6708PBWageningenthe Netherlands
| | | | - Lemeng Dong
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| | - Harro J. Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamthe Netherlands
| |
Collapse
|
18
|
Liu S, Lenoir CJG, Amaro TMMM, Rodriguez PA, Huitema E, Bos JIB. Virulence strategies of an insect herbivore and oomycete plant pathogen converge on host E3 SUMO ligase SIZ1. THE NEW PHYTOLOGIST 2022; 235:1599-1614. [PMID: 35491752 PMCID: PMC9545238 DOI: 10.1111/nph.18184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Pathogens and pests secrete proteins (effectors) to interfere with plant immunity through modification of host target functions and disruption of immune signalling networks. The extent of convergence between pathogen and herbivorous insect virulence strategies is largely unexplored. We found that effectors from the oomycete pathogen, Phytophthora capsici, and the major aphid pest, Myzus persicae target the host immune regulator SIZ1, an E3 SUMO ligase. We used transient expression assays in Nicotiana benthamiana as well as Arabidopsis mutants to further characterize biological role of effector-SIZ1 interactions in planta. We show that the oomycete and aphid effector, which both contribute to virulence, feature different activities towards SIZ1. While M. persicae effector Mp64 increases SIZ1 protein levels in transient assays, P. capsici effector CRN83_152 enhances SIZ1-E3 SUMO ligase activity in vivo. SIZ1 contributes to host susceptibility to aphids and an oomycete pathogen. Knockout of SIZ1 in Arabidopsis decreased susceptibility to aphids, independent of SNC1, PAD4 and EDS1. Similarly SIZ1 knockdown in N. benthamiana led to reduced P. capsici infection. Our results suggest convergence of distinct pathogen and pest virulence strategies on an E3 SUMO ligase to enhance host susceptibility.
Collapse
Affiliation(s)
- Shan Liu
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Camille J. G. Lenoir
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Tiago M. M. M. Amaro
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | | | - Edgar Huitema
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Jorunn I. B. Bos
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| |
Collapse
|
19
|
Chen D, Guo H, Chen S, Yue Q, Wang P, Chen X. Receptor-like kinase HAESA-like 1 positively regulates seed longevity in Arabidopsis. PLANTA 2022; 256:21. [PMID: 35763091 DOI: 10.1007/s00425-022-03942-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Based on the phenotypic, physiological and transcriptomic analysis, receptor-like kinase HAESA-like 1 was demonstrated to positively affect seed longevity in Arabidopsis. Seed longevity is very important for both genetic resource conservation and crop production. Receptor-like kinases (RLKs) are widely involved in plant growth, development and stress responses. However, the role of most RLKs, especially in seed longevity, is largely unknown. In this study, we report that Arabidopsis HAESA-like 1 (AtHSL1) positively regulated seed longevity. Disruption of HSL1 significantly decreased the germination rate to 50% at 7 days after cold stratification (DAC), compared with that of the wild type (93.5% at 7 DAC), after accelerated aging treatment. Expression of the HSL1 gene in hsl1 basically restored the defective phenotype (86.3%), while HSL1-overexpressing lines (98.3%) displayed slower accelerated aging than WT (93.5%). GUS staining revealed HSL1 was highly expressed universally, especially in young seedlings, mature seeds and embryos of imbibed seeds, and its expression could be induced by accelerated aging. No difference in the dyeing color and area of mucilage were identified between WT and hsl1. The soluble pectin content also was not different, while the adherent pectin content was significantly increased in hsl1. Global transcriptomics revealed that disruption of HSL1 mainly downregulated genes involved in trehalose synthesis, nucleotide sugar metabolism and protection and repair mechanisms. Therefore, an increase in adherent pectin content and downregulation of genes involved in trehalose synthesis may be the main reasons for decreasing seed longevity owing to disruption of HSL1 in Arabidopsis. Our work provides valuable information for understanding the function and mechanism of a receptor-like kinase, AtHSL1, in seed longevity.
Collapse
Affiliation(s)
- Defu Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongye Guo
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shuai Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qianying Yue
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Pei Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiwen Chen
- College of Life Sciences, Nankai University, Tianjin, 300071, China.
| |
Collapse
|
20
|
Grainge G, Nakabayashi K, Iza F, Leubner-Metzger G, Steinbrecher T. Gas-Plasma-Activated Water Impact on Photo-Dependent Dormancy Mechanisms in Nicotiana tabacum Seeds. Int J Mol Sci 2022; 23:6709. [PMID: 35743152 PMCID: PMC9223463 DOI: 10.3390/ijms23126709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/05/2023] Open
Abstract
Seeds sense temperature, nutrient levels and light conditions to inform decision making on the timing of germination. Limited light availability for photoblastic species results in irregular germination timing and losses of population germination percentage. Seed industries are therefore looking for interventions to mitigate this risk. A growing area of research is water treated with gas plasma (GPAW), in which the formed solution is a complex consisting of reactive oxygen and nitrogen species. Gas plasma technology is widely used for sterilisation and is an emerging technology in the food processing industry. The use of the GPAW on seeds has previously led to an increase in germination performance, often attributed to bolstered antioxidant defence mechanisms. However, there is a limited understanding of how the solution may influence the mechanisms that govern seed dormancy and whether photoreceptor-driven germination mechanisms are affected. In our work, we studied how GPAW can influence the mechanisms that govern photo-dependent dormancy, isolating the effects at low fluence response (LFR) and very low fluence response (VLFR). The two defined light intensity thresholds affect germination through different phytochrome photoreceptors, PHYB and PHYA, respectively; we found that GPAW showed a significant increase in population germination percentage under VLFR and further described how each treatment affects key physiological regulators.
Collapse
Affiliation(s)
- Giles Grainge
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (G.G.); (K.N.); (G.L.-M.)
| | - Kazumi Nakabayashi
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (G.G.); (K.N.); (G.L.-M.)
| | - Felipe Iza
- Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Leicestershire LE11 3TU, UK;
- Division of Advanced Nuclear Engineering, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (G.G.); (K.N.); (G.L.-M.)
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University, CZ-78371 Olomouc, Czech Republic
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK; (G.G.); (K.N.); (G.L.-M.)
| |
Collapse
|
21
|
Li C, Lei C, Wang K, Tan M, Xu F, Wang J, Zheng Y. MADS2 regulates priming defence in postharvest peach through combined salicylic acid and abscisic acid signaling. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3787-3806. [PMID: 35266534 DOI: 10.1093/jxb/erac099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
MADS-box genes play well-documented roles in plant development, but relatively little is known regarding their involvement in defence responses. In this study, pre-treatment of peach (Prunus persica) fruit with β-aminobutyric acid (BABA) activated resistance against Rhizopus stolonifer, leading to a significant delay in the symptomatic appearance of disease. This was associated with an integrated defence response that included a H2O2 burst, ABA accumulation, and callose deposition. cDNA library screening identified nucleus-localized MADS2 as an interacting partner with NPR1, and this was further confirmed by yeast two-hybrid, luciferase complementation imaging, and co-immunoprecipitation assays. The DNA-binding activity of NPR1 conferred by the NPR1-MADS2 complex was required for the transcription of SA-dependent pathogenesis-related (PR) and ABA-inducible CalS genes in order to gain the BABA-induced resistance, in which MAPK1-induced post-translational modification of MADS2 was also involved. In accordance with this, overexpression of PpMADS2 in Arabidopsis potentiated the transcription of a group of PR genes and conferred fungal resistance in the transgenic plants. Conversely, Arabidopsis mads2-knockout lines showed high sensitivity to the fungal pathogen. Our results indicate that MADS2 positively participates in BABA-elicited defence in peach through a combination of SA-dependent NPR1 activation and ABA signaling-induced callose accumulation, and that this defence is also related to the post-translational modification of MADS2 by MAPK1 for signal amplification.
Collapse
Affiliation(s)
- Chunhong Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P.R. China
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Changyi Lei
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Kaituo Wang
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Meilin Tan
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Feng Xu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, P.R. China
| | - Jinsong Wang
- College of Biology and Food Science, Chongqing Three Gorges University, Chongqing 404000, P.R. China
| | - Yonghua Zheng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095 Jiangsu, P.R. China
| |
Collapse
|
22
|
Zhang Y, Yin Q, Qin W, Gao H, Du J, Chen J, Li H, Zhou G, Wu H, Wu AM. The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3477-3495. [PMID: 35188965 DOI: 10.1093/jxb/erac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The production of Arabidopsis seed mucilage involves complex polysaccharide biosynthetic pathways and developmental processes in seed epidermal cells. Although the polysaccharide components of Arabidopsis seed mucilage have been identified, their regulatory mechanism requires further investigation. Here, we show that Class II KNOX gene family members KNAT3 and KNAT7 play an essential role in regulating mucilage production in the early developmental stages of Arabidopsis seeds. Double mutant knat3knat7 resulted in defective seed mucilage production and columellae formation, whereas knat3 showed a normal phenotype compared with wild type, and the mucilage thickness in knat7 was slightly disturbed. Rhamnogalacturonan I (RG-I) and its biosynthetic substrates galacturonic acid and rhamnose were reduced in both the adherent and soluble mucilage of knat3knat7. Comparative transcriptome analysis on whole seeds suggested that polysaccharide, glucosinolate and anthocyanin biosynthetic pathways were specifically repressed in knat3knat7. Transient co-expression of KNAT3 and KNAT7 with promoter regions of candidate genes in Arabidopsis protoplasts revealed that both KNAT3 and KNAT7 act as positive regulators of the RG-I biosynthetic gene MUCILAGE-MODIFIED 4 (MUM4, AT1G53500). Collectively, our results demonstrate that KNAT3 and KNAT7 are multifunctional transcription factors in secondary cell wall development and redundantly modulate mucilage biosynthesis in Arabidopsis seeds.
Collapse
Affiliation(s)
- Yuanyuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Qi Yin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Wenqi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Han Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- College of life sciences, South China Agricultural University. Guangzhou, 510642, China
| | - Jinge Du
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Jiajun Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
| | - Gongke Zhou
- College of Resource and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
- College of life sciences, South China Agricultural University. Guangzhou, 510642, China
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University. Guangzhou, 510642, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
| |
Collapse
|
23
|
Grant-Grant S, Schaffhauser M, Baeza-Gonzalez P, Gao F, Conéjéro G, Vidal EA, Gaymard F, Dubos C, Curie C, Roschzttardtz H. B3 Transcription Factors Determine Iron Distribution and FERRITIN Gene Expression in Embryo but Do Not Control Total Seed Iron Content. FRONTIERS IN PLANT SCIENCE 2022; 13:870078. [PMID: 35599858 PMCID: PMC9120844 DOI: 10.3389/fpls.2022.870078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/21/2022] [Indexed: 05/26/2023]
Abstract
Iron is an essential micronutrient for humans and other organisms. Its deficiency is one of the leading causes of anemia worldwide. The world health organization has proposed that an alternative to increasing iron content in food is through crop biofortification. One of the most consumed part of crops is the seed, however, little is known about how iron accumulation in seed occurs and how it is regulated. B3 transcription factors play a critical role in the accumulation of storage compounds such as proteins and lipids. Their role in seed maturation has been well characterized. However, their relevance in accumulation and distribution of micronutrients like iron remains unknown. In Arabidopsis thaliana and other plant models, three master regulators belonging to the B3 transcription factors family have been identified: FUSCA3 (FUS3), LEAFY COTYLEDON2 (LEC2), and ABSCISIC ACID INSENSITIVE 3 (ABI3). In this work, we studied how seed iron homeostasis is affected in B3 transcription factors mutants using histological and molecular approaches. We determined that iron distribution is modified in abi3, lec2, and fus3 embryo mutants. For abi3-6 and fus3-3 mutant embryos, iron was less accumulated in vacuoles of cells surrounding provasculature compared with wild type embryos. lec2-1 embryos showed no difference in the pattern of iron distribution in hypocotyl, but a dramatic decrease of iron was observed in cotyledons. Interestingly, for the three mutant genotypes, total iron content in dry mutant seeds showed no difference compared to wild type. At the molecular level, we showed that genes encoding the iron storage ferritins proteins are misregulated in mutant seeds. Altogether our results support a role of the B3 transcription factors ABI3, LEC2, and FUS3 in maintaining iron homeostasis in Arabidopsis embryos.
Collapse
Affiliation(s)
- Susana Grant-Grant
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Macarena Schaffhauser
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Baeza-Gonzalez
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fei Gao
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Geneviève Conéjéro
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Elena A. Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Frederic Gaymard
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Christian Dubos
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Catherine Curie
- IPSiM, Univ. Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Hannetz Roschzttardtz
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
24
|
Shin S, Chairattanawat C, Yamaoka Y, Yang Q, Lee Y, Hwang JU. Early seed development requires the A-type ATP-binding cassette protein ABCA10. PLANT PHYSIOLOGY 2022; 189:360-374. [PMID: 35166840 PMCID: PMC9070825 DOI: 10.1093/plphys/kiac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/06/2022] [Indexed: 05/11/2023]
Abstract
A-type ATP-binding cassette (ABCA) proteins transport lipids and lipid-based molecules in humans, and their malfunction is associated with various inherited diseases. Although plant genomes encode many ABCA transporters, their molecular and physiological functions remain largely unknown. Seeds are rapidly developing organs that rely on the biosynthesis and transport of large quantities of lipids to generate new membranes and storage lipids. In this study, we characterized the Arabidopsis (Arabidopsis thaliana) ABCA10 transporter, which is selectively expressed in female gametophytes and early developing seeds. By 3 d after flowering (DAF), seeds from the abca10 loss-of-function mutant exhibited a smaller chalazal endosperm than those of the wild-type. By 4 DAF, their endosperm nuclei occupied a smaller area than those of the wild-type. The endosperm nuclei of the mutants also failed to distribute evenly inside the seed coat and stayed aggregated instead, possibly due to inadequate expansion of abca10 endosperm. This endosperm defect might have retarded abca10 embryo development. At 7 DAF, a substantial portion of abca10 embryos remained at the globular or earlier developmental stages, whereas wild-type embryos were at the torpedo or later stages. ABCA10 is likely involved in lipid metabolism, as ABCA10 overexpression induced the overaccumulation of triacylglycerol but did not change the carbohydrate or protein contents in seeds. In agreement, ABCA10 localized to the endoplasmic reticulum (ER), the major site of lipid biosynthesis. Our results reveal that ABCA10 plays an essential role in early seed development, possibly by transporting substrates for lipid metabolism to the ER.
Collapse
Affiliation(s)
- Seungjun Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | | | - Yasuyo Yamaoka
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Qianying Yang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Youngsook Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Department of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | | |
Collapse
|
25
|
Nounurai P, Afifah A, Kittisenachai S, Roytrakul S. Phosphorylation of CAD1, PLDdelta, NDT1, RPM1 Proteins Induce Resistance in Tomatoes Infected by Ralstonia solanacearum. PLANTS 2022; 11:plants11060726. [PMID: 35336608 PMCID: PMC8954572 DOI: 10.3390/plants11060726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/20/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Ralstonia solanacaerum is one of the most devastating bacteria causing bacterial wilt disease in more than 200 species of plants, especially those belonging to the family Solanaceae. To cope with this pathogen, plants have evolved different resistance mechanisms depending on signal transduction after perception. Phosphorylation is the central regulatory component of the signal transduction pathway. We investigated a comparative phosphoproteomics analysis of the stems of resistant and susceptible tomatoes at 15 min and 30 min after inoculation with Ralstonia solanacearum to determine the phosphorylated proteins involved in induced resistance. Phosphoprotein profiling analyses led to the identification of 969 phosphoproteins classified into 10 functional categories. Among these, six phosphoproteins were uniquely identified in resistant plants including cinnamyl alcohol dehydrogenase 1 (CAD1), mitogen-activated protein kinase kinase kinase 18 (MAPKKK18), phospholipase D delta (PLDDELTA), nicotinamide adenine dinucleotide transporter 1 (NDT1), B3 domain-containing transcription factor VRN1, and disease resistance protein RPM1 (RPM1). These proteins are typically involved in defense mechanisms across different plant species. qRT-PCR analyses were performed to evaluate the level of expression of these genes in resistant and susceptible tomatoes. This study provides useful data, leading to an understanding of the early defense mechanisms of tomatoes against R. solanacearum.
Collapse
Affiliation(s)
- Prachumporn Nounurai
- Innovative Plant Biotechnology and Precision Agriculture Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
- Correspondence: (P.N.); (S.R.); Tel.: +66-25646700 (P.N. & S.R.)
| | - Anis Afifah
- Molecular and Applied Microbiology Laboratory, Diponegoro University, Jawa Tengah 50275, Indonesia;
| | - Suthathip Kittisenachai
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
- Correspondence: (P.N.); (S.R.); Tel.: +66-25646700 (P.N. & S.R.)
| |
Collapse
|
26
|
Škiljaica A, Jagić M, Vuk T, Leljak Levanić D, Bauer N, Markulin L. Evaluation of reference genes for RT-qPCR gene expression analysis in Arabidopsis thaliana exposed to elevated temperatures. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:367-379. [PMID: 34990067 DOI: 10.1111/plb.13382] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Increases in environmental temperature are directly linked to the issue of climate change and are known to significantly disrupt plant growth and development. Studies of gene expression in plants commonly include RT-qPCR but the reliability of the method depends on the use of suitable reference genes for data normalization. Despite this, no reference genes have been validated specifically for experiments in Arabidopsis thaliana employing treatments with elevated temperature. Here, ten genes were selected for expression stability analysis based on the screening of available literature and microarray data from temperature-treated A. thaliana. Expression levels of candidate reference genes were measured in 12-day-old seedlings, rosette leaves and flower buds of 5-week-old A. thaliana plants exposed to five different temperatures (22°C, 27°C, 32°C, 37°C and 42°C) and their expression stabilities were assessed using four statistical algorithms (BestKeeper, geNorm, NormFinder and comparative ΔCq method). This study provides reliable reference genes for use in A. thaliana RT-qPCR expression analyses employing elevated temperature treatments, namely OGIO and PUX7 in seedlings, UBC21 and PUX7 in leaves, TIP41 and UBC21 in buds, and TIP41 and UBC21 in all three tissues combined. Orthologues of these genes can be of potential use in less studied plants, especially agricultural species heavily affected by climate change.
Collapse
Affiliation(s)
- A Škiljaica
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - M Jagić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - T Vuk
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - D Leljak Levanić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - N Bauer
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - L Markulin
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
27
|
Baker CR, Stewart JJ, Amstutz CL, Ching LG, Johnson JD, Niyogi KK, Adams WW, Demmig‐Adams B. Genotype-dependent contribution of CBF transcription factors to long-term acclimation to high light and cool temperature. PLANT, CELL & ENVIRONMENT 2022; 45:392-411. [PMID: 34799867 PMCID: PMC9299779 DOI: 10.1111/pce.14231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
When grown under cool temperature, winter annuals upregulate photosynthetic capacity as well as freezing tolerance. Here, the role of three cold-induced C-repeat-binding factor (CBF1-3) transcription factors in photosynthetic upregulation and freezing tolerance was examined in two Arabidopsis thaliana ecotypes originating from Italy (IT) or Sweden (SW), and their corresponding CBF1-3-deficient mutant lines it:cbf123 and sw:cbf123. Photosynthetic, morphological and freezing-tolerance phenotypes, as well as gene expression profiles, were characterized in plants grown from the seedling stage under different combinations of light level and temperature. Under high light and cool (HLC) growth temperature, a greater role of CBF1-3 in IT versus SW was evident from both phenotypic and transcriptomic data, especially with respect to photosynthetic upregulation and freezing tolerance of whole plants. Overall, features of SW were consistent with a different approach to HLC acclimation than seen in IT, and an ability of SW to reach the new homeostasis through the involvement of transcriptional controls other than CBF1-3. These results provide tools and direction for further mechanistic analysis of the transcriptional control of approaches to cold acclimation suitable for either persistence through brief cold spells or for maximisation of productivity in environments with continuous low temperatures.
Collapse
Affiliation(s)
- Christopher R. Baker
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jared J. Stewart
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Cynthia L. Amstutz
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Lindsey G. Ching
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jeffrey D. Johnson
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Krishna K. Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical InstituteUniversity of CaliforniaBerkeleyCaliforniaUSA
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - William W. Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| | - Barbara Demmig‐Adams
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderColoradoUSA
| |
Collapse
|
28
|
Yin X, Bai YL, Ye T, Yu M, Wu Y, Feng YQ. Cinnamoyl coA: NADP oxidoreductase-like 1 regulates abscisic acid response by modulating phaseic acid homeostasis in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:860-872. [PMID: 34718526 DOI: 10.1093/jxb/erab474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Phaseic acid (PA), a main catabolite of abscisic acid (ABA), is structurally related to ABA and possesses ABA-like hormonal activity. However, the comprehensive metabolism pathway and roles of PA are not well understood. Here, using homologous alignment and expression pattern analysis, we identified in Arabidopsis the previously named CRL1 (Cinnamoyl coA: NADP oxidoreductase-like 1) as a PA reductase that catalyses PA to dihydrophaseic acid. The function of CRL1 and the potential role of PA were studied in transgenic CRL1 plants. Overexpression of CRL1 resulted in decreased ABA sensitivity in seed germination and attenuated drought tolerance. In contrast, increased ABA sensitivity and elevated drought tolerance was observed in down-regulated and loss-of-function crl1 mutants. Tyr162 in the conserved motif is the key residue in CRL1 to catalyse PA. Accelerated seed germination and earlier flowering phenotype were also observed in overexpressing lines, while retarded seed germination and delayed flowering occurred in crl1 mutants which accumulated more PA, but less dihydrophaseic acid than the wild type. This study demonstrates that PA plays diverse functions in drought tolerance, seed germination and flowering in an ABA-like manner, which may increase the adaptive plasticity of plants.
Collapse
Affiliation(s)
- Xiaoming Yin
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Ya-Li Bai
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Tiantian Ye
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Min Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, PR China
| |
Collapse
|
29
|
Omenge KM, Rümpler F, Kathalingam SS, Furch ACU, Theißen G. Studying the Function of Phytoplasma Effector Proteins Using a Chemical-Inducible Expression System in Transgenic Plants. Int J Mol Sci 2021; 22:ijms222413582. [PMID: 34948378 PMCID: PMC8703313 DOI: 10.3390/ijms222413582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Phytoplasmas are bacterial pathogens that live mainly in the phloem of their plant hosts. They dramatically manipulate plant development by secreting effector proteins that target developmental proteins of their hosts. Traditionally, the effects of individual effector proteins have been studied by ectopic overexpression using strong, ubiquitously active promoters in transgenic model plants. However, the impact of phytoplasma infection on the host plants depends on the intensity and timing of infection with respect to the developmental stage of the host. To facilitate investigations addressing the timing of effector protein activity, we have established chemical-inducible expression systems for the three most well-characterized phytoplasma effector proteins, SECRETED ASTER YELLOWS WITCHES’ BROOM PROTEIN 11 (SAP11), SAP54 and TENGU in transgenic Arabidopsis thaliana. We induced gene expression either continuously, or at germination stage, seedling stage, or flowering stage. mRNA expression was determined by quantitative reverse transcription PCR, protein accumulation by confocal laser scanning microscopy of GFP fusion proteins. Our data reveal tight regulation of effector gene expression and strong upregulation after induction. Phenotypic analyses showed differences in disease phenotypes depending on the timing of induction. Comparative phenotype analysis revealed so far unreported similarities in disease phenotypes, with all three effector proteins interfering with flower development and shoot branching, indicating a surprising functional redundancy of SAP54, SAP11 and TENGU. However, subtle but mechanistically important differences were also observed, especially affecting the branching pattern of the plants.
Collapse
Affiliation(s)
- Keziah M. Omenge
- Department of Genetics, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (K.M.O.); (F.R.); (S.S.K.)
| | - Florian Rümpler
- Department of Genetics, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (K.M.O.); (F.R.); (S.S.K.)
| | - Subha Suvetha Kathalingam
- Department of Genetics, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (K.M.O.); (F.R.); (S.S.K.)
| | - Alexandra C. U. Furch
- Department of Plant Physiology, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany;
| | - Günter Theißen
- Department of Genetics, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany; (K.M.O.); (F.R.); (S.S.K.)
- Correspondence:
| |
Collapse
|
30
|
Erazo-Garcia MP, Sotelo-Proaño AR, Ramirez-Villacis DX, Garcés-Carrera S, Leon-Reyes A. Methyl jasmonate-induced resistance to Delia platura (Diptera: Anthomyiidae) in Lupinus mutabilis. PEST MANAGEMENT SCIENCE 2021; 77:5382-5395. [PMID: 34313385 DOI: 10.1002/ps.6578] [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: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Andean lupin (Lupinus mutabilis Sweet) is an important leguminous crop from South America with a high protein content. In Ecuador, lupin yields are severely affected by the infestation of Delia platura larvae on germinating seeds. The application of elicitor molecules with activity against herbivorous insects to control D. platura infestation constitutes an unexplored and promising alternative for chemical insecticides. In this study, methyl jasmonate (MeJA), hexanoic acid, menadione sodium bisulfite, and DL-β-aminobutyric acid were evaluated for their ability to induce resistance against D. platura in three commercial lupin cultivars. RESULTS Only seeds pretreated with MeJA significantly impaired insect performance during choice and no-choice assays. Additionally, fitness indicators such as seed germination and growth were not affected by MeJA treatment. To investigate the molecular mechanisms behind the MeJA-mediated resistance, RT-qPCR assays were performed. First, RT-qPCR reference genes were validated, showing that LmUBC was the most stable reference gene. Next, expression analysis over time revealed that MeJA application up-regulated the activity of the jasmonic acid biosynthetic genes LmLOX2 and LmAOS, together with other jasmonate-related defense genes, such as LmTPS1, LmTPS4, LmPI2, LmMBL, LmL/ODC, LmCSD1, and LmPOD. CONCLUSION This study indicates that MeJA can be used as an environmentally friendly elicitor molecule to protect Andean lupin from D. platura attack without fitness cost. MeJA application induces plant defense responses to insects in Andean lupin that may be modulated by the onset of terpenoid biosynthesis, proteinase inhibitors, lectins, polyamines, and antioxidative enzymes. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Maria P Erazo-Garcia
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Adolfo R Sotelo-Proaño
- Laboratorio de Entomología, Departamento de Protección Vegetal, Estación Experimental Santa Catalina, Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sandra Garcés-Carrera
- Laboratorio de Entomología, Departamento de Protección Vegetal, Estación Experimental Santa Catalina, Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| |
Collapse
|
31
|
Ashraf M, Mao Q, Hong J, Shi L, Ran X, Liaquat F, Uzair M, Liang W, Fernie AR, Shi J. HSP70-16 and VDAC3 jointly inhibit seed germination under cold stress in Arabidopsis. PLANT, CELL & ENVIRONMENT 2021; 44:3616-3627. [PMID: 34173257 DOI: 10.1111/pce.14138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/09/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid (ABA) transport plays a crucial role in seed germination under unfavourable conditions such as cold stress. Both heat shock protein 70 (HSP70) and voltage-dependent anion channel (VDAC) protein are involved in cold stress responses in Arabidopsis. However, their roles in seed germination with regard to ABA signaling remain unknown. Here we demonstrated that Arabidopsis HSP70-16 and VDAC3 jointly suppress seed germination under cold stress conditions. At 4°C, both HSP70-16 and VDAC3 facilitated the efflux of ABA from the endosperm to the embryo and thus inhibited seed germination. HSP70-16 interacted with VDAC3 on the plasma membrane and in the nucleus, and the interplay between HSP70-16 and VDAC3 activated the opening of the VDAC3 ion channel. Our work established a novel function of HSP70-16 in seed germination under cold stress and a possible association of VDAC3 activity with ABA transportation from endosperm to embryo under cold stress conditions. This study reveals that HSP70-16 interacts with VDAC3 and facilitates the opening of the VDAC3 ion channel, which influences ABA efflux from endosperm to embryo, thus negatively regulates seed germination under cold stress.
Collapse
Affiliation(s)
- Muhammad Ashraf
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qionglei Mao
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoruo Ran
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fiza Liaquat
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Uzair
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
32
|
Née G, Châtel-Innocenti G, Meimoun P, Leymarie J, Montrichard F, Satour P, Bailly C, Issakidis-Bourguet E. A New Role for Plastid Thioredoxins in Seed Physiology in Relation to Hormone Regulation. Int J Mol Sci 2021; 22:ijms221910395. [PMID: 34638735 PMCID: PMC8508614 DOI: 10.3390/ijms221910395] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 01/16/2023] Open
Abstract
In Arabidopsis seeds, ROS have been shown to be enabling actors of cellular signaling pathways promoting germination, but their accumulation under stress conditions or during aging leads to a decrease in the ability to germinate. Previous biochemical work revealed that a specific class of plastid thioredoxins (Trxs), the y-type Trxs, can fulfill antioxidant functions. Among the ten plastidial Trx isoforms identified in Arabidopsis, Trx y1 mRNA is the most abundant in dry seeds. We hypothesized that Trx y1 and Trx y2 would play an important role in seed physiology as antioxidants. Using reverse genetics, we found important changes in the corresponding Arabidopsis mutant seeds. They display remarkable traits such as increased longevity and higher and faster germination in conditions of reduced water availability or oxidative stress. These phenotypes suggest that Trxs y do not play an antioxidant role in seeds, as further evidenced by no changes in global ROS contents and protein redox status found in the corresponding mutant seeds. Instead, we provide evidence that marker genes of ABA and GAs pathways are perturbed in mutant seeds, together with their sensitivity to specific hormone inhibitors. Altogether, our results suggest that Trxs y function in Arabidopsis seeds is not linked to their previously identified antioxidant roles and reveal a new role for plastid Trxs linked to hormone regulation.
Collapse
Affiliation(s)
- Guillaume Née
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, F-91405 Orsay, France
| | - Gilles Châtel-Innocenti
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, F-91405 Orsay, France
| | - Patrice Meimoun
- CNRS, Laboratoire de Biologie du Développement, Sorbonne Université, F-75005 Paris, France
| | - Juliette Leymarie
- CNRS, Laboratoire de Biologie du Développement, Sorbonne Université, F-75005 Paris, France
| | - Françoise Montrichard
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d'Angers, F-49071 Beaucouzé, France
| | - Pascale Satour
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d'Angers, F-49071 Beaucouzé, France
| | - Christophe Bailly
- CNRS, Laboratoire de Biologie du Développement, Sorbonne Université, F-75005 Paris, France
| | - Emmanuelle Issakidis-Bourguet
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Université Evry, Université Paris-Saclay, F-91405 Orsay, France
| |
Collapse
|
33
|
Evaluation of Angelica decursiva reference genes under various stimuli for RT-qPCR data normalization. Sci Rep 2021; 11:18993. [PMID: 34556773 PMCID: PMC8460625 DOI: 10.1038/s41598-021-98434-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the RT-qPCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This RT-qPCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the RT-qPCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of RT-qPCR for an accurate and far-reaching gene expression analysis in this medicinal plant.
Collapse
|
34
|
Albuquerque GMR, Fonseca FCA, Boiteux LS, Borges RCF, Miller RNG, Lopes CA, Souza EB, Fonseca MEN. Stability analysis of reference genes for RT-qPCR assays involving compatible and incompatible Ralstonia solanacearum-tomato 'Hawaii 7996' interactions. Sci Rep 2021; 11:18719. [PMID: 34548514 PMCID: PMC8455670 DOI: 10.1038/s41598-021-97854-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/31/2021] [Indexed: 11/26/2022] Open
Abstract
Reverse transcription-quantitative PCR (RT-qPCR) is an analytical tool for gene expression quantification. Reference genes are not yet available for gene expression analysis during interactions of Ralstonia solanacearum with ‘Hawaii 7996’ (the most stable source of resistance in tomato). Here, we carried out a multi-algorithm stability analysis of eight candidate reference genes during interactions of ‘Hawaii 7996’ with one incompatible/avirulent and two compatible/virulent (= resistance-breaking) bacterial isolates. Samples were taken at 24- and 96-h post-inoculation (HPI). Analyses were performed using the ∆∆Ct method and expression stability was estimated using BestKeeper, NormFinder, and geNorm algorithms. TIP41 and EF1α (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and TIP41 (with BestKeeper), were the best combinations for mRNA normalization in incompatible interactions at 24 HPI and 96 HPI. The most stable genes in global compatible and incompatible interactions at 24 HPI and 96 HPI were PDS and TIP41 (with geNorm), TIP41 and ACT (with NormFinder), and UBI3 and PDS/EXP (with BestKeeper). Global analyses on the basis of the three algorithms across 20 R. solanacearum-tomato experimental conditions identified UBI3, TIP41 and ACT as the best choices as reference tomato genes in this important pathosystem.
Collapse
Affiliation(s)
- Greecy M R Albuquerque
- Department of Agronomy, Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE, Brazil.
| | - Fernando C A Fonseca
- Departament of Academic Areas, Instituto Federal de Goiás (IFG), Águas Lindas,, GO, Brazil
| | - Leonardo S Boiteux
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
| | - Rafaela C F Borges
- Plant Pathology Department, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Robert N G Miller
- Plant Pathology Department, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil.,Department of Cell Biology, ICB, Universidade de Brasília (UnB), Brasília, DF, Brazil
| | - Carlos A Lopes
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
| | - Elineide B Souza
- Department of Biology, Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE, Brazil
| | - Maria Esther N Fonseca
- National Center for Vegetable Crops Research, Embrapa Vegetables (CNPH), Brasília, DF, Brazil
| |
Collapse
|
35
|
de Saint Germain A, Jacobs A, Brun G, Pouvreau JB, Braem L, Cornu D, Clavé G, Baudu E, Steinmetz V, Servajean V, Wicke S, Gevaert K, Simier P, Goormachtig S, Delavault P, Boyer FD. A Phelipanche ramosa KAI2 protein perceives strigolactones and isothiocyanates enzymatically. PLANT COMMUNICATIONS 2021; 2:100166. [PMID: 34746757 PMCID: PMC8553955 DOI: 10.1016/j.xplc.2021.100166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 05/18/2023]
Abstract
Phelipanche ramosa is an obligate root-parasitic weed that threatens major crops in central Europe. In order to germinate, it must perceive various structurally divergent host-exuded signals, including isothiocyanates (ITCs) and strigolactones (SLs). However, the receptors involved are still uncharacterized. Here, we identify five putative SL receptors in P. ramosa and show that PrKAI2d3 is involved in the stimulation of seed germination. We demonstrate the high plasticity of PrKAI2d3, which allows it to interact with different chemicals, including ITCs. The SL perception mechanism of PrKAI2d3 is similar to that of endogenous SLs in non-parasitic plants. We provide evidence that PrKAI2d3 enzymatic activity confers hypersensitivity to SLs. Additionally, we demonstrate that methylbutenolide-OH binds PrKAI2d3 and stimulates P. ramosa germination with bioactivity comparable to that of ITCs. This study demonstrates that P. ramosa has extended its signal perception system during evolution, a fact that should be considered for the development of specific and efficient biocontrol methods.
Collapse
Affiliation(s)
| | - Anse Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Guillaume Brun
- Laboratoire de Biologie et Pathologie Végétales (LBPV), Equipe d’Accueil 1157, Université de Nantes, 44000 Nantes, France
- Institute for Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Jean-Bernard Pouvreau
- Laboratoire de Biologie et Pathologie Végétales (LBPV), Equipe d’Accueil 1157, Université de Nantes, 44000 Nantes, France
| | - Lukas Braem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - David Cornu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Clavé
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Emmanuelle Baudu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Vincent Steinmetz
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Vincent Servajean
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Susann Wicke
- Institute for Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Philippe Simier
- Laboratoire de Biologie et Pathologie Végétales (LBPV), Equipe d’Accueil 1157, Université de Nantes, 44000 Nantes, France
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Philippe Delavault
- Laboratoire de Biologie et Pathologie Végétales (LBPV), Equipe d’Accueil 1157, Université de Nantes, 44000 Nantes, France
| | - François-Didier Boyer
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
- Corresponding author
| |
Collapse
|
36
|
Color-Specific Recovery to Extreme High-Light Stress in Plants. Life (Basel) 2021; 11:life11080812. [PMID: 34440556 PMCID: PMC8398727 DOI: 10.3390/life11080812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 11/17/2022] Open
Abstract
Plants pigments, such as chlorophyll and carotenoids, absorb light within specific wavelength ranges, impacting their response to environmental light changes. Although the color-specific response of plants to natural levels of light is well described, extreme high-light stress is still being discussed as a general response, without considering the impact of wavelengths in particular response processes. In this study, we explored how the plant proteome coordinated the response and recovery to extreme light conditions (21,000 µmol m-2 s-1) under different wavelengths. Changes at the protein and mRNA levels were measured, together with the photosynthetic parameters of plants under extreme high-light conditions. The changes in abundance of four proteins involved in photoinhibition, and in the biosynthesis/assembly of PSII (PsbS, PsbH, PsbR, and Psb28) in both light treatments were measured. The blue-light treatment presented a three-fold higher non-photochemical quenching and did not change the level of the oxygen-evolving complex (OEC) or the photosystem II (PSII) complex components when compared to the control, but significantly increased psbS transcripts. The red-light treatment caused a higher abundance of PSII and OEC proteins but kept the level of psbS transcripts the same as the control. Interestingly, the blue light stimulated a more efficient energy dissipation mechanism when compared to the red light. In addition, extreme high-light stress mechanisms activated by blue light involve the role of OEC through increasing PsbS transcript levels. In the proteomics spatial analysis, we report disparate activation of multiple stress pathways under three differently damaged zones as the enriched function of light stress only found in the medium-damaged zone of the red LED treatment. The results indicate that the impact of extreme high-light stress on the proteomic level is wavelength-dependent.
Collapse
|
37
|
Dorone Y, Boeynaems S, Flores E, Jin B, Hateley S, Bossi F, Lazarus E, Pennington JG, Michiels E, De Decker M, Vints K, Baatsen P, Bassel GW, Otegui MS, Holehouse AS, Exposito-Alonso M, Sukenik S, Gitler AD, Rhee SY. A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell 2021; 184:4284-4298.e27. [PMID: 34233164 PMCID: PMC8513799 DOI: 10.1016/j.cell.2021.06.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 03/22/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022]
Abstract
Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. We identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.
Collapse
Affiliation(s)
- Yanniv Dorone
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Benjamin Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Shannon Hateley
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Flavia Bossi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Elena Lazarus
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Janice G Pennington
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Emiel Michiels
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Mathias De Decker
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), 3000 Leuven, Belgium
| | - Katlijn Vints
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - Pieter Baatsen
- EM-platform@VIB Bio Imaging Core and VIB Center for Brain and Disease Research, KU Leuven, 3000 Leuven, Belgium
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Marisa S Otegui
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA; Department of Botany, University of Wisconsin, Madison, WI 53706, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, UC Merced, Merced, CA 95340, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| |
Collapse
|
38
|
Sharma S, Vengavasi K, Kumar MN, Yadav SK, Pandey R. Expression of potential reference genes in response to macronutrient stress in rice and soybean. Gene 2021; 792:145742. [PMID: 34051336 DOI: 10.1016/j.gene.2021.145742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 02/04/2023]
Abstract
Given the complexity of nutrient stress responses and the availability of a few validated reference genes, we aimed to identify robust and stable reference genes for macronutrient stress in rice and soybean. Ten potential reference genes were evaluated using geNorm, NormFinder, BestKeeper, Comparative ΔCt method, and RefFinder algorithms under low and completely starved conditions of nitrogen (N), phosphorus (P), potassium (K), and sulphur (S). Results revealed distinct sets of reference gene pairs, showing stable expression under different experimental conditions. The gene pairs TIP41/UBC(9/10/18) and F-box/UBC10 were most stable in rice and soybean, respectively under N stress. Under P stress, UBC9/UBC10 in rice and F-Box/UBC10 in soybean were most stable. Similarly, TIP41/UBC10 in rice and RING FINGER/UBC9 in soybean were the best gene pairs under K stress while F-Box/TIP41 in rice and UBC9/UBC10 in soybean were the most stable gene pairs under S stress. These reference gene pairs were validated by quantifying the expression levels of high-affinity transporters like NRT2.1/NRT2.5, PT1, AKT1, and SULTR1 for N, P, K, and S stress, respectively. This study reiterates the importance of choosing reference genes based on crop species and the experimental conditions, in order to obtain concrete answers to missing links of gene regulation in response to macronutrient deficiencies.
Collapse
Affiliation(s)
- Sandeep Sharma
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Krishnapriya Vengavasi
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - M Nagaraj Kumar
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Shiv Kumar Yadav
- Division of Seed Science and Technology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agriculture Research Institute, New Delhi 110012, India.
| |
Collapse
|
39
|
Strobbe S, Verstraete J, Stove C, Van Der Straeten D. Metabolic engineering provides insight into the regulation of thiamin biosynthesis in plants. PLANT PHYSIOLOGY 2021; 186:1832-1847. [PMID: 33944954 PMCID: PMC8331165 DOI: 10.1093/plphys/kiab198] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/06/2021] [Indexed: 05/06/2023]
Abstract
Thiamin (or thiamine) is a water-soluble B-vitamin (B1), which is required, in the form of thiamin pyrophosphate, as an essential cofactor in crucial carbon metabolism reactions in all forms of life. To ensure adequate metabolic functioning, humans rely on a sufficient dietary supply of thiamin. Increasing thiamin levels in plants via metabolic engineering is a powerful strategy to alleviate vitamin B1 malnutrition and thus improve global human health. These engineering strategies rely on comprehensive knowledge of plant thiamin metabolism and its regulation. Here, multiple metabolic engineering strategies were examined in the model plant Arabidopsis thaliana. This was achieved by constitutive overexpression of the three biosynthesis genes responsible for B1 synthesis, HMP-P synthase (THIC), HET-P synthase (THI1), and HMP-P kinase/TMP pyrophosphorylase (TH1), either separate or in combination. By monitoring the levels of thiamin, its phosphorylated entities, and its biosynthetic intermediates, we gained insight into the effect of either strategy on thiamin biosynthesis. Moreover, expression analysis of thiamin biosynthesis genes showed the plant's intriguing ability to respond to alterations in the pathway. Overall, we revealed the necessity to balance the pyrimidine and thiazole branches of thiamin biosynthesis and assessed its biosynthetic intermediates. Furthermore, the accumulation of nonphosphorylated intermediates demonstrated the inefficiency of endogenous thiamin salvage mechanisms. These results serve as guidelines in the development of novel thiamin metabolic engineering strategies.
Collapse
Affiliation(s)
- Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, B-9000 Ghent, Belgium
| | - Jana Verstraete
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, B-9000 Ghent, Belgium
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Ghent University, B-9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, B-9000 Ghent, Belgium
- Author for communication:
| |
Collapse
|
40
|
Ramachandran P, Augstein F, Mazumdar S, Nguyen TV, Minina EA, Melnyk CW, Carlsbecker A. Abscisic acid signaling activates distinct VND transcription factors to promote xylem differentiation in Arabidopsis. Curr Biol 2021; 31:3153-3161.e5. [PMID: 34043949 DOI: 10.1016/j.cub.2021.04.057] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/03/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022]
Abstract
Plants display remarkable abilities to adjust growth and development to environmental conditions, such as the amount of available water. This developmental plasticity is apparent not only in root and shoot growth rates, but also in tissue patterning and cell morphology.1,2 We have previously shown that in response to limited water availability, Arabidopsis thaliana root displays changes in xylem morphology, mediated by the non-cell-autonomous action of abscisic acid, ABA.2 Here, we show, through analyses of ABA response reporters and tissue-specific suppression of ABA signaling, that xylem cells themselves act as primary signaling centers governing both xylem cell fate and xylem differentiation rate, revealing the cell-autonomous control of multiple aspects of xylem development by ABA. ABA rapidly activates the expression of genes encoding VASCULAR-RELATED NAC DOMAIN (VND) transcription factors. Molecular and genetic analyses revealed that the two ABA-mediated xylem developmental changes are regulated by distinct members of this transcription factor family, with VND2 and VND3 promoting differentiation rate of metaxylem cells, while VND7 promotes the conversion of metaxylem toward protoxylem morphology. This phenomenon shows how different aspects of developmental plasticity can be interlinked, yet genetically separable. Moreover, similarities in phenotypic and molecular responses to ABA in diverse species indicate evolutionary conservation of the ABA-xylem development regulatory network among eudicots. Hence, this study gives molecular insights into how environmental stress modifies plant vascular anatomy and has potential relevance for water use optimization and adaptation to drought conditions.
Collapse
Affiliation(s)
- Prashanth Ramachandran
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Frauke Augstein
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Shamik Mazumdar
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Thanh Van Nguyen
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Charles W Melnyk
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Ullsv. 24E, SE-756 51 Uppsala, Sweden
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, SE-756 51 Uppsala, Sweden.
| |
Collapse
|
41
|
Ribeiro-Oliveira JP, Silveira LED, Pinto LVA, Silva EAA, Hilhorst HWM. Clues on an intraspecific communication system in seed-seedling transition. PHYSIOLOGIA PLANTARUM 2021; 172:1609-1618. [PMID: 33661531 DOI: 10.1111/ppl.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/08/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
How much interactivity is in a seed-seedling transition system? We hypothesize that seed-seed, seed-seedling, and seedling-seedling interactions can drive the early plant development in artificial growth systems directly due to mutual stimulation phenomena. To test the hypothesis, we performed seed germination measurements, gene expression in germination sensu stricto, water dynamics in germinating seeds, and information theory. For a biological model, we used Solanum lycocarpum A. St.-Hil. seeds. This is a neotropical species with high intraspecific variability in the seed sample. Our findings demonstrate that the dynamic and transient seed-seedling transition system is influenced by the number of individuals (seed or seedling) in the artificial system. In addition, we also discuss that: (1) the information entropy enables the quantification of system disturbance relative to individuals at the same physiological stage (seed-seed or seedling-seedling), which may be determinant for embryo growth during germination and (2) the intraspecific communication in seed-seedling transition systems formed by germinating seeds has the potential to alter the expression pattern of key genes for embryo development. Therefore, the phenomenon of mutual stimulation during the germination process can be an important aspect of seed-seedling transition, especially in laboratory conditions.
Collapse
Affiliation(s)
- João Paulo Ribeiro-Oliveira
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, Brazil
- Departamento de Produção e Melhoramento Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu, Brazil
| | - Lilian E D Silveira
- Departamento de Produção e Melhoramento Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu, Brazil
| | - Lilian V A Pinto
- Instituto Federal de Educação Ciência e Tecnologia do Sul de Minas Gerais, Inconfidentes, Brazil
| | - Edvaldo A A Silva
- Departamento de Produção e Melhoramento Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu, Brazil
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
42
|
Alaguero-Cordovilla A, Sánchez-García AB, Ibáñez S, Albacete A, Cano A, Acosta M, Pérez-Pérez JM. An auxin-mediated regulatory framework for wound-induced adventitious root formation in tomato shoot explants. PLANT, CELL & ENVIRONMENT 2021; 44:1642-1662. [PMID: 33464573 DOI: 10.1111/pce.14001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 05/24/2023]
Abstract
Adventitious roots (ARs) are produced from non-root tissues in response to different environmental signals, such as abiotic stresses, or after wounding, in a complex developmental process that requires hormonal crosstalk. Here, we characterized AR formation in young seedlings of Solanum lycopersicum cv. 'Micro-Tom' after whole root excision by means of physiological, genetic and molecular approaches. We found that a regulated basipetal auxin transport from the shoot and local auxin biosynthesis triggered by wounding are both required for the re-establishment of internal auxin gradients within the vasculature. This promotes cell proliferation at the distal cambium near the wound in well-defined positions of the basal hypocotyl and during a narrow developmental window. In addition, a pre-established pattern of differential auxin responses along the apical-basal axis of the hypocotyl and an as of yet unknown cell-autonomous inhibitory pathway contribute to the temporal and spatial patterning of the newly formed ARs on isolated hypocotyl explants. Our work provides an experimental outline for the dissection of wound-induced AR formation in tomato, a species that is suitable for molecular identification of gene regulatory networks via forward and reverse genetics approaches.
Collapse
Affiliation(s)
| | | | - Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Alfonso Albacete
- Present address: Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), La Alberca, Spain
- CEBAS-CSIC, Department of Plant Nutrition, Campus Universitario de Espinardo, Espinardo, Murcia, Spain
| | - Antonio Cano
- Departamento de Biología Vegetal, Universidad de Murcia, Murcia, Spain
| | - Manuel Acosta
- Departamento de Biología Vegetal, Universidad de Murcia, Murcia, Spain
| | | |
Collapse
|
43
|
Linardić M, Braybrook SA. Identification and selection of optimal reference genes for qPCR-based gene expression analysis in Fucus distichus under various abiotic stresses. PLoS One 2021; 16:e0233249. [PMID: 33909633 PMCID: PMC8081170 DOI: 10.1371/journal.pone.0233249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/18/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative gene expression analysis is an important tool in the scientist's belt. The identification of evenly expressed reference genes is necessary for accurate quantitative gene expression analysis, whether by traditional RT-PCR (reverse-transcription polymerase chain reaction) or by qRT-PCR (quantitative real-time PCR; qPCR). In the Stramenopiles (the major line of eukaryotes that includes brown algae) there is a noted lack of known reference genes for such studies, largely due to the absence of available molecular tools. Here we present a set of nine reference genes (Elongation Factor 1 alpha (EF1A), Elongation Factor 2 alpha (EF2A), Elongation Factor 1 beta (EF1B), 14-3-3 Protein, Ubiquitin Conjugating Enzyme (UBCE2), Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH), Actin Related Protein Complex (ARP2/3), Ribosomal Protein (40s; S23), and Actin) for the brown alga Fucus distichus. These reference genes were tested on adult sporophytes across six abiotic stress conditions (desiccation, light and temperature modification, hormone addition, pollutant exposure, nutrient addition, and wounding). Suitability of these genes as reference genes was quantitatively evaluated across conditions using standard methods and the majority of the tested genes were evaluated favorably. However, we show that normalization genes should be chosen on a condition-by-condition basis. We provide a recommendation that at least two reference genes be used per experiment, a list of recommended pairs for the conditions tested here, and a procedure for identifying a suitable set for an experimenter's unique design. With the recent expansion of interest in brown algal biology and accompanied molecular tools development, the variety of experimental conditions tested here makes this study a valuable resource for future work in basic biology and understanding stress responses in the brown algal lineage.
Collapse
Affiliation(s)
- Marina Linardić
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Energy Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Siobhan A. Braybrook
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Energy Institute of Genomics and Proteomics, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|
44
|
Ding A, Tang X, Yang D, Wang M, Ren A, Xu Z, Hu R, Zhou G, O’Neill M, Kong Y. ERF4 and MYB52 transcription factors play antagonistic roles in regulating homogalacturonan de-methylesterification in Arabidopsis seed coat mucilage. THE PLANT CELL 2021; 33:381-403. [PMID: 33709105 PMCID: PMC8136884 DOI: 10.1093/plcell/koaa031] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/17/2020] [Indexed: 05/05/2023]
Abstract
Homogalacturonan (HG), a component of pectin, is synthesized in the Golgi apparatus in its fully methylesterified form. It is then secreted into the apoplast where it is typically de-methylesterified by pectin methylesterases (PME). Secretion and de-esterification are critical for normal pectin function, yet the underlying transcriptional regulation mechanisms remain largely unknown. Here, we uncovered a mechanism that fine-tunes the degree of HG de-methylesterification (DM) in the mucilage that surrounds Arabidopsis thaliana seeds. We demonstrate that the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor (TF) ERF4 is a transcriptional repressor that positively regulates HG DM. ERF4 expression is confined to epidermal cells in the early stages of seed coat development. The adhesiveness of the erf4 mutant mucilage was decreased as a result of an increased DM caused by a decrease in PME activity. Molecular and genetic analyses revealed that ERF4 positively regulates HG DM by suppressing the expression of three PME INHIBITOR genes (PMEIs) and SUBTILISIN-LIKE SERINE PROTEASE 1.7 (SBT1.7). ERF4 shares common targets with the TF MYB52, which also regulates pectin DM. Nevertheless, the erf4-2 myb52 double mutant seeds have a wild-type mucilage phenotype. We provide evidence that ERF4 and MYB52 regulate downstream gene expression in an opposite manner by antagonizing each other's DNA-binding ability through a physical interaction. Together, our findings reveal that pectin DM in the seed coat is fine-tuned by an ERF4-MYB52 transcriptional complex.
Collapse
Affiliation(s)
- Anming Ding
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Xianfeng Tang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao 266101, China
| | - Dahai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Meng Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Angyan Ren
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Zongchang Xu
- Key Laboratory of Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, China
| | - Ruibo Hu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences (CAS), Qingdao 266101, China
| | - Gongke Zhou
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257000, China
| | - Malcolm O’Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Yingzhen Kong
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| |
Collapse
|
45
|
A Raf-like kinase is required for smoke-induced seed dormancy in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2021; 118:2020636118. [PMID: 33795513 DOI: 10.1073/pnas.2020636118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants sense and integrate diverse stimuli to determine the timing for germination. A smoke compound, 3,4,5-trimethylfuran-2(5H)-one (trimethylbutenolide, TMB), has been identified to inhibit the seed germination of higher plants. To understand the mode of action, we examined various physiological and molecular aspects of the TMB-dependent inhibition of seed germination in Arabidopsis thaliana The results indicated that the effect of TMB is due to the enhanced physiological dormancy, which is modulated by other dormancy regulatory cues such as after-ripening, stratification, and ABA/GA signaling. In addition, gene expression profiling showed that TMB caused genome-wide transcriptional changes, altering the expression of a series of dormancy-related genes. Based on the TMB-responsive physiological contexts in Arabidopsis, we performed mutant screening to isolate genetic components that underpin the TMB-induced seed dormancy. As a result, the TMB-RESISTANT1 (TES1) gene in Arabidopsis, encoding a B2 group Raf-like kinase, was identified. Phenotypic analysis of the tes1 mutant implicated that TES1 has a critical role in the TMB-responsive gene expression and the inhibition of seed germination. Taken together, we propose that plants have been equipped with a TMB sensory pathway through which the TMB induces the seed dormancy in a TES1-dependent way.
Collapse
|
46
|
Lu J, Le Hir R, Gómez-Páez DM, Coen O, Péchoux C, Jasinski S, Magnani E. The nucellus: between cell elimination and sugar transport. PLANT PHYSIOLOGY 2021; 185:478-490. [PMID: 33721907 PMCID: PMC8133628 DOI: 10.1093/plphys/kiaa045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/10/2020] [Indexed: 05/29/2023]
Abstract
The architecture of the seed is shaped by the processes of tissue partitioning, which determines the volume ratio of maternal and zygotic tissues, and nutrient partitioning, which regulates nutrient distribution among tissues. In angiosperms, early seed development is characterized by antagonistic development of the nucellus maternal tissue and the endosperm fertilization product to become the main sugar sink. This process marked the evolution of angiosperms and outlines the most ancient seed architectures. In Arabidopsis, the endosperm partially eliminates the nucellus and imports sugars from the seed coat. Here, we show that the nucellus is symplasmically connected to the chalaza, the seed nutrient unloading zone, and works as both a sugar sink and source alongside the seed coat. After fertilization, the transient nucellus accumulates starch early on and releases it in the apoplasmic space during its elimination. By contrast, the persistent nucellus exports sugars toward the endosperm through the SWEET4 hexose facilitator. Finally, we analyzed sugar metabolism and transport in the transparent testa 16 mutant, which fails to undergo nucellus cell elimination, which shed light on the coordination between tissue and nutrient partitioning. Overall, this study identifies a path of sugar transport in the Arabidopsis seed and describes a link between sugar redistribution and the nucellus cell-elimination program.
Collapse
Affiliation(s)
- Jing Lu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
- École Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, bat 360, 91405 Orsay Cedex, France
| | - Rozenn Le Hir
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Dennys-Marcela Gómez-Páez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Olivier Coen
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
- École Doctorale 567 Sciences du Végétal, University Paris-Sud, University of Paris-Saclay, bat 360, 91405 Orsay Cedex, France
| | - Christine Péchoux
- INRAE, Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas Cedex, France
| | - Sophie Jasinski
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| | - Enrico Magnani
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, CNRS, University of Paris-Saclay, Route de St-Cyr (RD10), 78026 Versailles Cedex, France
| |
Collapse
|
47
|
Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover. Sci Rep 2021; 11:3269. [PMID: 33558610 PMCID: PMC7870939 DOI: 10.1038/s41598-021-82633-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/19/2021] [Indexed: 11/08/2022] Open
Abstract
The forage species Caucasian clover (Trifolium ambiguum M. Bieb.), a groundcover plant, is resistant to both cold and drought. However, reference genes for qRT-PCR-based analysis of Caucasian clover are lacking. In this study, 12 reference genes were selected on the basis of transcriptomic data. These genes were used to determine the most stably expressed genes in various organs of Caucasian clover under cold, salt and drought stress for qRT-PCR-based analysis. Reference gene stability was analyzed by geNorm, NormFinder, BestKeeper, the ∆Ct method and RefFinder. Under salt stress, RCD1 and PPIL3 were the most stable reference genes in the leaves, and NLI1 and RCD1 were the most stable references genes in the roots. Under low-temperature stress, APA and EFTu-GTP were the most stable reference genes in the leaves, and the RCD1 and NLI2 genes were highly stable in the roots. Under 10% PEG-6000 stress, NLI1 and NLI2 were highly stable in the leaves, and RCD1 and PPIL3 were the most stable in the roots. Overall, RCD1 and NLI2 were the most stable reference genes in organs under normal conditions and across all samples. The most and least stable reference genes were validated by assessing their appropriateness for normalization via WRKY genes.
Collapse
|
48
|
Chen J, Zhou J, Hong Y, Li Z, Cheng X, Zheng A, Zhang Y, Song J, Xie G, Chen C, Yuan M, Wang T, Chen Q. Genome-wide identification of ubiquitin proteasome subunits as superior reference genes for transcript normalization during receptacle development in strawberry cultivars. BMC Genomics 2021; 22:88. [PMID: 33509086 PMCID: PMC7845027 DOI: 10.1186/s12864-021-07393-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
Background Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars. Results The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the “Commonly used” and “Traditional” HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development. Conclusion These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07393-9.
Collapse
Affiliation(s)
- Jianqing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China. .,FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jinyu Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Yanhong Hong
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Zekun Li
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Xiangyu Cheng
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Aiying Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Yilin Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Juanjuan Song
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Guifeng Xie
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Changmei Chen
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Meng Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Tengyun Wang
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China
| | - Qingxi Chen
- College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China.
| |
Collapse
|
49
|
Wang W, Hu S, Cao Y, Chen R, Wang Z, Cao X. Selection and evaluation of reference genes for qRT-PCR of Scutellaria baicalensis Georgi under different experimental conditions. Mol Biol Rep 2021; 48:1115-1126. [PMID: 33511512 PMCID: PMC7842394 DOI: 10.1007/s11033-021-06153-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/12/2021] [Indexed: 10/28/2022]
Abstract
Scutellaria baicalensis Georgi is a famous medicinal plant with its dried roots having been used as a traditional Chinese medicinal for more than 2000 years. Although its genome sequence has previously been published and molecular biology methods have been used to study this species, no suitable internal reference genes have been investigated for standardization of gene expression via quantitative real-time polymerase chain reaction (qRT-PCR). Here, the stabilities of 10 candidate reference genes, ACT11, ACT7, α-TUB, β-TUB, GAPDH, UBC, RPL, SAM, HSP70, and PP2A, were analyzed by four different procedures of GeNorm, NormFinder, BestKeeper, and RefFinder. Their expression stabilities were evaluated under various conditions, including different tissue types (root, stem, leaf, and flower), hormone stimuli treatments (methyl jasmonate, salicylic acid, and abscisic acid), and abiotic stresses (heavy metal, salt, drought, cold, and wounding). The results indicated that β-TUB was the most stable gene for all tested samples, while ACT11 was the most unstable. The most stable reference gene was not consistent under different conditions. β-TUB exhibited the highest stability for different tissue types and abiotic stresses, while for hormone stimuli treatments, ACT7 showed the highest stability. To confirm the applicability of suitable reference genes, we selected to SbF6H and SbF8H as target genes to analyze their expression levels in different tissues. This study helps to the accurate quantification of the relative expression levels of interest genes in S. baicalensis via qRT-PCR analysis.
Collapse
Affiliation(s)
- Wentao Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Suying Hu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Yao Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Rui Chen
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China
| | - Zhezhi Wang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
| | - Xiaoyan Cao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi'an, China.
| |
Collapse
|
50
|
Pérez-Martín L, Busoms S, Tolrà R, Poschenrieder C. Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure. Int J Mol Sci 2021; 22:1226. [PMID: 33513755 PMCID: PMC7865540 DOI: 10.3390/ijms22031226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c-). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c-) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress.
Collapse
Affiliation(s)
| | | | | | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, C/de la Vall Moronta s/n, E-08193 Bellaterra, Spain; (L.P.-M.); (S.B.); (R.T.)
| |
Collapse
|