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Sun H, Li C, Li S, Ma J, Li S, Li X, Gao C, Yang R, Ma N, Yang J, Yang P, He X, Hu T. Identification and validation of stable reference genes for RT-qPCR analyses of Kobresia littledalei seedlings. BMC PLANT BIOLOGY 2024; 24:389. [PMID: 38730341 PMCID: PMC11088182 DOI: 10.1186/s12870-024-04924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/18/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Kobreisa littledalei, belonging to the Cyperaceae family is the first Kobresia species with a reference genome and the most dominant species in Qinghai-Tibet Plateau alpine meadows. It has several resistance genes which could be used to breed improved crop varieties. Reverse Transcription Quantitative Real-Time Polymerase Chain Reaction (RT-qPCR) is a popular and accurate gene expression analysis method. Its reliability depends on the expression levels of reference genes, which vary by species, tissues and environments. However, K.littledalei lacks a stable and normalized reference gene for RT-qPCR analysis. RESULTS The stability of 13 potential reference genes was tested and the stable reference genes were selected for RT-qPCR normalization for the expression analysis in the different tissues of K. littledalei under two abiotic stresses (salt and drought) and two hormonal treatments (abscisic acid (ABA) and gibberellin (GA)). Five algorithms were used to assess the stability of putative reference genes. The results showed a variation amongst the methods, and the same reference genes showed tissue expression differences under the same conditions. The stability of combining two reference genes was better than a single one. The expression levels of ACTIN were stable in leaves and stems under normal conditions, in leaves under drought stress and in roots under ABA treatment. The expression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expression was stable in the roots under the control conditions and salt stress and in stems exposed to drought stress. Expression levels of superoxide dismutase (SOD) were stable in stems of ABA-treated plants and in the roots under drought stress. Moreover, RPL6 expression was stable in the leaves and stems under salt stress and in the stems of the GA-treated plants. EF1-alpha expression was stable in leaves under ABA and GA treatments. The expression levels of 28 S were stable in the roots under GA treatment. In general, ACTIN and GAPDH could be employed as housekeeping genes for K. littledalei under different treatments. CONCLUSION This study identified the best RT-qPCR reference genes for different K. littledalei tissues under five experimental conditions. ACTIN and GAPDH genes can be employed as the ideal housekeeping genes for expression analysis under different conditions. This is the first study to investigate the stable reference genes for normalized gene expression analysis of K. littledalei under different conditions. The results could aid molecular biology and gene function research on Kobresia and other related species.
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Affiliation(s)
- Haoyang Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Chunping Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Siyu Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jiaxin Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Shuo Li
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xin Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Cai Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Rongchen Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Nan Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Jing Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Peizhi Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China
| | - Xueqing He
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi Province, PR China.
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Bharadwaj R, Noceda C, Mohanapriya G, Kumar SR, Thiers KLL, Costa JH, Macedo ES, Kumari A, Gupta KJ, Srivastava S, Adholeya A, Oliveira M, Velada I, Sircar D, Sathishkumar R, Arnholdt-Schmitt B. Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness. FRONTIERS IN PLANT SCIENCE 2021; 12:686274. [PMID: 34659277 PMCID: PMC8518632 DOI: 10.3389/fpls.2021.686274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/10/2021] [Indexed: 05/05/2023]
Abstract
Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Gunasekharan Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Sarma Rajeev Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Karine Leitão Lima Thiers
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - José Hélio Costa
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Aprajita Kumari
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources Institute (TERI), TERI Gram, Gurugram, India
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and Its Applications, Universidade de Évora, Évora, Portugal
| | - Isabel Velada
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Birgit Arnholdt-Schmitt
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
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Costa JH, Mohanapriya G, Bharadwaj R, Noceda C, Thiers KLL, Aziz S, Srivastava S, Oliveira M, Gupta KJ, Kumari A, Sircar D, Kumar SR, Achra A, Sathishkumar R, Adholeya A, Arnholdt-Schmitt B. ROS/RNS Balancing, Aerobic Fermentation Regulation and Cell Cycle Control - a Complex Early Trait ('CoV-MAC-TED') for Combating SARS-CoV-2-Induced Cell Reprogramming. Front Immunol 2021; 12:673692. [PMID: 34305903 PMCID: PMC8293103 DOI: 10.3389/fimmu.2021.673692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/17/2021] [Indexed: 12/19/2022] Open
Abstract
In a perspective entitled 'From plant survival under severe stress to anti-viral human defense' we raised and justified the hypothesis that transcript level profiles of justified target genes established from in vitro somatic embryogenesis (SE) induction in plants as a reference compared to virus-induced profiles can identify differential virus signatures that link to harmful reprogramming. A standard profile of selected genes named 'ReprogVirus' was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait. For data collection, the 'ReprogVirus platform' was initiated. This initiative aims to identify in a common effort across scientific boundaries critical virus footprints from diverse virus origins and variants as a basis for anti-viral strategy design. This approach is open for validation and extension. In the present study, we initiated validation by experimental transcriptome data available in public domain combined with advancing plant wet lab research. We compared plant-adapted transcriptomes according to 'RegroVirus' complemented by alternative oxidase (AOX) genes during de novo programming under SE-inducing conditions with in vitro corona virus-induced transcriptome profiles. This approach enabled identifying a major complex trait for early de novo programming during SARS-CoV-2 infection, called 'CoV-MAC-TED'. It consists of unbalanced ROS/RNS levels, which are connected to increased aerobic fermentation that links to alpha-tubulin-based cell restructuration and progression of cell cycle. We conclude that anti-viral/anti-SARS-CoV-2 strategies need to rigorously target 'CoV-MAC-TED' in primary infected nose and mouth cells through prophylactic and very early therapeutic strategies. We also discuss potential strategies in the view of the beneficial role of AOX for resilient behavior in plants. Furthermore, following the general observation that ROS/RNS equilibration/redox homeostasis is of utmost importance at the very beginning of viral infection, we highlight that 'de-stressing' disease and social handling should be seen as essential part of anti-viral/anti-SARS-CoV-2 strategies.
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Affiliation(s)
- José Hélio Costa
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Gunasekaran Mohanapriya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Revuru Bharadwaj
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Carlos Noceda
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Cell and Molecular Biotechnology of Plants (BIOCEMP)/Industrial Biotechnology and Bioproducts, Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Shahid Aziz
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
| | - Shivani Srivastava
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gurugram, India
| | - Manuela Oliveira
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Mathematics and CIMA - Center for Research on Mathematics and Its Applications, Universidade de Évora, Évora, Portugal
| | - Kapuganti Jagadis Gupta
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Aprajita Kumari
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Debabrata Sircar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Sarma Rajeev Kumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Arvind Achra
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences & Dr Ram Manohar Lohia Hospital, New Delhi, India
| | - Ramalingam Sathishkumar
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Alok Adholeya
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
- Centre for Mycorrhizal Research, Sustainable Agriculture Division, The Energy and Resources, Institute (TERI), TERI Gram, Gurugram, India
| | - Birgit Arnholdt-Schmitt
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Non-Institutional Competence Focus (NICFocus) ‘Functional Cell Reprogramming and Organism Plasticity’ (FunCROP), coordinated from Foros de Vale de Figueira, Alentejo, Portugal
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Maia RA, da Cruz Saraiva KD, Roque ALM, Thiers KLL, Dos Santos CP, da Silva JHM, Feijó DF, Arnholdt-Schmitt B, Costa JH. Differential expression of recently duplicated PTOX genes in Glycine max during plant development and stress conditions. J Bioenerg Biomembr 2019; 51:355-370. [PMID: 31506801 DOI: 10.1007/s10863-019-09810-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Plastid terminal oxidase (PTOX) is a chloroplast enzyme that catalyzes oxidation of plastoquinol (PQH2) and reduction of molecular oxygen to water. Its function has been associated with carotenoid biosynthesis, chlororespiration and environmental stress responses in plants. In the majority of plant species, a single gene encodes the protein and little is known about events of PTOX gene duplication and their implication to plant metabolism. Previously, two putative PTOX (PTOX1 and 2) genes were identified in Glycine max, but the evolutionary origin and the specific function of each gene was not explored. Phylogenetic analyses revealed that this gene duplication occurred apparently during speciation involving the Glycine genus ancestor, an event absent in all other available plant leguminous genomes. Gene expression evaluated by RT-qPCR and RNA-seq data revealed that both PTOX genes are ubiquitously expressed in G. max tissues, but their mRNA levels varied during development and stress conditions. In development, PTOX1 was predominant in young tissues, while PTOX2 was more expressed in aged tissues. Under stress conditions, the PTOX transcripts varied according to stress severity, i.e., PTOX1 mRNA was prevalent under mild or moderate stresses while PTOX2 was predominant in drastic stresses. Despite the high identity between proteins (97%), molecular docking revealed that PTOX1 has higher affinity to substrate plastoquinol than PTOX2. Overall, our results indicate a functional relevance of this gene duplication in G. max metabolism, whereas PTOX1 could be associated with chloroplast effectiveness and PTOX2 to senescence and/or apoptosis.
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Affiliation(s)
- Rachel Alves Maia
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
- Federal Institute of Education, Science and Technology of Paraíba - IFPB, Campus Princesa Isabel, 58755-000, BR-426, S/N - Rural Zone, Princesa Isabel, Paraíba, Brazil
| | - André Luiz Maia Roque
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Clesivan Pereira Dos Santos
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | | | - Daniel Ferreira Feijó
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Birgit Arnholdt-Schmitt
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
- Functional Cell Reprogramming and Organism Plasticity (FunCrop - virtual network), EU Marie Curie Chair, ICAAM, University of Évora, Apartado 94, 7002-554, Évora, Portugal
- Science and Technology Park Alentejo (PACT), 7005-841, Évora, Portugal
| | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil.
- Functional Cell Reprogramming and Organism Plasticity (FunCrop - virtual network), EU Marie Curie Chair, ICAAM, University of Évora, Apartado 94, 7002-554, Évora, Portugal.
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5
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Mohanapriya G, Bharadwaj R, Noceda C, Costa JH, Kumar SR, Sathishkumar R, Thiers KLL, Santos Macedo E, Silva S, Annicchiarico P, Groot SP, Kodde J, Kumari A, Gupta KJ, Arnholdt-Schmitt B. Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis-A Role Relevant for Seed Vigor Prediction and Plant Robustness. FRONTIERS IN PLANT SCIENCE 2019; 10:1134. [PMID: 31611888 PMCID: PMC6776121 DOI: 10.3389/fpls.2019.01134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)-stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.
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Affiliation(s)
- Gunasekaran Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Carlos Noceda
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Cell and Molecular Biology of Plants (BPOCEMP)/Industrial Biotechnology and Bioproducts, Department of Sciences of the Vidaydela Agriculture, University of the Armed Forces-ESPE, Milagro, Ecuador
- Faculty of Engineering, State University of Milagro (UNEMI), Milagro, Ecuador
| | - José Hélio Costa
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Sarma Rajeev Kumar
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Sofia Silva
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Steven P.C. Groot
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Jan Kodde
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Aprajita Kumari
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Birgit Arnholdt-Schmitt
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- CERNAS-Research Center for Natural Resources, Environment and Society, Department of Environment, Escola Superior Agrária de Coimbra, Coimbra, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
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A Driving Bioinformatics Approach to Explore Co-regulation of AOX Gene Family Members During Growth and Development. Methods Mol Biol 2018; 1670:219-224. [PMID: 28871546 DOI: 10.1007/978-1-4939-7292-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The alternative oxidase (AOX) gene family is a hot candidate for functional marker development that could help plant breeding on yield stability through more robust plants based on multi-stress tolerance. However, there is missing knowledge on the interplay between gene family members that might interfere with the efficiency of marker development. It is common view that AOX1 and AOX2 have different physiological roles. Nevertheless, both family member groups act in terms of molecular-biochemical function as "typical" alternative oxidases and co-regulation of AOX1 and AOX2 had been reported. Although conserved sequence differences had been identified, the basis for differential effects on physiology regulation is not sufficiently explored.This protocol gives instructions for a bioinformatics approach that supports discovering potential interaction of AOX family members in regulating growth and development. It further provides a strategy to elucidate the relevance of gene sequence diversity and copy number variation for final functionality in target tissues and finally the whole plant. Thus, overall this protocol provides the means for efficiently identifying plant AOX variants as functional marker candidates related to growth and development.
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