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da Silva VCH, Martins MCM, Calderan-Rodrigues MJ, Artins A, Monte Bello CC, Gupta S, Sobreira TJP, Riaño-Pachón DM, Mafra V, Caldana C. Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C 4 Species Setaria viridis, a Suitable Model for Biomass Crops. Front Plant Sci 2021; 12:637508. [PMID: 33927734 PMCID: PMC8078139 DOI: 10.3389/fpls.2021.637508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
The Target of Rapamycin (TOR) kinase pathway integrates energy and nutrient availability into metabolism promoting growth in eukaryotes. The overall higher efficiency on nutrient use translated into faster growth rates in C4 grass plants led to the investigation of differential transcriptional and metabolic responses to short-term chemical TOR complex (TORC) suppression in the model Setaria viridis. In addition to previously described responses to TORC inhibition (i.e., general growth arrest, translational repression, and primary metabolism reprogramming) in Arabidopsis thaliana (C3), the magnitude of changes was smaller in S. viridis, particularly regarding nutrient use efficiency and C allocation and partitioning that promote biosynthetic growth. Besides photosynthetic differences, S. viridis and A. thaliana present several specificities that classify them into distinct lineages, which also contribute to the observed alterations mediated by TOR. Indeed, cell wall metabolism seems to be distinctly regulated according to each cell wall type, as synthesis of non-pectic polysaccharides were affected in S. viridis, whilst assembly and structure in A. thaliana. Our results indicate that the metabolic network needed to achieve faster growth seems to be less stringently controlled by TORC in S. viridis.
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Affiliation(s)
| | | | | | - Anthony Artins
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Saurabh Gupta
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | | | | | - Valéria Mafra
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Camila Caldana
- National Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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Martins PK, Mafra V, de Souza WR, Ribeiro AP, Vinecky F, Basso MF, da Cunha BADB, Kobayashi AK, Molinari HBC. Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis. Sci Rep 2016; 6:28348. [PMID: 27321675 PMCID: PMC4913262 DOI: 10.1038/srep28348] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 12/28/2022] Open
Abstract
Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but reliable results depend on the use of stable reference genes for proper normalization. This study proposed to test the expression stability of 13 candidate reference genes in Setaria viridis, a monocot species recently proposed as a new C4 model plant. Gene expression stability of these genes was assayed across different tissues and developmental stages of Setaria and under drought or aluminum stress. In general, our results showed Protein Kinase, RNA Binding Protein and SDH as the most stable genes. Moreover, pairwise analysis showed that two reference genes were sufficient to normalize the gene expression data under each condition. By contrast, GAPDH and ACT were the least stably expressed genes tested. Validation of suitable reference genes was carried out to profile the expression of P5CS and GolS during abiotic stress. In addition, normalization of gene expression of SuSy, involved in sugar metabolism, was assayed in the developmental dataset. This study provides a list of reliable reference genes for transcript normalization in S. viridis in different tissues and stages of development and under abiotic stresses, which will facilitate genetic studies in this monocot model plant.
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Affiliation(s)
- Polyana Kelly Martins
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Valéria Mafra
- Brazilian Bioethanol Science and Technology Laboratory/Brazilian Center of Research in Energy and Materials, Campinas, SP, 13083-100, Brazil
| | - Wagner Rodrigo de Souza
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Ana Paula Ribeiro
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Felipe Vinecky
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | - Marcos Fernando Basso
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
| | | | - Adilson Kenji Kobayashi
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasília, DF, 70770-901, Brazil
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Mafra V, Martins PK, Francisco CS, Ribeiro-Alves M, Freitas-Astúa J, Machado MA. Candidatus Liberibacter americanus induces significant reprogramming of the transcriptome of the susceptible citrus genotype. BMC Genomics 2013; 14:247. [PMID: 23586643 PMCID: PMC3635983 DOI: 10.1186/1471-2164-14-247] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/26/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Citrus huanglongbing (HLB) disease is caused by endogenous, phloem-restricted, Gram negative, uncultured bacteria named Candidatus Liberibacter africanus (CaLaf), Ca. L. asiaticus (CaLas), and Ca. L. americanus (CaLam), depending on the continent where the bacteria were first detected. The Asian citrus psyllid vector, Diaphorina citri, transmits CaLas and CaLam and both Liberibacter species are present in Brazil. Several studies of the transcriptional response of citrus plants manifesting HLB symptoms have been reported, but only for CaLas infection. This study evaluated the transcriptional reprogramming of a susceptible genotype of sweet orange challenged with CaLam, using a customized 385K microarray containing approximately 32,000 unigene transcripts. We analyzed global changes in gene expression of CaLam-infected leaves of sweet orange during the symptomatic stage of infection and compared the results with previously published microarray studies that used CaLas-infected plants. Twenty candidate genes were selected to validate the expression profiles in symptomatic and asymptomatic PCR-positive leaves infected with CaLas or CaLam. RESULTS The microarray analysis identified 633 differentially expressed genes during the symptomatic stage of CaLam infection. Among them, 418 (66%) were upregulated and 215 (34%) were down regulated. Five hundred and fourteen genes (81%) were orthologs of genes from Arabidopsis thaliana. Gene set enrichment analysis (GSEA) revealed that several of the transcripts encoded transporters associated with the endomembrane system, especially zinc transport. Among the most biologically relevant gene transcripts in GSEA were those related to signaling, metabolism and/or stimulus to hormones, genes responding to stress and pathogenesis, biosynthesis of secondary metabolites, oxidative stress and transcription factors belonging to different families. Real time PCR of 20 candidate genes validated the expression pattern of some genes in symptomatic and asymptomatic leaves infected with CaLam or CaLas. CONCLUSIONS Many gene transcripts and biological processes are significantly altered upon CaLam infection. Some of them had been identified in response to CaLas infection, while others had not been previously reported. These data will be useful for selecting target genes for genetic engineering to control HLB.
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Affiliation(s)
- Valéria Mafra
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, Brazil
- Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Polyana K Martins
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, Brazil
| | - Carolina S Francisco
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, Brazil
| | - Marcelo Ribeiro-Alves
- Laboratório de Pesquisa em Farmacogenética / Instituto de Pesquisa Clínica Evandro Chagas (IPEC) – Fiocruz, Rio de Janeiro, Brazil
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, Brazil
- Embrapa Cassava & Fruits, Cruz das Almas, Bahia, Brazil
| | - Marcos A Machado
- Centro de Citricultura Sylvio Moreira, Instituto Agronômico de Campinas, Cordeirópolis, São Paulo, Brazil
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Mafra V, Kubo KS, Alves-Ferreira M, Ribeiro-Alves M, Stuart RM, Boava LP, Rodrigues CM, Machado MA. Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PLoS One 2012; 7:e31263. [PMID: 22347455 PMCID: PMC3276578 DOI: 10.1371/journal.pone.0031263] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 01/04/2012] [Indexed: 11/19/2022] Open
Abstract
Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress.
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Affiliation(s)
- Valéria Mafra
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas-São Paulo, Brazil
| | - Karen S. Kubo
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas-São Paulo, Brazil
| | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular Vegetal, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Rodrigo M. Stuart
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
- Instituto de Biologia, Universidade Estadual de Campinas, Campinas-São Paulo, Brazil
| | - Leonardo P. Boava
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
| | - Carolina M. Rodrigues
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
| | - Marcos A. Machado
- Laboratório de Biotecnologia, Centro de Citricultura Sylvio Moreira, Cordeirópolis-São Paulo, Brazil
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