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Santos IR, Ribeiro DG, Távora FTPK, Maximiano MR, Rabelo AC, Rios TB, Reis Junior FB, Megías M, Silva LP, Mehta A. Priming of defense-related genes in Brassica oleracea var. capitata using concentrated metabolites produced by Rhizobium tropici CIAT 899. Braz J Microbiol 2022; 53:595-604. [PMID: 35318614 PMCID: PMC9151945 DOI: 10.1007/s42770-022-00722-4] [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: 08/31/2021] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
To verify the potential of metabolites extracted from Rhizobium tropici to trigger the priming of defense responses in cruciferous plants, we analyzed the expression of defense-related genes by qRT-PCR. Brassica oleracea var. capitata, susceptible to Xanthomonas campestris pv. campestris, were grown in greenhouse conditions. At 18 days after sowing, plants were inoculated with 1 mL of 1% concentrated metabolites produced by R. tropici (CM-RT) in the root. In a second experiment, leaves were sprayed with 1 mL of a solution containing 1% CM-RT. Aerial and root tissue were collected separately at 0 (non-treated control condition), 24, and 48 h after application, submitted to RNA extraction and gene expression analysis by qRT-PCR. The results showed that, after root treatment with CM-RT, most evaluated genes were upregulated at 24 h after application and downregulated at 48 h after application in roots, while in leaves, genes were downregulated both at 24 and 48 h after application. On the other hand, leaf treatment with CM-RT showed that most evaluated genes in leaves and roots were upregulated at 24 and 48 h after application. These results indicate that the effect of CM-RT applied in roots seems restricted to the applied region and is not sustained, while the application in leaves results in a more systemic response and maintenance of the effect of CM-RT for a longer period. The results obtained in this study emphasize the biotechnological potential of using metabolites of R. tropici as an elicitor of active defense responses in plants.
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Affiliation(s)
- Ivonaldo Reis Santos
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
- Programa de Pós-Graduação Em Ciências Biológicas (Biologia Molecular), Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF CEP 70910-900 Brazil
| | - Daiane Gonzaga Ribeiro
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
- Programa de Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica de Brasília/Campus II, Brasília, CEP 70790160 Brazil
| | - Fabiano Touzdjian Pinheiro Kohlrausch Távora
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
- Programa de Pós-Graduação Em Ciências Biológicas (Imunologia e DIP/Genética E Biotecnologia, Universidade Federal de, Juiz de Fora, Campus Universitário, Rua José Lourenço Kelmer, s/n - São Pedro, Juiz de Fora, MG CEP 36036-900 Brazil
| | - Mariana Rocha Maximiano
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
- Programa de Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica de Brasília/Campus II, Brasília, CEP 70790160 Brazil
| | - Ana Carolina Rabelo
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
| | - Thuanny Borba Rios
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
| | | | - Manuel Megías
- Departamento de Microbiología Y Parasitología, Universidad de Sevilla, Apdo Postal 874, 41080 Sevilla, Spain
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
- Programa de Pós-Graduação Em Ciências Biológicas (Biologia Molecular), Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF CEP 70910-900 Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos E Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, DF CEP 70770-917 Brazil
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Tortosa M, Velasco P, Rodríguez VM, Cartea ME. Changes in Brassica oleracea Leaves Infected With Xanthomonas campestris pv. campestris by Proteomics Analysis. FRONTIERS IN PLANT SCIENCE 2022; 12:781984. [PMID: 35211128 PMCID: PMC8860909 DOI: 10.3389/fpls.2021.781984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Understanding plant's response mechanisms against pathogenesis is fundamental for the development of resistant crop varieties and more productive agriculture. In this regard, "omic" approaches are heralded as valuable technologies. In this work, combining isobaric tags for relative and absolute quantification (iTRAQ) technology with mass spectrometry, the proteomes from leaves of Brassica oleracea plants infected with Xanthomonas campestris pv. campestris (Xcc), and control plants at two different post-infection times were compared. Stronger proteomic changes were obtained at 12 days post-infection in comparison with 3 days. The responses observed involved different cell processes, from primary metabolism, such as photosynthesis or photorespiration, to other complex processes such as redox homeostasis, hormone signaling, or defense mechanisms. Most of the proteins decreased in the earlier response were involved in energetic metabolism, whereas later response was characterized by a recovery of primary metabolism. Furthermore, our results indicated that proteolysis machinery and reactive oxygen species (ROS) homeostasis could be key processes during this plant-pathogen interaction. Current data provide new insights into molecular mechanisms that may be involved in defense responses of B. oleracea to Xcc.
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Affiliation(s)
| | | | | | - María Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain
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Hahn J, Koch D, Niehaus K, Ortseifen V. Analysis of Gum proteins involved in xanthan biosynthesis throughout multiple cell fractions in a "single-tube". J Proteomics 2022; 257:104513. [PMID: 35149254 DOI: 10.1016/j.jprot.2022.104513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 10/19/2022]
Abstract
Xanthomonas is a phytopathogenic bacterium and of industrial interest due to its capability to produce xanthan, used as a thickener and emulsifier in the food and non-food industry. Until now, proteome analyses of Xcc lacking a detailed view on the proteins involved in xanthan biosynthesis. The proteins involved in the biosynthesis of this polysaccharide are located near, in or at the cell membrane. This study aims to establish a robust and rapid protocol for a comprehensive proteome analysis of Xcc strains, without the need to isolate different cell fractions. Therefore, a method for the analysis of the whole cell proteome was compared to the isolation of specific fractions regarding the total number of identified proteins, the overlap, and the differences between the approaches. The whole cell proteome analysis with extended peptide separation methods resulted in more than 3254 identified proteins covering 73.1% of the whole proteome. The protocol was used to study xanthan production in a label-free quantification approach. Expression profiles of 8 Gum proteins were compared between the stationary and logarithmic growth phase. Differential expression levels within the operon structure indicate a complex regulatory mechanism for xanthan biosynthesis. Data are available via ProteomeXchange with identifier PXD027261. SIGNIFICANCE: Bacteria are metabolite factories with a wide variety of natural products. Thus, proteome analyses play a crucial role to understand the biological processes within a cell behind the biosynthesis of those metabolites. Proteins involved in the biosynthesis of secreted products are often organised on, in or around the membrane allowing metabolite channelling. Experiments targeting those biosynthesis pathways on protein level often require the analysis of multiple cell fractions like cytosolic, inner, and outer membrane. This is time consuming and demands different protocols. The protocol presented here is a rapid and robust solution to study biosynthetic pathways of biological or biotechnological interest in a single approach on protein level, where gene products are partitioned across multiple cell fractions. The use of a single method also simplifies the comparison of different experiments, for example, production vs. nonproduction conditions.
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Affiliation(s)
- Julia Hahn
- Proteome- and Metabolome Research, Faculty of Biology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Daniel Koch
- Jungbunzlauer Austria AG, Pernhofen 1, 2064 Wulzeshofen, Austria
| | - Karsten Niehaus
- Proteome- and Metabolome Research, Faculty of Biology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Vera Ortseifen
- Proteome- and Metabolome Research, Faculty of Biology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany.
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Shaw RK, Shen Y, Wang J, Sheng X, Zhao Z, Yu H, Gu H. Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L. FRONTIERS IN PLANT SCIENCE 2021; 12:742553. [PMID: 34938304 PMCID: PMC8687090 DOI: 10.3389/fpls.2021.742553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Brassica oleracea is one of the most important species of the Brassicaceae family encompassing several economically important vegetables produced and consumed worldwide. But its sustainability is challenged by a range of pathogens, among which black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most serious and destructive seed borne bacterial disease, causing huge yield losses. Host-plant resistance could act as the most effective and efficient solution to curb black rot disease for sustainable production of B. oleracea. Recently, 'omics' technologies have emerged as promising tools to understand the host-pathogen interactions, thereby gaining a deeper insight into the resistance mechanisms. In this review, we have summarized the recent achievements made in the emerging omics technologies to tackle the black rot challenge in B. oleracea. With an integrated approach of the omics technologies such as genomics, proteomics, transcriptomics, and metabolomics, it would allow better understanding of the complex molecular mechanisms underlying black rot resistance. Due to the availability of sequencing data, genomics and transcriptomics have progressed as expected for black rot resistance, however, other omics approaches like proteomics and metabolomics are lagging behind, necessitating a holistic and targeted approach to address the complex questions of Xcc-Brassica interactions. Genomic studies revealed that the black rot resistance is a complex trait and is mostly controlled by quantitative trait locus (QTL) with minor effects. Transcriptomic analysis divulged the genes related to photosynthesis, glucosinolate biosynthesis and catabolism, phenylpropanoid biosynthesis pathway, ROS scavenging, calcium signalling, hormonal synthesis and signalling pathway are being differentially expressed upon Xcc infection. Comparative proteomic analysis in relation to susceptible and/or resistance interactions with Xcc identified the involvement of proteins related to photosynthesis, protein biosynthesis, processing and degradation, energy metabolism, innate immunity, redox homeostasis, and defence response and signalling pathways in Xcc-Brassica interaction. Specifically, most of the studies focused on the regulation of the photosynthesis-related proteins as a resistance response in both early and later stages of infection. Metabolomic studies suggested that glucosinolates (GSLs), especially aliphatic and indolic GSLs, its subsequent hydrolysis products, and defensive metabolites synthesized by jasmonic acid (JA)-mediated phenylpropanoid biosynthesis pathway are involved in disease resistance mechanisms against Xcc in Brassica species. Multi-omics analysis showed that JA signalling pathway is regulating resistance against hemibiotrophic pathogen like Xcc. So, the bonhomie between omics technologies and plant breeding is going to trigger major breakthroughs in the field of crop improvement by developing superior cultivars with broad-spectrum resistance. If multi-omics tools are implemented at the right scale, we may be able to achieve the maximum benefits from the minimum. In this review, we have also discussed the challenges, future prospects, and the way forward in the application of omics technologies to accelerate the breeding of B. oleracea for disease resistance. A deeper insight about the current knowledge on omics can offer promising results in the breeding of high-quality disease-resistant crops.
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Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Ribeiro DG, Carmo LST, Santos IR, Almeida RF, Silva LP, Oliveira-Neto OB, Scherwinski-Pereira JE, Mehta A. MALDI TOF MS-profiling: Applications for bacterial and plant sample differentiation and biological variability assessment. J Proteomics 2019; 213:103619. [PMID: 31846767 DOI: 10.1016/j.jprot.2019.103619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/06/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
Abstract
In this study, we evaluated the potential use of MALDI-TOF MS Profiling for the differentiation of biological samples submitted to different treatments. We compared the bacterium Xanthomonas campestris pv. campestris (Xcc), grown in culture medium and in vivo (recovered from the plant). Plant samples were also analyzed and included explants at different somatic embryogenesis (SE) stages, as well as leaves from Brassica oleracea and Arabidopsis thaliana inoculated with Xcc, at different time points. The results showed that bacteria and highly divergent plant samples, such as those from embryogenic stages, can be unequivocally differentiated and the clustering was in accordance with proteomic analysis performed by 2-DE. These results show an important application of MALDI-TOF MS Profiling to select and prioritize samples to be analyzed prior to more complex approaches including transcriptomics and proteomics. We also show that in plant-pathogen interactions, when more subtle differences are obtained, the main contribution of MALDI-TOF MS Profiling is in the assessment of experimental variability. This is relevant since reproducibility is a challenging issue when dealing with complex experimental conditions such as plant-pathogen interactions. We propose the use of MALDI-TOF MS Profiling to aid researchers in minimizing experimental variability unrelated to the condition being analyzed. SIGNIFICANCE: MALDI-Profiling offers an inexpensive, rapid and reliable approach for investigating the protein profile to assess sample differentiation and experimental variability in microorganisms and plants and can be highly useful to analyze samples prior to more complex and expensive techniques such as proteomics and transcriptomics.
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Affiliation(s)
- Daiane Gonzaga Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil; Departamento de Botânica, Universidade de Brasília, Campus Universitário Darcy Ribeiro, CEP 70919-970 Brasília, DF, Brazil
| | - Lílian Silveira Travassos Carmo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil
| | - Ivonaldo Reis Santos
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil; Departamento de Botânica, Universidade de Brasília, Campus Universitário Darcy Ribeiro, CEP 70919-970 Brasília, DF, Brazil
| | - Raphael Ferreira Almeida
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil; Departamento de Botânica, Universidade de Brasília, Campus Universitário Darcy Ribeiro, CEP 70919-970 Brasília, DF, Brazil
| | - Luciano Paulino Silva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil
| | - Osmundo Brilhante Oliveira-Neto
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil; Departamento de Bioquímica e Biologia Molecular, Escola de Medicina, FACIPLAC, CEP 72460-000 Brasília, DF, Brazil
| | - Jonny Everson Scherwinski-Pereira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5 Norte (final), CEP 70770-917 Brasília, DF, Brazil.
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Santos C, Nogueira FCS, Domont GB, Fontes W, Prado GS, Habibi P, Santos VO, Oliveira-Neto OB, Grossi-de-Sá MF, Jorrín-Novo JV, Franco OL, Mehta A. Proteomic Analysis and Functional Validation of a Brassica oleracea Endochitinase Involved in Resistance to Xanthomonas campestris. FRONTIERS IN PLANT SCIENCE 2019; 10:414. [PMID: 31031780 PMCID: PMC6473119 DOI: 10.3389/fpls.2019.00414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 05/02/2023]
Abstract
Black rot is a severe disease caused by the bacterium Xanthomonas campestris pv. campestris (Xcc), which can lead to substantial losses in cruciferous vegetable production worldwide. Although the use of resistant cultivars is the main strategy to control this disease, there are limited sources of resistance. In this study, we used the LC-MS/MS technique to analyze young cabbage leaves and chloroplast-enriched samples at 24 h after infection by Xcc, using both susceptible (Veloce) and resistant (Astrus) cultivars. A comparison between susceptible Xcc-inoculated plants and the control condition, as well as between resistant Xcc-inoculated plants with the control was performed and more than 300 differentially abundant proteins were identified in each comparison. The chloroplast enriched samples contributed with the identification of 600 additional protein species in the resistant interaction and 900 in the susceptible one, which were not detected in total leaf sample. We further determined the expression levels for 30 genes encoding the identified differential proteins by qRT-PCR. CHI-B4 like gene, encoding an endochitinase showing a high increased abundance in resistant Xcc-inoculated leaves, was selected for functional validation by overexpression in Arabidopsis thaliana. Compared to the wild type (Col-0), transgenic plants were highly resistant to Xcc indicating that CHI-B4 like gene could be an interesting candidate to be used in genetic breeding programs aiming at black rot resistance.
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Affiliation(s)
- Cristiane Santos
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Fábio C. S. Nogueira
- Proteomics Unit, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B. Domont
- Proteomics Unit, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wagner Fontes
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | | | - Peyman Habibi
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Department of Bioprocess Engineering and Biotechnology, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Osmundo B. Oliveira-Neto
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Departamento de Bioquímica e Biologia Molecular, Escola de Medicina, Faculdades Integradas da União Educacional do Planalto Central, Brasília, Brazil
| | - Maria Fatima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Centro de Analises Proteomicas e Bioquimica, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Jesus V. Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Córdoba, Spain
| | - Octavio L. Franco
- Departamento de Biologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
- Centro de Analises Proteomicas e Bioquimica, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Brazil
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Santos LS, Maximiano MR, Megias E, Pappas M, Ribeiro SG, Mehta A. Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris. Mol Biol Rep 2019; 46:3523-3529. [PMID: 30945070 DOI: 10.1007/s11033-019-04779-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/21/2019] [Indexed: 12/19/2022]
Abstract
Brassica oleracea var. capitata (cabbage) is an economically important crop affected by black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). MicroRNAs (miRNAs) play an important role in plant defense modulation and therefore the analysis of these molecules can help better understand plant-pathogen interactions. In this study, we report the differential expression of four miRNAs that seem to participate in the plant response to Xcc infection. Northern Blot and RT-qPCR techniques were used to measure miRNA expression in resistant (União) and susceptible (Kenzan) cultivars. From 6 miRNAs analyzed, 4 were detected and differentially expressed, showing a down- and upregulated expression profile in susceptible and resistant cultivars, respectively. These results suggest that miR156, miR167, miR169, and miR390 could play a role in B. oleracea resistance enhancement against Xcc and could be explored as potential resistance markers in B. oleracea-Xcc interaction.
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Affiliation(s)
- Lucas Souza Santos
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Centro Universitário do Distrito Federal, SEP/SUL EQ 704/904 Conj.A, Brasília, DF, CEP 70390-045, Brazil
| | - Mariana Rocha Maximiano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n - Campus Universitário, Bairro São Pedro, Juiz de Fora, MG, CEP 36036-900, Brazil
| | - Esaú Megias
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
- Universidad de Cádiz, Calle Ancha, 16, 11001, Cádiz, Spain
| | - Marília Pappas
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
| | - Simone Graça Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Av. W5, Norte (final), Brasília, DF, CEP 70770-917, Brazil.
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Abstract
BACKGROUND With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of 'omics applications. This adds an extra layer of complexity to the analysis and interpretation, in particular when inferential univariate methods are applied en masse. It is well-known that mass univariate testing suffers from multiplicity issues and although this has been well documented for simple comparative tests, few approaches have focussed on more complex explanatory structures. RESULTS Two frameworks are introduced incorporating corrections for multiplicity whilst maintaining appropriate structure in the explanatory variables. Within this paradigm, a choice has to be made as to whether multiplicity corrections should be applied to the saturated model, putting emphasis on controlling the rate of false positives, or to the predictive model, where emphasis is on model selection. This choice has implications for both the ranking and selection of the response variables identified as differentially expressed. The theoretical difference is demonstrated between the two approaches along with an empirical study of lipid composition in Arabidopsis under differing levels of salt stress. CONCLUSIONS Multiplicity corrections have an inherent weakness when the full explanatory structure is not properly incorporated. Although a unifying 'single best' recommendation is not provided, two reasonable alternatives are provided and the applicability of these approaches is discussed for different scenarios where the aims of analysis will differ. The key result is that the point at which multiplicity is incorporated into the analysis will fundamentally change the interpretation of the results, and the choice of approach should therefore be driven by the specific aims of the experiment.
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Affiliation(s)
- Kirsty L. Hassall
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ UK
| | - Andrew Mead
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ UK
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Maximiano MR, Oliveira-Neto OB, Franco OL, Mehta A. Validation of an in vitro system for studies of pathogenicity mechanisms in Xanthomonas campestris. FEMS Microbiol Lett 2017; 364:4494362. [PMID: 29040467 DOI: 10.1093/femsle/fnx217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/11/2017] [Indexed: 01/16/2023] Open
Abstract
Several minimal media capable of inducing pathogenicity genes have been used to study plant-pathogen interactions. An in planta assay to study a closer interaction between the bacteria and the host was also developed and has been employed by our group. In order to determine whether growth medium could be improved to better approximate in planta conditions beyond that offered by the defined minimal medium XVM1, we compared the expression of 20 Xanthomonas campestris pv. campestris (Xcc) genes by quantitative reverse transcription - polymerase chain reaction (qRT-PCR) under in vivo (bacteria recovered from the plant) and in vitro (rich medium NYG, minimal medium XVM1 and XVM1 + leaf extract) growth systems. The results showed a higher expression level of the genes in the in planta system when compared to growth in culture media. In planta growth is closest to a real interaction condition and captures the complexity of the plant cell environment; however, this system has some limitations. The main finding of our work is that the addition of plant extract to XVM1 medium results in a gene expression profile that better matches the in planta profile, when compared with the XVM1 medium alone, giving support to the use of plant extract to study pathogenicity mechanisms in Xanthomonas.
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Affiliation(s)
- Mariana Rocha Maximiano
- Embrapa Recursos Genéticos e Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, Distrito Federal 70770-917, Brazil.,Programa de Pós-Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, Minas Gerais, 36036-330, Brazil
| | - Osmundo B Oliveira-Neto
- Embrapa Recursos Genéticos e Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, Distrito Federal 70770-917, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Biológicas (Imunologia e DIP/Genética e Biotecnologia), Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, S/n - Martelos, Juiz de Fora, Minas Gerais, 36036-330, Brazil.,S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Av. Tamandaré, 6000, Campo Grande, Mato Grosso do Sul, 79117-900, Brazil.,Centro de Analises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916N, Modulo C, Sala 219, Brasília, Distrito Federal 70790-100, Brazil
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, PBI, Av. W/5 Norte Final, Brasília, Distrito Federal 70770-917, Brazil
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