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Zhang J, Aroca A, Hervás M, Navarro JA, Moreno I, Xie Y, Romero LC, Gotor C. Analysis of sulfide signaling in rice highlights specific drought responses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5130-5145. [PMID: 38808567 PMCID: PMC11349868 DOI: 10.1093/jxb/erae249] [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: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 05/30/2024]
Abstract
Hydrogen sulfide regulates essential plant processes, including adaptation responses to stress situations, and the best characterized mechanism of action of sulfide consists of the post-translational modification of persulfidation. In this study, we reveal the first persulfidation proteome described in rice including 3443 different persulfidated proteins that participate in a broad range of biological processes and metabolic pathways. In addition, comparative proteomics revealed specific proteins involved in sulfide signaling during drought responses. Several proteins are involved in the maintenance of cellular redox homeostasis, the tricarboxylic acid cycle and energy-related pathways, and ion transmembrane transport and cellular water homeostasis, with the aquaporin family showing the highest differential levels of persulfidation. We revealed that water transport activity is regulated by sulfide which correlates with an increasing level of persulfidation of aquaporins. Our findings emphasize the impact of persulfidation on total ATP levels, fatty acid composition, levels of reactive oxygen species, antioxidant enzymatic activities, and relative water content. Interestingly, the role of persulfidation in aquaporin transport activity as an adaptation response in rice differs from current knowledge of Arabidopsis, which highlights the distinct role of sulfide in improving rice tolerance to drought.
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Affiliation(s)
- Jing Zhang
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Angeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Manuel Hervás
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - José A Navarro
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Yanjie Xie
- Laboratory Center of Life Sciences, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Seville, Spain
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2
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Nguyen DT, Zavadil Kokáš F, Gonin M, Lavarenne J, Colin M, Gantet P, Bergougnoux V. Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2024; 24:438. [PMID: 38778283 PMCID: PMC11110440 DOI: 10.1186/s12870-024-05160-y] [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: 06/16/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. RESULTS Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. CONCLUSIONS This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.
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Affiliation(s)
- Dieu Thu Nguyen
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Department of Biochemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Filip Zavadil Kokáš
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- Present address: Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Mathieu Gonin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jérémy Lavarenne
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Colin
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czechia.
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Koh E, Goh W, Julca I, Villanueva E, Mutwil M. PEO: Plant Expression Omnibus - a comparative transcriptomic database for 103 Archaeplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1592-1603. [PMID: 38050352 DOI: 10.1111/tpj.16566] [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: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
The Plant Expression Omnibus (PEO) is a web application that provides biologists with access to gene expression insights across over 100 plant species, ~60 000 manually annotated RNA-seq samples, and more than 4 million genes. The tool allows users to explore the expression patterns of genes across different organs, identify organ-specific genes, and discover top co-expressed genes for any gene of interest. PEO also provides functional annotations for each gene, allowing for the identification of genetic modules and pathways. PEO is designed to facilitate comparative kingdom-wide gene expression analysis and provide a valuable resource for plant biology research. We provide two case studies to demonstrate the utility of PEO in identifying candidate genes in pollen coat biosynthesis in Arabidopsis and investigating the biosynthetic pathway components of capsaicin in Capsicum annuum. The database is freely available at https://expression.plant.tools/.
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Affiliation(s)
- Eugene Koh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - William Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Irene Julca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Erielle Villanueva
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
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4
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Orduña L, Santiago A, Navarro-Payá D, Zhang C, Wong DCJ, Matus JT. Aggregated gene co-expression networks predict transcription factor regulatory landscapes in grapevine. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6522-6540. [PMID: 37668374 DOI: 10.1093/jxb/erad344] [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: 04/25/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets from three different tissues (leaf, berry, and 'all organs'). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied aggGCNs to study several transcription factor gene families, showing their capacity for detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC, and multiple specialized metabolic pathways. Specifically, transcription factor gene- and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino acid pathways. This network was validated using DNA affinity purification sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks in other crops and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.
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Affiliation(s)
- Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
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García-Calderón M, Vignane T, Filipovic MR, Ruiz MT, Romero LC, Márquez AJ, Gotor C, Aroca A. Persulfidation protects from oxidative stress under nonphotorespiratory conditions in Arabidopsis. THE NEW PHYTOLOGIST 2023; 238:1431-1445. [PMID: 36840421 DOI: 10.1111/nph.18838] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen sulfide is a signaling molecule in plants that regulates essential biological processes through protein persulfidation. However, little is known about sulfide-mediated regulation in relation to photorespiration. Here, we performed label-free quantitative proteomic analysis and observed a high impact on protein persulfidation levels when plants grown under nonphotorespiratory conditions were transferred to air, with 98.7% of the identified proteins being more persulfidated under suppressed photorespiration. Interestingly, a higher level of reactive oxygen species (ROS) was detected under nonphotorespiratory conditions. Analysis of the effect of sulfide on aspects associated with non- or photorespiratory growth conditions has demonstrated that it protects plants grown under suppressed photorespiration. Thus, sulfide amends the imbalance of carbon/nitrogen and restores ATP levels to concentrations like those of air-grown plants; balances the high level of ROS in plants under nonphotorespiratory conditions to reach a cellular redox state similar to that in air-grown plants; and regulates stomatal closure, to decrease the high guard cell ROS levels and induce stomatal aperture. In this way, sulfide signals the CO2 -dependent stomata movement, in the opposite direction of the established abscisic acid-dependent movement. Our findings suggest that the high persulfidation level under suppressed photorespiration reveals an essential role of sulfide signaling under these conditions.
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Affiliation(s)
- Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Prof. García González 1, 41012, Sevilla, Spain
| | - Thibaut Vignane
- Leibniz Institute for Analytical Sciences, ISAS e.V., 44227, Dortmund, Germany
| | - Milos R Filipovic
- Leibniz Institute for Analytical Sciences, ISAS e.V., 44227, Dortmund, Germany
| | - M Teresa Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| | - Antonio J Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Prof. García González 1, 41012, Sevilla, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
| | - Angeles Aroca
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, Prof. García González 1, 41012, Sevilla, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis (Universidad de Sevilla, Consejo Superior de Investigaciones Científicas), Américo Vespucio 49, 41092, Sevilla, Spain
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6
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Jurado-Flores A, Gotor C, Romero LC. Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation. Antioxidants (Basel) 2023; 12:antiox12040789. [PMID: 37107163 PMCID: PMC10135009 DOI: 10.3390/antiox12040789] [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: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Hydrogen sulfide (H2S) acts as a signaling molecule in plants, bacteria, and mammals, regulating various physiological and pathological processes. The molecular mechanism by which hydrogen sulfide exerts its action involves the posttranslational modification of cysteine residues to form a persulfidated thiol motif. This research aimed to study the regulation of protein persulfidation. We used a label-free quantitative approach to measure the protein persulfidation profile in leaves under different growth conditions such as light regimen and carbon deprivation. The proteomic analysis identified a total of 4599 differentially persulfidated proteins, of which 1115 were differentially persulfidated between light and dark conditions. The 544 proteins that were more persulfidated in the dark were analyzed, and showed significant enrichment in functions and pathways related to protein folding and processing in the endoplasmic reticulum. Under light conditions, the persulfidation profile changed, and the number of differentially persulfidated proteins increased up to 913, with the proteasome and ubiquitin-dependent and ubiquitin-independent catabolic processes being the most-affected biological processes. Under carbon starvation conditions, a cluster of 1405 proteins was affected by a reduction in their persulfidation, being involved in metabolic processes that provide primary metabolites to essential energy pathways and including enzymes involved in sulfur assimilation and sulfide production.
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Affiliation(s)
- Ana Jurado-Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
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7
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Khodaeiaminjan M, Knoch D, Ndella Thiaw MR, Marchetti CF, Kořínková N, Techer A, Nguyen TD, Chu J, Bertholomey V, Doridant I, Gantet P, Graner A, Neumann K, Bergougnoux V. Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1125672. [PMID: 37077626 PMCID: PMC10106628 DOI: 10.3389/fpls.2023.1125672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.
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Affiliation(s)
- Mortaza Khodaeiaminjan
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- *Correspondence: Mortaza Khodaeiaminjan, ; Véronique Bergougnoux,
| | - Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | | - Cintia F. Marchetti
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Nikola Kořínková
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Alexie Techer
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Thu D. Nguyen
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
| | - Jianting Chu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Valentin Bertholomey
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Ingrid Doridant
- Limagrain Field Seeds, Traits and Technologies, Groupe Limagrain Centre de Recherche, Chappes, France
| | - Pascal Gantet
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- Unité Mixte de Recherche DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Andreas Graner
- Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Kerstin Neumann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Véronique Bergougnoux
- Czech Advanced Technology and Research Institute, Palacký University in Olomouc, Olomouc, Czechia
- *Correspondence: Mortaza Khodaeiaminjan, ; Véronique Bergougnoux,
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8
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Liu X, Kou X, Bai S, Luo Y, Wang Z, Xie L, Deng P, Zhang H, Wang C, Wang Y, Zhao J, Ji W. Identification of Differentially Expressed Genes in Resistant Tetraploid Wheat ( Triticum turgidum) under Sitobion avenae (F.) Infestation. Int J Mol Sci 2022; 23:ijms23116012. [PMID: 35682692 PMCID: PMC9180832 DOI: 10.3390/ijms23116012] [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: 04/24/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023] Open
Abstract
The grain aphid Sitobion avenae (Fabricius) is one of the most destructive pests of wheat (Triticum aestivum). Deployment of resistant wheat germplasm appears as an excellent solution for this problem. Elite bread wheat cultivars only have limited resistance to this pest. The present study was carried out to investigate the potential of the tetraploid wheat (Triticum turgidum) variety Lanmai, which showed high resistance to S. avenae at both seedling and adult plant stages, as a source of resistance genes. Based on apterous adult aphids’ fecundity tests and choice bioassays, Lanmai has been shown to display antixenosis and antibiosis. Suppression subtractive hybridization (SSH) was employed to identify and isolate the putative candidate defense genes in Lanmai against S. avenae infestation. A total of 134 expressed sequence tags (ESTs) were identified and categorized based on their putative functions. RT-qPCR analysis of 30 selected genes confirmed their differential expression over time between the resistant wheat variety Lanmai and susceptible wheat variety Polan305 during S. avenae infestation. There were 11 genes related to the photosynthesis process, and only 3 genes showed higher expression in Lanmai than in Polan305 after S. avenae infestation. Gene expression analysis also revealed that Lanmai played a critical role in salicylic acid and jasmonic acid pathways after S. avenae infestation. This study provided further insights into the role of defense signaling networks in wheat resistance to S. avenae and indicates that the resistant tetraploid wheat variety Lanmai may provide a valuable resource for aphid tolerance improvement in wheat.
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Affiliation(s)
- Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
- Correspondence: (X.L.); (W.J.)
| | - Xudan Kou
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Shichao Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Yufeng Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Zhenyu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Lincai Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (X.K.); (S.B.); (Y.L.); (Z.W.); (L.X.); (P.D.); (H.Z.); (C.W.); (Y.W.); (J.Z.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Xianyang 712100, China
- Correspondence: (X.L.); (W.J.)
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9
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Tregear JW, Richaud F, Collin M, Esbelin J, Parrinello H, Cochard B, Nodichao L, Morcillo F, Adam H, Jouannic S. Micro-RNA-Regulated SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Expression and Cytokinin Accumulation Distinguish Early-Developing Male and Female Inflorescences in Oil Palm (Elaeis guineensis). PLANTS 2022; 11:plants11050685. [PMID: 35270155 PMCID: PMC8912876 DOI: 10.3390/plants11050685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Sexual differentiation of inflorescences and flowers is important for reproduction and affects crop plant productivity. We report here on a molecular study of the process of sexual differentiation in the immature inflorescence of oil palm (Elaeis guineensis). This species is monoecious and exhibits gender diphasy, producing male and female inflorescences separately on the same plant in alternation. Three main approaches were used: small RNA-seq to characterise and study the expression of miRNA genes; RNA-seq to monitor mRNA accumulation patterns; hormone quantification to assess the role of cytokinins and auxins in inflorescence differentiation. Our study allowed the characterisation of 30 previously unreported palm MIRNA genes. In differential gene and miRNA expression studies, we identified a number of key developmental genes and miRNA-mRNA target modules previously described in relation to their developmental regulatory role in the cereal panicle, notably the miR156/529/535-SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) gene regulatory module. Gene enrichment analysis highlighted the importance of hormone-related genes, and this observation was corroborated by the detection of much higher levels of cytokinins in the female inflorescence. Our data illustrate the importance of branching regulation within the developmental window studied, during which the female inflorescence, unlike its male counterpart, produces flower clusters on new successive axes by sympodial growth.
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Affiliation(s)
- James W. Tregear
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- Correspondence:
| | - Frédérique Richaud
- CIRAD, UMR AGAP, 34398 Montpellier, France;
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Myriam Collin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Jennifer Esbelin
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France;
| | | | | | - Fabienne Morcillo
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
- CIRAD, UMR DIADE, 34394 Montpellier, France
| | - Hélène Adam
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
| | - Stefan Jouannic
- DIADE, University of Montpellier, CIRAD, IRD, 34394 Montpellier, France; (M.C.); (J.E.); (F.M.); (H.A.); (S.J.)
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10
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Ma X, Yan H, Yang J, Liu Y, Li Z, Sheng M, Cao Y, Yu X, Yi X, Xu W, Su Z. PlantGSAD: a comprehensive gene set annotation database for plant species. Nucleic Acids Res 2021; 50:D1456-D1467. [PMID: 34534340 PMCID: PMC8728169 DOI: 10.1093/nar/gkab794] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
With the accumulation of massive data sets from high-throughput experiments and the rapid emergence of new types of omics data, gene sets have become more diverse and essential for the refinement of gene annotation at multidimensional levels. Accordingly, we collected and defined 236 007 gene sets across different categories for 44 plant species in the Plant Gene Set Annotation Database (PlantGSAD). These gene sets were divided into nine main categories covering many functional subcategories, such as trait ontology, co-expression modules, chromatin states, and liquid-liquid phase separation. The annotations from the collected gene sets covered all of the genes in the Brassicaceae species Arabidopsis and Poaceae species Oryza sativa. Several GSEA tools are implemented in PlantGSAD to improve the efficiency of the analysis, including custom SEA for a flexible strategy based on customized annotations, SEACOMPARE for the cross-comparison of SEA results, and integrated visualization features for ontological analysis that intuitively reflects their parent-child relationships. In summary, PlantGSAD provides numerous gene sets for multiple plant species and highly efficient analysis tools. We believe that PlantGSAD will become a multifunctional analysis platform that can be used to predict and elucidate the functions and mechanisms of genes of interest. PlantGSAD is publicly available at http://systemsbiology.cau.edu.cn/PlantGSEAv2/.
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Affiliation(s)
- Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hengyu Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jiaotong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yue Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhongqiu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Minghao Sheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yaxin Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xinyue Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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11
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Hosni H, Diallo A, Morcillo F, Vaissayre V, Collin M, Tranchant-Dubreuil C, Dussert S, Joët T, Castaño F, Marquínez X, Stauffer FW, Hodel DR, Castillo Mont JJ, Adam H, Jouannic S, Tregear JW. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote). ANNALS OF BOTANY 2021; 128:231-240. [PMID: 33978714 PMCID: PMC8324030 DOI: 10.1093/aob/mcab060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/07/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. METHODS We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. KEY RESULTS A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. CONCLUSIONS The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.
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Affiliation(s)
- Hanene Hosni
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Abdoulaye Diallo
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Fabienne Morcillo
- CIRAD, DIADE, Montpellier, France
- DIADE, Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Virginie Vaissayre
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Myriam Collin
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | | | - Stéphane Dussert
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Thierry Joët
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Felipe Castaño
- Universidad Industrial de Santander, Escuela de Biología, Calle, Bucaramanga, Colombia
| | - Xavier Marquínez
- Universidad Nacional de Colombia, Departamento de Biología, Carrera, Bogotá, Colombia
| | - Fred W Stauffer
- Conservatoire et Jardin botaniques de la Ville de Genève, Université de Genève, Laboratoire de Systématique Végétale et Biodiversité, Chambésy, Switzerland
| | - Donald R Hodel
- University of California, Cooperative Extension, Alhambra, CA, USA
| | | | - Hélène Adam
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - Stefan Jouannic
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
| | - James W Tregear
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, Montpellier, France
- For correspondence. E-mail
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12
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Yang Y, Zhang X, Wu L, Zhang L, Liu G, Xia C, Liu X, Kong X. Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date. BMC Genomics 2021; 22:468. [PMID: 34162321 PMCID: PMC8220847 DOI: 10.1186/s12864-021-07797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07797-7.
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Affiliation(s)
- Yuxin Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xueying Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Lifen Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.,Hebei sub-center of National Maize Improvement Center of China, Key Laboratory of Crop Germplasm Resources of Northern China (Ministry of Education), College of Agronomy, Hebei Agricultural University, 071001, Baoding, China
| | - Lichao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Guoxiang Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Chuan Xia
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xu Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiuying Kong
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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13
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Innovation, conservation, and repurposing of gene function in root cell type development. Cell 2021; 184:3333-3348.e19. [PMID: 34010619 DOI: 10.1016/j.cell.2021.04.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022]
Abstract
Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals.
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14
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Jurado-Flores A, Romero LC, Gotor C. Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of H 2S Signaling by Protein Persulfidation. Antioxidants (Basel) 2021; 10:508. [PMID: 33805243 PMCID: PMC8064375 DOI: 10.3390/antiox10040508] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/10/2021] [Accepted: 03/22/2021] [Indexed: 01/18/2023] Open
Abstract
Hydrogen sulfide (H2S)-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the posttranslational modification of cysteine residues to form a persulfidated thiol motif. We developed a comparative and label-free quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in N-starved Arabidopsis thaliana roots by using the tag-switch method. In this work, we identified 5214 unique proteins from root tissue that were persulfidated, 1674 of which were quantitatively analyzed and found to show altered persulfidation levels in vivo under N deprivation. These proteins represented almost 13% of the entire annotated proteome in Arabidopsis. Bioinformatic analysis revealed that persulfidated proteins were involved in a wide range of biological functions, regulating important processes such as primary metabolism, plant responses to stresses, growth and development, RNA translation and protein degradation. Quantitative mass spectrometry analysis allowed us to obtain a comprehensive view of hydrogen sulfide signaling via changes in the persulfidation levels of key protein targets involved in ubiquitin-dependent protein degradation and autophagy, among others.
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Affiliation(s)
| | - Luis C. Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain;
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain;
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15
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Heydarian Z, Gruber M, Coutu C, Glick BR, Hegedus DD. Gene expression patterns in shoots of Camelina sativa with enhanced salinity tolerance provided by plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase or expression of the corresponding acdS gene. Sci Rep 2021; 11:4260. [PMID: 33608579 PMCID: PMC7895925 DOI: 10.1038/s41598-021-83629-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/28/2022] Open
Abstract
Growth of plants in soil inoculated with plant growth promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase or expression of the corresponding acdS gene in transgenic lines reduces the decline in shoot length, shoot weight and photosynthetic capacity triggered by salt stress in Camelina sativa. Reducing the levels of ethylene attenuated the salt stress response as inferred from decreases in the expression of genes involved in development, senescence, chlorosis and leaf abscission that are highly induced by salt to levels that may otherwise have a negative effect on plant growth and productivity. Growing plants in soil treated with Pseudomonas migulae 8R6 negatively affected ethylene signaling, auxin and JA biosynthesis and signalling, but had a positive effect on the regulation of genes involved in GA signaling. In plants expressing acdS, the expression of the genes involved in auxin signalling was positively affected, while the expression of genes involved in cytokinin degradation and ethylene biosynthesis were negatively affected. Moreover, fine-tuning of ABA signaling appears to result from the application of ACC deaminase in response to salt treatment. Moderate expression of acdS under the control of the root specific rolD promoter or growing plants in soil treated with P. migulae 8R6 were more effective in reducing the expression of the genes involved in ethylene production and/or signaling than expression of acdS under the more active Cauliflower Mosaic Virus 35S promoter.
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Affiliation(s)
- Zohreh Heydarian
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.,Department of Biotechnology, School of Agriculture, University of Shiraz, Bajgah, Shiraz, Fars, Iran
| | - Margaret Gruber
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. .,Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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16
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Ramšak Ž, Petek M, Baebler Š. RNA Sequencing Analyses for Deciphering Potato Molecular Responses. Methods Mol Biol 2021; 2354:57-94. [PMID: 34448155 DOI: 10.1007/978-1-0716-1609-3_3] [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]
Abstract
Understanding the molecular mechanisms of potato development and responses to environmental stressors is of utmost importance for achieving stable crop yields. RNA sequencing (RNA-Seq) provides an insight into responses of all of the organism genes to the environmental and developmental cues and thus provides insights into underlying modes of action. In this chapter, we guide a researcher through some of the most important steps in the analysis of transcriptomics data. The initial topic of experimental design is followed by a more wet-lab-oriented section on RNA-Seq sample preparation. Next, we present intermediate steps of data retrieval, quality control, mapping, and differential expression of the dataset and a section on how to expose your data to the public (i.e., public repositories) and make it findable, accessible, interoperable, and reusable (FAIR). In the last four sections, we describe specific tools or Web applications, which ease the exploration of generated results in the context of their gene function and network-based visualizations, specifically GoMapMan, GSEA, DiNAR, and Biomine Explorer. All sections are accompanied by potato dataset examples and include general hints and tricks, as well as potato specificities that one should be aware of.
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Affiliation(s)
- Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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17
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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18
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Laureano-Marín AM, Aroca Á, Pérez-Pérez ME, Yruela I, Jurado-Flores A, Moreno I, Crespo JL, Romero LC, Gotor C. Abscisic Acid-Triggered Persulfidation of the Cys Protease ATG4 Mediates Regulation of Autophagy by Sulfide. THE PLANT CELL 2020; 32:3902-3920. [PMID: 33037147 PMCID: PMC7721334 DOI: 10.1105/tpc.20.00766] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
Hydrogen sulfide is a signaling molecule that regulates essential processes in plants, such as autophagy. In Arabidopsis (Arabidopsis thaliana), hydrogen sulfide negatively regulates autophagy independently of reactive oxygen species via an unknown mechanism. Comparative and quantitative proteomic analysis was used to detect abscisic acid-triggered persulfidation that reveals a main role in the control of autophagy mediated by the autophagy-related (ATG) Cys protease AtATG4a. This protease undergoes specific persulfidation of Cys170 that is a part of the characteristic catalytic Cys-His-Asp triad of Cys proteases. Regulation of the ATG4 activity by persulfidation was tested in a heterologous assay using the Chlamydomonas reinhardtii CrATG8 protein as a substrate. Sulfide significantly and reversibly inactivates AtATG4a. The biological significance of the reversible inhibition of the ATG4 by sulfide is supported by the results obtained in Arabidopsis leaves under basal and autophagy-activating conditions. A significant increase in the overall ATG4 proteolytic activity in Arabidopsis was detected under nitrogen starvation and osmotic stress and can be inhibited by sulfide. Therefore, the data strongly suggest that the negative regulation of autophagy by sulfide is mediated by specific persulfidation of the ATG4 protease.
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Affiliation(s)
- Ana M Laureano-Marín
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - M Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, 50059 Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to Consejo Superior de Investigaciones Científicas, 50059 Zaragoza, Spain
| | - Ana Jurado-Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
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19
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Huang K, Zhou S, Shen K, Zhou Y, Wang F, Jiang X. Elucidation of the miR164c-Guided Gene/Protein Interaction Network Controlling Seed Vigor in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:589005. [PMID: 33281848 PMCID: PMC7688992 DOI: 10.3389/fpls.2020.589005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/26/2020] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) play important roles in various aspects of plant physiology and metabolism. The expression level of miR164c is negatively correlated with seed vigor in rice (Oryza sativa L.); however, the mechanism of seed vigor regulation by miR164c remains unknown. Anti-aging capacity is an important indicator of seed vigor. Here, we report an miR164c-guided gene/protein interaction network that regulates the anti-aging ability of rice seeds. Seeds of the wild-type (WT) rice cultivar "Kasalath" and its transgenic derivatives, miR164c-silenced line (MIM164c) and miR164c overexpression line (OE164c), with significant differences in anti-aging capacity, showed significant differences in gene and protein expression levels. The differentially expressed genes (DEGs) or proteins were significantly enriched in six metabolic functional categories related to seed vigor, including "stress response," "protein processing in endoplasmic reticulum (ER)," "embryo development," "serine-type endopeptidase inhibitor," "energy metabolism," and "other." Differences in the expression levels of genes or proteins related to energy metabolism, serine endopeptidase, and stress response in seeds under normal storage conditions may be associated with anti-aging capacity. The results of gene/protein interaction analyses suggest that miR164c first targets PSK5, and the PSK5 protein then interacts with the ubiquitin-associated gene RPS27AA, which simultaneously impacts the genes/proteins in the six above-mentioned functional categories. Expression levels of some of the key genes and proteins in the interaction network were verified by real-time fluorescence quantitative PCR (RT-qPCR) and multiple reaction monitoring mass spectrometry (MRM-MS), respectively. Thus, the present study provides new insights into the miRNA-mediated gene and protein interaction network that regulates seed vigor.
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Affiliation(s)
- Kerui Huang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shiqi Zhou
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Kaimin Shen
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yan Zhou
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Feng Wang
- College of Life Sciences, Hunan Normal University, Changsha, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, China
| | - Xiaocheng Jiang
- College of Life Sciences, Hunan Normal University, Changsha, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, China
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20
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Fass MI, Rivarola M, Ehrenbolger GF, Maringolo CA, Montecchia JF, Quiroz F, García-García F, Blázquez JD, Hopp HE, Heinz RA, Paniego NB, Lia VV. Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis. Sci Rep 2020; 10:13347. [PMID: 32770047 PMCID: PMC7414910 DOI: 10.1038/s41598-020-70315-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/24/2020] [Indexed: 12/24/2022] Open
Abstract
Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotinia-sunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense.
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Affiliation(s)
- Mónica I Fass
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina.
| | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Guillermo F Ehrenbolger
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Carla A Maringolo
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce, Balcarce, Argentina
| | - Juan F Montecchia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Facundo Quiroz
- Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce, Balcarce, Argentina
| | | | - Joaquín Dopazo Blázquez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.,INB-ELIXIR-Es, FPS, Hospital Virgen del Rocío, 42013, Sevilla, Spain
| | - H Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina.,Departamento de Fisiología, Biología Molecular y Celular (FBMC), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA), 1428, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham B1686IGC, Buenos Aires, Argentina
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21
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Wong DCJ. Network aggregation improves gene function prediction of grapevine gene co-expression networks. PLANT MOLECULAR BIOLOGY 2020; 103:425-441. [PMID: 32266646 DOI: 10.1007/s11103-020-01001-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/21/2020] [Indexed: 05/08/2023]
Abstract
Aggregation across multiple networks highlights robust co-expression interactions and improves the functional connectivity of grapevine gene co-expression networks. In recent years, the rapid accumulation of transcriptome datasets from diverse experimental conditions has enabled the widespread use of gene co-expression network (GCN) analysis in plants. In grapevine, GCN analysis has shown great promise for gene function prediction, however, measurable progress is currently lacking. Using accumulated microarray datasets from the grapevine whole-genome array (33 experiments, 1359 samples), we explored how meta-analysis through aggregation influences the functional connectivity (performance) of derived networks using guilt-by-association neighbor voting. Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringent) and 300 (relaxed) ranked genes were evaluated. We observed that aggregating across multiple networks improves performance dramatically, with the aggregate outperforming the majority of functional terms across individual networks. Network sparsity and size (i.e. the number of samples and aggregates) were key factors influencing performance while the choice of annotation scheme had little. Systematic comparison with various state-of-the-art microarray and RNA-seq networks was also performed, however, none outperformed the aggregate microarray network despite having good predictive performance. Repeating these series of tests using a functional enrichment-based performance metric also showed remarkably consistent findings with guilt-by-association neighbor voting. To demonstrate its functionality, we explore the function and transcriptional regulation of grapevine EXPANSIN genes. We envisage that network aggregation will offer new and unique opportunities for gene function prediction in future grapevine functional genomics studies. To this end, we make the aggregate networks and associated metadata publicly available at VTC-Agg (https://sites.google.com/view/vtc-agg).
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia.
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22
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Stavrinides AK, Dussert S, Combes MC, Fock-Bastide I, Severac D, Minier J, Bastos-Siqueira A, Demolombe V, Hem S, Lashermes P, Joët T. Seed comparative genomics in three coffee species identify desiccation tolerance mechanisms in intermediate seeds. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1418-1433. [PMID: 31790120 PMCID: PMC7031068 DOI: 10.1093/jxb/erz508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/10/2019] [Indexed: 05/13/2023]
Abstract
In contrast to desiccation-tolerant 'orthodox' seeds, so-called 'intermediate' seeds cannot survive complete drying and are short-lived. All species of the genus Coffea produce intermediate seeds, but they show a considerable variability in seed desiccation tolerance (DT), which may help to decipher the molecular basis of seed DT in plants. We performed a comparative transcriptome analysis of developing seeds in three coffee species with contrasting desiccation tolerance. Seeds of all species shared a major transcriptional switch during late maturation that governs a general slow-down of metabolism. However, numerous key stress-related genes, including those coding for the late embryogenesis abundant protein EM6 and the osmosensitive calcium channel ERD4, were up-regulated during DT acquisition in the two species with high seed DT, C. arabica and C. eugenioides. By contrast, we detected up-regulation of numerous genes involved in the metabolism, transport, and perception of auxin in C. canephora seeds with low DT. Moreover, species with high DT showed a stronger down-regulation of the mitochondrial machinery dedicated to the tricarboxylic acid cycle and oxidative phosphorylation. Accordingly, respiration measurements during seed dehydration demonstrated that intermediate seeds with the highest DT are better prepared to cease respiration and avoid oxidative stresses.
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Affiliation(s)
| | | | | | | | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier Cedex 5, France
| | | | | | - Vincent Demolombe
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Sonia Hem
- BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | | | - Thierry Joët
- IRD, Université Montpellier, UMR DIADE, Montpellier, France
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23
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Molina-Contreras MJ, Paulišić S, Then C, Moreno-Romero J, Pastor-Andreu P, Morelli L, Roig-Villanova I, Jenkins H, Hallab A, Gan X, Gomez-Cadenas A, Tsiantis M, Rodríguez-Concepción M, Martínez-García JF. Photoreceptor Activity Contributes to Contrasting Responses to Shade in Cardamine and Arabidopsis Seedlings. THE PLANT CELL 2019; 31:2649-2663. [PMID: 31530733 PMCID: PMC6881134 DOI: 10.1105/tpc.19.00275] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/22/2019] [Accepted: 09/13/2019] [Indexed: 05/08/2023]
Abstract
Plants have evolved two major ways to deal with nearby vegetation or shade: avoidance and tolerance. Moreover, some plants respond to shade in different ways; for example, Arabidopsis (Arabidopsis thaliana) undergoes an avoidance response to shade produced by vegetation, but its close relative Cardamine hirsuta tolerates shade. How plants adopt opposite strategies to respond to the same environmental challenge is unknown. Here, using a genetic strategy, we identified the C. hirsuta slender in shade1 mutants, which produce strongly elongated hypocotyls in response to shade. These mutants lack the phytochrome A (phyA) photoreceptor. Our findings suggest that C. hirsuta has evolved a highly efficient phyA-dependent pathway that suppresses hypocotyl elongation when challenged by shade from nearby vegetation. This suppression relies, at least in part, on stronger phyA activity in C. hirsuta; this is achieved by increased ChPHYA expression and protein accumulation combined with a stronger specific intrinsic repressor activity. We suggest that modulation of photoreceptor activity is a powerful mechanism in nature to achieve physiological variation (shade tolerance versus avoidance) for species to colonize different habitats.
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Affiliation(s)
- Maria Jose Molina-Contreras
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Christiane Then
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Jordi Moreno-Romero
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Pedro Pastor-Andreu
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Luca Morelli
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Irma Roig-Villanova
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Huw Jenkins
- Department of Plant Sciences, University of Oxford, Oxford OX1 3BR, United Kingdom
| | - Asis Hallab
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Xiangchao Gan
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Aurelio Gomez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, 12071 Castello de la Plana, Spain
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Manuel Rodríguez-Concepción
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
| | - Jaime F Martínez-García
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas -Institut de Recerca i Tecnologies Agroalimentaries - Universitat Autònoma de Barcelona - Universitat de Barcelona, 08193 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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24
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Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B. MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. MOLECULAR PLANT 2019; 12:879-892. [PMID: 30639314 DOI: 10.1016/j.molp.2019.01.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 01/01/2019] [Indexed: 05/18/2023]
Abstract
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
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Affiliation(s)
- Rainer Schwacke
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Gabriel Y Ponce-Soto
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, The Arctic University of Norway, Biology Building, 9037 Tromsø, Norway
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
| | - Borjana Arsova
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Asis Hallab
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Department of Systems Regulation, 14476 Potsdam-Golm, Germany
| | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany.
| | - Björn Usadel
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany; Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
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25
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Featherston J, Arakaki Y, Hanschen ER, Ferris PJ, Michod RE, Olson BJSC, Nozaki H, Durand PM. The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage. Mol Biol Evol 2019; 35:855-870. [PMID: 29294063 DOI: 10.1093/molbev/msx332] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.
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Affiliation(s)
- Jonathan Featherston
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa.,Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
| | - Yoko Arakaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Erik R Hanschen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Patrick J Ferris
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | - Richard E Michod
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
| | | | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Hongo, Japan
| | - Pierre M Durand
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
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26
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García I, Arenas-Alfonseca L, Moreno I, Gotor C, Romero LC. HCN Regulates Cellular Processes through Posttranslational Modification of Proteins by S-cyanylation. PLANT PHYSIOLOGY 2019; 179:107-123. [PMID: 30377236 PMCID: PMC6324243 DOI: 10.1104/pp.18.01083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/23/2018] [Indexed: 05/07/2023]
Abstract
Hydrogen cyanide (HCN) is coproduced with ethylene in plant cells and is primarily enzymatically detoxified by the mitochondrial β-CYANOALANINE SYNTHASE (CAS-C1). Permanent or transient depletion of CAS-C1 activity in Arabidopsis (Arabidopsis thaliana) results in physiological alterations in the plant that suggest that HCN acts as a gasotransmitter molecule. Label-free quantitative proteomic analysis of mitochondrially enriched samples isolated from the wild type and cas-c1 mutant revealed significant changes in protein content, identifying 451 proteins that are absent or less abundant in cas-c1 and 353 proteins that are only present or more abundant in cas-c1 Gene ontology classification of these proteins identified proteomic changes that explain the root hairless phenotype and the altered immune response observed in the cas-c1 mutant. The mechanism of action of cyanide as a signaling molecule was addressed using two proteomic approaches aimed at identifying the S-cyanylation of Cys as a posttranslational modification of proteins. Both the 2-imino-thiazolidine chemical method and the direct untargeted analysis of proteins using liquid chromatography-tandem mass spectrometry identified a set of 163 proteins susceptible to S-cyanylation that included SEDOHEPTULOSE 1,7-BISPHOSPHATASE (SBPase), the PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 20-3 (CYP20-3), and ENOLASE2 (ENO2). In vitro analysis of these enzymes showed that S-cyanylation of SBPase Cys74, CYP20-3 Cys259, and ENO2 Cys346 residues affected their enzymatic activity. Gene Ontology classification and protein-protein interaction cluster analysis showed that S-cyanylation is involved in the regulation of primary metabolic pathways, such as glycolysis, and the Calvin and S-adenosyl-Met cycles.
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Affiliation(s)
- Irene García
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Lucía Arenas-Alfonseca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49, 41092 Sevilla, Spain
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Heydarian Z, Yu M, Gruber M, Coutu C, Robinson SJ, Hegedus DD. Changes in gene expression in Camelina sativa roots and vegetative tissues in response to salinity stress. Sci Rep 2018; 8:9804. [PMID: 29955098 PMCID: PMC6023900 DOI: 10.1038/s41598-018-28204-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 06/14/2018] [Indexed: 12/19/2022] Open
Abstract
The response of Camelina sativa to salt stress was examined. Salt reduced shoot, but not root length. Root and shoot weight were affected by salt, as was photosynthetic capacity. Salt did not alter micro-element concentration in shoots, but increased macro-element (Ca and Mg) levels. Gene expression patterns in shoots indicated that salt stress may have led to shuttling of Na+ from the cytoplasm to the tonoplast and to an increase in K+ and Ca+2 import into the cytoplasm. In roots, gene expression patterns indicated that Na+ was exported from the cytoplasm by the SOS pathway and that K+ was imported in response to salt. Genes involved in chelation and storage were up-regulated in shoots, while metal detoxification appeared to involve various export mechanisms in roots. In shoots, genes involved in secondary metabolism leading to lignin, anthocyanin and wax production were up-regulated. Partial genome partitioning was observed in roots and shoots based on the expression of homeologous genes from the three C. sativa sub-genomes. Sub-genome I and II were involved in the response to salinity stress to about the same degree, while about 10% more differentially-expressed genes were associated with sub-genome III.
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Affiliation(s)
- Zohreh Heydarian
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
- Department of Biotechnology, School of Agriculture, University of Shiraz, Bajgah, Shiraz, Fars, Iran
| | - Min Yu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Margaret Gruber
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Cathy Coutu
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Stephen J Robinson
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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Heydarian Z, Gruber M, Glick BR, Hegedus DD. Gene Expression Patterns in Roots of Camelina sativa With Enhanced Salinity Tolerance Arising From Inoculation of Soil With Plant Growth Promoting Bacteria Producing 1-Aminocyclopropane-1-Carboxylate Deaminase or Expression the Corresponding acdS Gene. Front Microbiol 2018; 9:1297. [PMID: 30013518 PMCID: PMC6036250 DOI: 10.3389/fmicb.2018.01297] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 05/28/2018] [Indexed: 12/19/2022] Open
Abstract
Camelina sativa treated with plant growth-promoting bacteria (PGPB) producing 1-aminocyclopropane-1-carboxylate deaminase (acdS) or transgenic lines expressing acdS exhibit increased salinity tolerance. AcdS reduces the level of stress ethylene to below the point where it is inhibitory to plant growth. The study determined that several mechanisms appear to be responsible for the increased salinity tolerance and that the effect of acdS on gene expression patterns in C. sativa roots during salt stress is a function of how it is delivered. Growth in soil treated with the PGPB (Pseudomonas migulae 8R6) mostly affected ethylene- and abscisic acid-dependent signaling in a positive way, while expression of acdS in transgenic lines under the control of the broadly active CaMV 35S promoter or the root-specific rolD promoter affected auxin, jasmonic acid and brassinosteroid signaling and/biosynthesis. The expression of genes involved in minor carbohydrate metabolism were also up-regulated, mainly in roots of lines expressing acdS. Expression of acdS also affected the expression of genes involved in modulating the level of reactive oxygen species (ROS) to prevent cellular damage, while permitting ROS-dependent signal transduction. Though the root is not a photosynthetic tissue, acdS had a positive effect on the expression of genes involved in photosynthesis.
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Affiliation(s)
- Zohreh Heydarian
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada.,Department of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Dwayne D Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, SK, Canada.,Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Tsai CH, Uygun S, Roston R, Shiu SH, Benning C. Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas. PLANT PHYSIOLOGY 2018; 176:2007-2023. [PMID: 29288234 PMCID: PMC5841715 DOI: 10.1104/pp.17.01546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/26/2017] [Indexed: 05/20/2023]
Abstract
Facing adverse conditions such as nitrogen (N) deprivation, microalgae enter cellular quiescence, a reversible cell cycle arrest with drastic changes in metabolism allowing cells to remain viable. Recovering from N deprivation and quiescence is an active and orderly process as we are showing here for Chlamydomonas reinhardtii We conducted comparative transcriptomics on this alga to discern processes relevant to quiescence in the context of N deprivation and recovery following refeeding. A mutant with slow recovery from N deprivation, compromised hydrolysis of triacylglycerols7 (cht7), was included to better define the regulatory processes governing the respective transitions. We identified an ordered set of biological processes with expression patterns that showed sequential reversal following N resupply and uncovered acclimation responses specific to the recovery phase. Biochemical assays and microscopy validated selected inferences made based on the transcriptional analyses. These comprise (1) the restoration of N source preference and cellular bioenergetics during the early stage of recovery; (2) flagellum-based motility in the mid to late stage of recovery; and (3) recovery phase-specific gene groups cooperating in the rapid replenishment of chloroplast proteins. In the cht7 mutant, a large number of programmed responses failed to readjust in a timely manner. Finally, evidence is provided for the involvement of the cAMP-protein kinase A pathway in gating the recovery. We conclude that the recovery from N deprivation represents not simply a reversal of processes directly following N deprivation, but a distinct cellular state.
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Affiliation(s)
- Chia-Hong Tsai
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sahra Uygun
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Genetics Program, Michigan State University, East Lansing, Michigan 48824
| | - Rebecca Roston
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Genetics Program, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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Abstract
Lysine acetylation is a key posttranslational modification that regulates diverse proteins involved in a range of biological processes. The role of histone acetylation in plant defense is well established, and it is known that pathogen effector proteins encoding acetyltransferases can directly acetylate host proteins to alter immunity. However, it is unclear whether endogenous plant enzymes can modulate protein acetylation during an immune response. Here, we investigate how the effector molecule HC-toxin (HCT), a histone deacetylase inhibitor produced by the fungal pathogen Cochliobolus carbonum race 1, promotes virulence in maize through altering protein acetylation. Using mass spectrometry, we globally quantified the abundance of 3,636 proteins and the levels of acetylation at 2,791 sites in maize plants treated with HCT as well as HCT-deficient or HCT-producing strains of C. carbonum Analyses of these data demonstrate that acetylation is a widespread posttranslational modification impacting proteins encoded by many intensively studied maize genes. Furthermore, the application of exogenous HCT enabled us to show that the activity of plant-encoded enzymes (histone deacetylases) can be modulated to alter acetylation of nonhistone proteins during an immune response. Collectively, these results provide a resource for further mechanistic studies examining the regulation of protein function by reversible acetylation and offer insight into the complex immune response triggered by virulent C. carbonum.
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Meyer J, Berger DK, Christensen SA, Murray SL. RNA-Seq analysis of resistant and susceptible sub-tropical maize lines reveals a role for kauralexins in resistance to grey leaf spot disease, caused by Cercospora zeina. BMC PLANT BIOLOGY 2017; 17:197. [PMID: 29132306 PMCID: PMC5683525 DOI: 10.1186/s12870-017-1137-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/18/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cercospora zeina is a foliar pathogen responsible for maize grey leaf spot in southern Africa that negatively impacts maize production. Plants use a variety of chemical and structural mechanisms to defend themselves against invading pathogens such as C. zeina, including the production of secondary metabolites with antimicrobial properties. In maize, a variety of biotic and abiotic stressors induce the accumulation of the terpenoid phytoalexins, zealexins and kauralexins. RESULTS C. zeina-susceptible line displayed pervasive rectangular grey leaf spot lesions, running parallel with the leaf veins in contrast to C. zeina-resistant line that had restricted disease symptoms. Analysis of the transcriptome of both lines indicated that genes involved in primary and secondary metabolism were up-regualted, and although different pathways were prioritized in each line, production of terpenoid compounds were common to both. Targeted phytoalexin analysis revealed that C. zeina-inoculated leaves accumulated zealexins and kauralexins. The resistant line shows a propensity toward accumulation of the kauralexin B series metabolites in response to infection, which contrasts with the susceptible line that preferentially accumulates the kauralexin A series. Kauralexin accumulation was correlated to expression of the kauralexin biosynthetic gene, ZmAn2 and a candidate biosynthetic gene, ZmKSL2. We report the expression of a putative copalyl diphosphate synthase gene that is induced by C. zeina in the resistant line exclusively. DISCUSSION This study shows that zealexins and kauralexins, and expression of their biosynthetic genes, are induced by C. zeina in both resistant and susceptible germplasm adapted to the southern African climate. The data presented here indicates that different forms of kauralexins accumulate in the resistant and susceptible maize lines in response to C. zeina, with the accumulation of kauralexin B compounds in a resistant maize line and kauralexin A compounds accumulating in the susceptible line.
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Affiliation(s)
- Jacqueline Meyer
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P/Bag X20, Hatfield, Gauteng, 0028, South Africa
- Centre for Proteomic and Genomic Research, Upper Level, St Peter's Mall, Cnr Anzio and Main Road, Observatory, Cape Town, 7925, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P/Bag X20, Hatfield, Gauteng, 0028, South Africa
| | - Shawn A Christensen
- Center for Medical, Agricultural, and Veterinary Entomology, United States Department of Agriculture, Agricultural Research Service, Chemistry Research Unit, Gainesville, Florida, 32608, USA
| | - Shane L Murray
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
- Centre for Proteomic and Genomic Research, Upper Level, St Peter's Mall, Cnr Anzio and Main Road, Observatory, Cape Town, 7925, South Africa.
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Grübler B, Merendino L, Twardziok SO, Mininno M, Allorent G, Chevalier F, Liebers M, Blanvillain R, Mayer KFX, Lerbs-Mache S, Ravanel S, Pfannschmidt T. Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1. PLANT PHYSIOLOGY 2017; 175:1203-1219. [PMID: 28935841 PMCID: PMC5664474 DOI: 10.1104/pp.17.00982] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/20/2017] [Indexed: 05/20/2023]
Abstract
Plants possessing dysfunctional plastids due to defects in pigment biosynthesis or translation are known to repress photosynthesis-associated nuclear genes via retrograde signals from the disturbed organelles toward the nucleus. These signals are thought to be essential for proper biogenesis and function of the plastid. Mutants lacking plastid-encoded RNA polymerase-associated proteins (PAPs) display a genetic arrest in eoplast-chloroplast transition leading to an albino phenotype in the light. Retrograde signaling in these mutants, therefore, could be expected to be similar as under conditions inducing plastid dysfunction. To answer this question, we performed plastome- and genomewide array analyses in the pap7-1 mutant of Arabidopsis (Arabidopsis thaliana). In parallel, we determined the potential overlap with light-regulated expression networks. To this end, we performed a comparative expression profiling approach using light- and dark-grown wild-type plants as relative control for the expression profiles obtained from light-grown pap7-1 mutants. Our data indicate a specific impact of retrograde signals on metabolism-related genes in pap7-1 mutants reflecting the starvation situation of the albino seedlings. In contrast, light regulation of PhANGs and other nuclear gene groups appears to be fully functional in this mutant, indicating that a block in chloroplast biogenesis per se does not repress expression of them as suggested by earlier studies. Only genes for light harvesting complex proteins displayed a significant repression indicating an exclusive retrograde impact on this gene family. Our results indicate that chloroplasts and arrested plastids each emit specific signals that control different target gene modules both in positive and negative manner.
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Affiliation(s)
- Björn Grübler
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Livia Merendino
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Sven O Twardziok
- Plant Genome and Systems Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Morgane Mininno
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Guillaume Allorent
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Fabien Chevalier
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Monique Liebers
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Robert Blanvillain
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Silva Lerbs-Mache
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Stéphane Ravanel
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
| | - Thomas Pfannschmidt
- LPCV, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France and
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Aroca A, Benito JM, Gotor C, Romero LC. Persulfidation proteome reveals the regulation of protein function by hydrogen sulfide in diverse biological processes in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4915-4927. [PMID: 28992305 PMCID: PMC5853657 DOI: 10.1093/jxb/erx294] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/28/2017] [Indexed: 05/20/2023]
Abstract
Hydrogen sulfide-mediated signaling pathways regulate many physiological and pathophysiological processes in mammalian and plant systems. The molecular mechanism by which hydrogen sulfide exerts its action involves the post-translational modification of cysteine residues to form a persulfidated thiol motif, a process called protein persulfidation. We have developed a comparative and quantitative proteomic analysis approach for the detection of endogenous persulfidated proteins in wild-type Arabidopsis and L-CYSTEINE DESULFHYDRASE 1 mutant leaves using the tag-switch method. The 2015 identified persulfidated proteins were isolated from plants grown under controlled conditions, and therefore, at least 5% of the entire Arabidopsis proteome may undergo persulfidation under baseline conditions. Bioinformatic analysis revealed that persulfidated cysteines participate in a wide range of biological functions, regulating important processes such as carbon metabolism, plant responses to abiotic and biotic stresses, plant growth and development, and RNA translation. Quantitative analysis in both genetic backgrounds reveals that protein persulfidation is mainly involved in primary metabolic pathways such as the tricarboxylic acid cycle, glycolysis, and the Calvin cycle, suggesting that this protein modification is a new regulatory component in these pathways.
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Affiliation(s)
| | - Juan M Benito
- Instituto de Investigaciones Química, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Avenida Américo Vespucio, Sevilla, Spain
| | | | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis
- Correspondence:
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Hu R, Xu Y, Yu C, He K, Tang Q, Jia C, He G, Wang X, Kong Y, Zhou G. Transcriptome analysis of genes involved in secondary cell wall biosynthesis in developing internodes of Miscanthus lutarioriparius. Sci Rep 2017; 7:9034. [PMID: 28831170 PMCID: PMC5567372 DOI: 10.1038/s41598-017-08690-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/12/2017] [Indexed: 11/08/2022] Open
Abstract
Miscanthus is a promising lignocellulosic bioenergy crop for bioethanol production. To identify candidate genes and regulation networks involved in secondary cell wall (SCW) development in Miscanthus, we performed de novo transcriptome analysis of a developing internode. According to the histological and in-situ histochemical analysis, an elongating internode of M. lutarioriparius can be divided into three distinct segments, the upper internode (UI), middle internode (MI) and basal internode (BI), each representing a different stage of SCW development. The transcriptome analysis generated approximately 300 million clean reads, which were de novo assembled into 79,705 unigenes. Nearly 65% of unigenes was annotated in seven public databases. Comparative profiling among the UI, MI and BI revealed four distinct clusters. Moreover, detailed expression profiling was analyzed for gene families and transcription factors (TFs) involved in SCW biosynthesis, assembly and modification. Based on the co-expression patterns, putative regulatory networks between TFs and SCW-associated genes were constructed. The work provided the first transcriptome analysis of SCW development in M. lutarioriparius. The results obtained provide novel insights into the biosynthesis and regulation of SCW in Miscanthus. In addition, the genes identified represent good candidates for further functional studies to unravel their roles in SCW biosynthesis and modification.
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Affiliation(s)
- Ruibo Hu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Yan Xu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Changjiang Yu
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Kang He
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Qi Tang
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Chunlin Jia
- Shandong Institute of Agricultural Sustainable Development, Jinan, 250100, P. R. China
| | - Guo He
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Xiaoyu Wang
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China
| | - Yingzhen Kong
- Key laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, P. R. China
| | - Gongke Zhou
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, P. R. China.
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Wong DCJ, Lopez Gutierrez R, Gambetta GA, Castellarin SD. Genome-wide analysis of cis-regulatory element structure and discovery of motif-driven gene co-expression networks in grapevine. DNA Res 2017; 24:311-326. [PMID: 28119334 PMCID: PMC5499852 DOI: 10.1093/dnares/dsw061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/13/2016] [Indexed: 11/29/2022] Open
Abstract
Coordinated transcriptional and metabolic reprogramming ensures a plant’s continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.
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Affiliation(s)
| | | | - Gregory Alan Gambetta
- Ecophysiologie et Génomique Fonctionnelle de la Vigne, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 33140 Villenave d'Ornon, France
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Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St Clair JB, Denver DR. Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics 2017; 18:558. [PMID: 28738815 PMCID: PMC5525293 DOI: 10.1186/s12864-017-3916-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. RESULTS We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/- 2 h from sunrise and sunset, and +/- 20 days from winter and summer solstices. Comparisons with published studies from other conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. CONCLUSIONS Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone conifers, and for identifying cyclic transcriptome components in other conifer species.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA.
| | - Peter C Dolan
- University of Minnesota - Morris, Morris, MN, 56267, USA
| | - Sanjuro Jogdeo
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - David B Neale
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - J Bradley St Clair
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA
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Wong DCJ, Amarasinghe R, Rodriguez-Delgado C, Eyles R, Pichersky E, Peakall R. Tissue-Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV-B Dependent Floral Volatile, Chiloglottone 1. FRONTIERS IN PLANT SCIENCE 2017; 8:1260. [PMID: 28769963 PMCID: PMC5515871 DOI: 10.3389/fpls.2017.01260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/04/2017] [Indexed: 05/29/2023]
Abstract
The Australian sexually deceptive orchid, Chiloglottis trapeziformis, employs a unique UV-B-dependent floral volatile, chiloglottone 1, for specific male wasp pollinator attraction. Chiloglottone 1 and related variants (2,5-dialkylcyclohexane-1,3-diones), represent a unique class of specialized metabolites presumed to be the product of cyclization between two fatty acid (FA) precursors. However, the genes involved in the biosynthesis of precursors, intermediates, and transcriptional regulation remains to be discovered. Chiloglottone 1 production occurs in the aggregation of calli (callus) on the labellum under continuous UV-B light. Therefore, deep sequencing, transcriptome assembly, and differential expression (DE) analysis were performed across different tissue types and UV-B treatments. Transcripts expressed in the callus and labellum (∼23,000 transcripts) were highly specialized and enriched for a diversity of known and novel metabolic pathways. DE analysis between chiloglottone-emitting callus versus the remainder of the labellum showed strong coordinated induction of entire FA biosynthesis and β-oxidation pathways including genes encoding Ketoacyl-ACP Synthase, Acyl-CoA Oxidase, and Multifunctional Protein. Phylogenetic analysis revealed potential gene duplicates with tissue-specific differential regulation including two Acyl-ACP Thioesterase B and a Ketoacyl-ACP Synthase genes. UV-B treatment induced the activation of UVR8-mediated signaling and large-scale transcriptome changes in both tissues, however, neither FA biosynthesis/β-oxidation nor other lipid metabolic pathways showed clear indications of concerted DE. Gene co-expression network analysis identified three callus-specific modules enriched with various lipid metabolism categories. These networks also highlight promising candidates involved in the cyclization of chiloglottone 1 intermediates (e.g., Bet v I and dimeric α,β barrel proteins) and orchestrating regulation of precursor pathways (e.g., AP2/ERF) given a strong co-regulation with FA biosynthesis/β-oxidation genes. Possible alternative biosynthetic routes for precursors (e.g., aldehyde dehydrogenases) were also indicated. Our comprehensive study constitutes the first step toward understanding the biosynthetic pathways involved in chiloglottone 1 production in Chiloglottis trapeziformis - supporting the roles of FA metabolism in planta, gene duplication as a potential source of new genes, and co-regulation of novel pathway genes in a tissue-specific manner. This study also provides a new and valuable resource for future discovery and comparative studies in plant specialized metabolism of other orchids and non-model plants.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Ranamalie Amarasinghe
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Claudia Rodriguez-Delgado
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Rodney Eyles
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann ArborMI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
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Duncan O, Trösch J, Fenske R, Taylor NL, Millar AH. Resource: Mapping the Triticum aestivum proteome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:601-616. [PMID: 27775198 DOI: 10.1111/tpj.13402] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 05/22/2023]
Abstract
Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. We present a large scale, publicly accessible proteome mapping of wheat consisting of 24 organ and developmental samples. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified, alongside hierarchical assessment of protein functional classes, their presence in different tissues and correlations between the abundance of functional classes of proteins. Gene-specific identifications and protein family relationships are accounted for in the organisation of the data and 202 new protein-coding transcripts identified by proteogenomic mapping. The interactive database will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function (www.wheatproteome.org).
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Affiliation(s)
- Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - Nicolas L Taylor
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
- School of Chemistry and Biochemistry, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, Crawley, WA, 6009, Australia
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Zhao K, Yang W, Zhou Y, Zhang J, Li Y, Ahmad S, Zhang Q. Comparative Transcriptome Reveals Benzenoid Biosynthesis Regulation as Inducer of Floral Scent in the Woody Plant Prunus mume. FRONTIERS IN PLANT SCIENCE 2017; 8:319. [PMID: 28344586 PMCID: PMC5345196 DOI: 10.3389/fpls.2017.00319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 05/08/2023]
Abstract
Mei (Prunus mume) is a peculiar woody ornamental plant famous for its inviting fragrance in winter. However, in this valuable plant, the mechanism behind floral volatile development remains poorly defined. Therefore, to explore the floral scent formation, a comparative transcriptome was conducted in order to identify the global transcripts specifying flower buds and blooming flowers of P. mume. Differentially expressed genes were identified between the two different stages showing great discrepancy in floral volatile production. Moreover, according to the expression specificity among the organs (stem, root, fruit, leaf), we summarized one gene cluster regulating the benzenoid floral scent. Significant gene changes were observed in accordance with the formation of benzenoid, thus pointing the pivotal roles of genes as well as cytochrome-P450s and short chain dehydrogenases in the benzenoid biosynthetic process. Further, transcription factors like EMISSION OF BENZENOID I and ODORANT I performed the same expression pattern suggesting key roles in the management of the downstream genes. Taken together, these data provide potential novel anchors for the benzenoid pathway, and the insight for the floral scent induction and regulation mechanism in woody plants.
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Hloušková P, Bergougnoux V. A subtracted cDNA library identifies genes up-regulated during PHOT1-mediated early step of de-etiolation in tomato (Solanum lycopersicum L.). BMC Genomics 2016; 17:291. [PMID: 27090636 PMCID: PMC4835860 DOI: 10.1186/s12864-016-2613-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/06/2016] [Indexed: 11/19/2022] Open
Abstract
Background De-etiolation is the switch from skoto- to photomorphogenesis, enabling the heterotrophic etiolated seedling to develop into an autotrophic plant. Upon exposure to blue light (BL), reduction of hypocotyl growth rate occurs in two phases: a rapid inhibition mediated by phototropin 1 (PHOT1) within the first 30–40 min of illumination, followed by the cryptochrome 1 (CRY1)-controlled establishment of the steady-state growth rate. Although some information is available for CRY1-mediated de-etiolation, less attention has been given to the PHOT1 phase of de-etiolation. Results We generated a subtracted cDNA library using the suppression subtractive hybridization method to investigate the molecular mechanisms of BL-induced de-etiolation in tomato (Solanum lycopersicum L.), an economically important crop. We focused our interest on the first 30 min following the exposure to BL when PHOT1 is required to induce the process. Our library generated 152 expressed sequence tags that were found to be rapidly accumulated upon exposure to BL and consequently potentially regulated by PHOT1. Annotation revealed that biological functions such as modification of chromatin structure, cell wall modification, and transcription/translation comprise an important part of events contributing to the establishment of photomorphogenesis in young tomato seedlings. Our conclusions based on bioinformatics data were supported by qRT-PCR analyses the specific investigation of V-H+-ATPase during de-etiolation in tomato. Conclusions Our study provides the first report dealing with understanding the PHOT1-mediated phase of de-etiolation. Using subtractive cDNA library, we were able to identify important regulatory mechanisms. The profound induction of transcription/translation, as well as modification of chromatin structure, is relevant in regard to the fact that the entry into photomorphogenesis is based on a deep reprograming of the cell. Also, we postulated that BL restrains the cell expansion by the rapid modification of the cell wall. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2613-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petra Hloušková
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research and Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71, Olomouc, Czech Republic
| | - Véronique Bergougnoux
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research and Faculty of Science, Palacký University in Olomouc, Šlechtitelů 11, CZ-783 71, Olomouc, Czech Republic.
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Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M. FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants. PLANT PHYSIOLOGY 2016; 170:1878-94. [PMID: 26754669 PMCID: PMC4775111 DOI: 10.1104/pp.15.01281] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/07/2016] [Indexed: 05/07/2023]
Abstract
Gene duplications generate new genes that can acquire similar but often diversified functions. Recent studies of gene coexpression networks have indicated that, not only genes, but also pathways can be multiplied and diversified to perform related functions in different parts of an organism. Identification of such diversified pathways, or modules, is needed to expand our knowledge of biological processes in plants and to understand how biological functions evolve. However, systematic explorations of modules remain scarce, and no user-friendly platform to identify them exists. We have established a statistical framework to identify modules and show that approximately one-third of the genes of a plant's genome participate in hundreds of multiplied modules. Using this framework as a basis, we implemented a platform that can explore and visualize multiplied modules in coexpression networks of eight plant species. To validate the usefulness of the platform, we identified and functionally characterized pollen- and root-specific cell wall modules that multiplied to confer tip growth in pollen tubes and root hairs, respectively. Furthermore, we identified multiplied modules involved in secondary metabolite synthesis and corroborated them by metabolite profiling of tobacco (Nicotiana tabacum) tissues. The interactive platform, referred to as FamNet, is available at http://www.gene2function.de/famnet.html.
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Affiliation(s)
- Colin Ruprecht
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Amelie Mendrinna
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Takayuki Tohge
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Arun Sampathkumar
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Sebastian Klie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Zoran Nikoloski
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Staffan Persson
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
| | - Marek Mutwil
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (C.R., T.T, S.K., A.R.F., Z.N., M.M.), School of Biosciences and Australian Research Council Centre of Excellence in Plant Cell Walls, University of Melbourne, Parkville, Victoria 3010, Australia (A.M., S.P.); andDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 (A.S.)
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Rasheed S, Bashir K, Matsui A, Tanaka M, Seki M. Transcriptomic Analysis of Soil-Grown Arabidopsis thaliana Roots and Shoots in Response to a Drought Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:180. [PMID: 26941754 PMCID: PMC4763085 DOI: 10.3389/fpls.2016.00180] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/02/2016] [Indexed: 05/04/2023]
Abstract
Drought stress has a negative impact on crop yield. Thus, understanding the molecular mechanisms responsible for plant drought stress tolerance is essential for improving this beneficial trait in crops. In the current study, a transcriptional analysis was conducted of gene regulatory networks in roots of soil-grown Arabidopsis plants in response to a drought stress treatment. A microarray analysis of drought-stressed roots and shoots was performed at 0, 1, 3, 5, 7, and 9 days. Results indicated that the expression of many drought stress-responsive genes and abscisic acid biosynthesis-related genes was differentially regulated in roots and shoots from days 3 to 9. The expression of cellular and metabolic process-related genes was up-regulated at an earlier time-point in roots than in shoots. In this regard, the expression of genes involved in oxidative signaling, chromatin structure, and cell wall modification also increased significantly in roots compared to shoots. Moreover, the increased expression of genes involved in the transport of amino acids and other solutes; including malate, iron, and sulfur, was observed in roots during the early time points following the initiation of the drought stress. These data suggest that plants may utilize these signaling channels and metabolic adjustments as adaptive responses in the early stages of a drought stress. Collectively, the results of the present study increases our understanding of the differences pertaining to the molecular mechanisms occurring in roots vs. shoots in response to a drought stress. Furthermore, these findings also aid in the selection of novel genes and promoters that can be used to potentially produce crop plants with increased drought tolerance.
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Affiliation(s)
- Sultana Rasheed
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource SciencesYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- CREST, Japan Science and Technology AgencySaitama, Japan
- *Correspondence: Motoaki Seki
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Tian C, Zuo Z, Qiu JL. Identification and Characterization of ABA-Responsive MicroRNAs in Rice. J Genet Genomics 2015; 42:393-402. [PMID: 26233894 DOI: 10.1016/j.jgg.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/22/2023]
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that silence genes through mRNA degradation or translational inhibition. The phytohormone abscisic acid (ABA) is essential for plant development and adaptation to abiotic and biotic stresses. In Arabidopsis, miRNAs are implicated in ABA functions. However, ABA-responsive miRNAs have not been systematically studied in rice. Here high throughput sequencing of small RNAs revealed that 107 miRNAs were differentially expressed in the rice ABA deficient mutant, Osaba1. Of these, 13 were confirmed by stem-loop RT-PCR. Among them, miR1425-5P, miR169a, miR169n, miR390-5P, miR397a and miR397b were up-regulated, but miR162b reduced in expression in Osaba1. The targets of these 13 miRNAs were predicted and validated by gene expression profiling. Interestingly, the expression levels of these miRNAs and their targets were regulated by ABA. Cleavage sites were detected on 7 of the miRNA targets by 5'-Rapid Amplification of cDNA Ends (5'-RACE). Finally, miR162b and its target OsTRE1 were shown to affect rice resistance to drought stress, suggesting that miR162b increases resistance to drought by targeting OsTRE1. Our work provides important information for further characterization and functional analysis of ABA-responsive miRNAs in rice.
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Affiliation(s)
- Caijuan Tian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhangli Zuo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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Aroca Á, Serna A, Gotor C, Romero LC. S-sulfhydration: a cysteine posttranslational modification in plant systems. PLANT PHYSIOLOGY 2015; 168:334-42. [PMID: 25810097 PMCID: PMC4424021 DOI: 10.1104/pp.15.00009] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/24/2015] [Indexed: 05/20/2023]
Abstract
Hydrogen sulfide is a highly reactive molecule that is currently accepted as a signaling compound. This molecule is as important as carbon monoxide in mammals and hydrogen peroxide in plants, as well as nitric oxide in both eukaryotic systems. Although many studies have been conducted on the physiological effects of hydrogen sulfide, the underlying mechanisms are poorly understood. One of the proposed mechanisms involves the posttranslational modification of protein cysteine residues, a process called S-sulfhydration. In this work, a modified biotin switch method was used for the detection of Arabidopsis (Arabidopsis thaliana) proteins modified by S-sulfhydration under physiological conditions. The presence of an S-sulfhydration-modified cysteine residue on cytosolic ascorbate peroxidase was demonstrated using liquid chromatography-tandem mass spectrometry analysis, and a total of 106 S-sulfhydrated proteins were identified. Immunoblot and enzyme activity analyses of some of these proteins showed that the sulfide added through S-sulfhydration reversibly regulates the functions of plant proteins in a manner similar to that described in mammalian systems.
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Affiliation(s)
- Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Seville, Spain (A.A., C.G., L.C.R.); andAB Sciex, 28108 Alcobendas, Madrid, Spain (A.S.)
| | - Antonio Serna
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Seville, Spain (A.A., C.G., L.C.R.); andAB Sciex, 28108 Alcobendas, Madrid, Spain (A.S.)
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Seville, Spain (A.A., C.G., L.C.R.); andAB Sciex, 28108 Alcobendas, Madrid, Spain (A.S.)
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, 41092 Seville, Spain (A.A., C.G., L.C.R.); andAB Sciex, 28108 Alcobendas, Madrid, Spain (A.S.)
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A co-expression gene network associated with developmental regulation of apple fruit acidity. Mol Genet Genomics 2015; 290:1247-63. [PMID: 25576355 DOI: 10.1007/s00438-014-0986-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 12/30/2014] [Indexed: 12/27/2022]
Abstract
Apple fruit acidity, which affects the fruit's overall taste and flavor to a large extent, is primarily determined by the concentration of malic acid. Previous studies demonstrated that the major QTL malic acid (Ma) on chromosome 16 is largely responsible for fruit acidity variations in apple. Recent advances suggested that a natural mutation that gives rise to a premature stop codon in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) is the genetic causal element underlying Ma. However, the natural mutation does not explain the developmental changes of fruit malate levels in a given genotype. Using RNA-seq data from the fruit of 'Golden Delicious' taken at 14 developmental stages from 1 week after full-bloom (WAF01) to harvest (WAF20), we characterized their transcriptomes in groups of high (12.2 ± 1.6 mg/g fw, WAF03-WAF08), mid (7.4 ± 0.5 mg/g fw, WAF01-WAF02 and WAF10-WAF14) and low (5.4 ± 0.4 mg/g fw, WAF16-WAF20) malate concentrations. Detailed analyses showed that a set of 3,066 genes (including Ma1) were expressed not only differentially (P FDR < 0.05) between the high and low malate groups (or between the early and late developmental stages) but also in significant (P < 0.05) correlation with malate concentrations. The 3,066 genes fell in 648 MapMan (sub-) bins or functional classes, and 19 of them were significantly (P FDR < 0.05) co-enriched or co-suppressed in a malate dependent manner. Network inferring using the 363 genes encompassed in the 19 (sub-) bins, identified a major co-expression network of 239 genes. Since the 239 genes were also differentially expressed between the early (WAF03-WAF08) and late (WAF16-WAF20) developmental stages, the major network was considered to be associated with developmental regulation of apple fruit acidity in 'Golden Delicious'.
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Gawehns F, Ma L, Bruning O, Houterman PM, Boeren S, Cornelissen BJC, Rep M, Takken FLW. The effector repertoire of Fusarium oxysporum determines the tomato xylem proteome composition following infection. FRONTIERS IN PLANT SCIENCE 2015; 6:967. [PMID: 26583031 PMCID: PMC4631825 DOI: 10.3389/fpls.2015.00967] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/22/2015] [Indexed: 05/14/2023]
Abstract
Plant pathogens secrete small proteins, of which some are effectors that promote infection. During colonization of the tomato xylem vessels the fungus Fusarium oxysporum f.sp. lycopersici (Fol) secretes small proteins that are referred to as SIX (Secreted In Xylem) proteins. Of these, Six1 (Avr3), Six3 (Avr2), Six5, and Six6 are required for full virulence, denoting them as effectors. To investigate their activities in the plant, the xylem sap proteome of plants inoculated with Fol wild-type or either AVR2, AVR3, SIX2, SIX5, or SIX6 knockout strains was analyzed with nano-Liquid Chromatography-Mass Spectrometry (nLC-MSMS). Compared to mock-inoculated sap 12 additional plant proteins appeared while 45 proteins were no longer detectable in the xylem sap of Fol-infected plants. Of the 285 proteins found in both uninfected and infected plants the abundance of 258 proteins changed significantly following infection. The xylem sap proteome of plants infected with four Fol effector knockout strains differed significantly from plants infected with wild-type Fol, while that of the SIX2-knockout inoculated plants remained unchanged. Besides an altered abundance of a core set of 24 differentially accumulated proteins (DAPs), each of the four effector knockout strains affected specifically the abundance of a subset of DAPs. Hence, Fol effectors have both unique and shared effects on the composition of the tomato xylem sap proteome.
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Affiliation(s)
- Fleur Gawehns
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Lisong Ma
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Oskar Bruning
- RNA Biology and Applied Bioinformatics Research Group and MAD: Dutch Genomics Service and Support Provider, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Petra M. Houterman
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen UniversityWageningen, Netherlands
| | - Ben J. C. Cornelissen
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
| | - Frank L. W. Takken
- Molecular Plant Pathology, Faculty of Science, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdam, Netherlands
- *Correspondence: Frank L. W. Takken
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Amar D, Frades I, Danek A, Goldberg T, Sharma SK, Hedley PE, Proux-Wera E, Andreasson E, Shamir R, Tzfadia O, Alexandersson E. Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. BMC PLANT BIOLOGY 2014; 14:329. [PMID: 25476999 PMCID: PMC4274702 DOI: 10.1186/s12870-014-0329-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/10/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. RESULTS We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. CONCLUSIONS We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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Affiliation(s)
- David Amar
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Itziar Frades
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Agnieszka Danek
- Institute of Informatics, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland.
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University of Munich, Arcisstraße 21, 80333, Munich, Germany.
| | - Sanjeev K Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Estelle Proux-Wera
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
- Current affiliation: SciLifeLab, Stockholm University, Universitetsvägen 10, 114 18, Stockholm, Sweden.
| | - Erik Andreasson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Oren Tzfadia
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
| | - Erik Alexandersson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res 2014; 43:D1010-7. [PMID: 25392409 PMCID: PMC4383956 DOI: 10.1093/nar/gku1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein–protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17 264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
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Affiliation(s)
- Rim Zaag
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean Philippe Tamby
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Cécile Guichard
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Zakia Tariq
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Guillem Rigaill
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Etienne Delannoy
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean-Pierre Renou
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Sandrine Balzergue
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Tristan Mary-Huard
- INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France UMRGV, INRA, Université Paris-Sud, CNRS, F-91190 Gif-sur-Yvette, Paris, France
| | - Sébastien Aubourg
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Marie-Laure Martin-Magniette
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
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Fang L, Tian R, Li X, Chen J, Wang S, Wang P, Zhang T. Cotton fiber elongation network revealed by expression profiling of longer fiber lines introgressed with different Gossypium barbadense chromosome segments. BMC Genomics 2014; 15:838. [PMID: 25273845 PMCID: PMC4190578 DOI: 10.1186/1471-2164-15-838] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/24/2014] [Indexed: 12/24/2022] Open
Abstract
Background Cotton fiber, a highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model. Fiber length, largely determined during the elongation stage, is a key property of fiber quality. Several studies using expressed sequence tags and microarray analysis have identified transcripts that accumulate preferentially during fiber elongation. To further show the mechanism of fiber elongation, we used Digital Gene Expression Tag Profiling to compare transcriptome data from longer fiber chromosome introgressed lines (CSILs) containing segments of various Gossypium barbadense chromosomes with data from its recurrent parent TM-1 during fiber elongation (from 5 DPA to 20 DPA). Results A large number of differentially expressed genes (DEGs) involved in carbohydrate, fatty acid and secondary metabolism, particularly cell wall biosynthesis, were highly upregulated during the fiber elongation stage, as determined by functional enrichment and pathway analysis. Furthermore, DEGs related to hormone responses and transcription factors showed upregulated expression levels in the CSILs. Moreover, metabolic and regulatory network analysis indicated that the same pathways were differentially altered, and distinct pathways exhibited altered gene expression, in the CSILs. Interestingly, mining of upregulated DEGs in the introgressed segments of these CSILs based on D-genome sequence data showed that these lines were enriched in glucuronosyltransferase, inositol-1, 4, 5-trisphosphate 3-kinase and desulfoglucosinolate sulfotransferase activity. These results were similar to the results of transcriptome analysis. Conclusions This report provides an integrative network about the molecular mechanisms controlling fiber length, which are mainly tied to carbohydrate metabolism, cell wall biosynthesis, fatty acid metabolism, secondary metabolism, hormone responses and Transcription factors. The results of this study provide new insights into the critical factors associated with cell elongation and will facilitate further research aimed at understanding the mechanisms underlying cotton fiber elongation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-838) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China.
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Rajasundaram D, Selbig J, Persson S, Klie S. Co-ordination and divergence of cell-specific transcription and translation of genes in arabidopsis root cells. ANNALS OF BOTANY 2014; 114:1109-23. [PMID: 25149544 PMCID: PMC4195562 DOI: 10.1093/aob/mcu151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS A key challenge in biology is to systematically investigate and integrate the different levels of information available at the global and single-cell level. Recent studies have elucidated spatiotemporal expression patterns of root cell types in Arabidopsis thaliana, and genome-wide quantification of polysome-associated mRNA levels, i.e. the translatome, has also been obtained for corresponding cell types. Translational control has been increasingly recognized as an important regulatory step in protein synthesis. The aim of this study was to investigate coupled transcription and translation by use of publicly available root datasets. METHODS Using cell-type-specific datasets of the root transcriptome and translatome of arabidopsis, a systematic assessment was made of the degree of co-ordination and divergence between these two levels of cellular organization. The computational analysis considered correlation and variation of expression across cell types at both system levels, and also provided insights into the degree of co-regulatory relationships that are preserved between the two processes. KEY RESULTS The overall correlation of expression and translation levels of genes resemble an almost bimodal distribution (mean/median value of 0·08/0·12), with a second, less strongly pronounced 'mode' for negative Pearson's correlation coefficient values. The analysis conducted also confirms that previously identified key transcriptional activators of secondary cell wall development display highly conserved patterns of transcription and translation across the investigated cell types. Moreover, the biological processes that display conserved and divergent patterns based on the cell-type-specific expression and translation levels were identified. CONCLUSIONS In agreement with previous studies in animal cells, a large degree of uncoupling was found between the transcriptome and translatome. However, components and processes were also identified that are under co-ordinated transcriptional and translational control in plant root cells.
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Affiliation(s)
- Dhivyaa Rajasundaram
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Joachim Selbig
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Staffan Persson
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sebastian Klie
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany Targenomix GmbH, Potsdam-Golm, 14476, Germany
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