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Abstract
Guide RNA design for CRISPR genome editing of gene families is a challenging task as usually good candidate sgRNAs are tagged with low scores precisely because they match several locations in the genome, thus time-consuming manual evaluation of targets is required. To address this issues, I have developed ARES-GT, a Python local command line tool compatible with any operative system. ARES-GT allows the selection of candidate sgRNAs that match multiple input query sequences, in addition of candidate sgRNAs that specifically match each query sequence. It also contemplates the use of unmapped contigs apart from complete genomes thus allowing the use of any genome provided by user and being able to handle intraspecies allelic variability and individual polymorphisms. ARES-GT is available at GitHub (https://github.com/eugomin/ARES-GT.git).
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Hloušková P, Černý M, Kořínková N, Luklová M, Minguet EG, Brzobohatý B, Galuszka P, Bergougnoux V. Affinity chromatography revealed 14-3-3 interactome of tomato (Solanum lycopersicum L.) during blue light-induced de-etiolation. J Proteomics 2018; 193:44-61. [PMID: 30583044 DOI: 10.1016/j.jprot.2018.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/09/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
De-etiolation is the first developmental process under light control allowing the heterotrophic seedling to become autotrophic. The phytohormones cytokinins (CKs) largely contribute to this process. Reversible phosphorylation is a key event of cell signaling, allowing proteins to become active or generating a binding site for specific protein interaction. 14-3-3 proteins regulate a variety of plant responses. The expression, hormonal regulation, and proteomic network under the control of 14-3-3s were addressed in tomato (Solanum lycopersicum L.) during blue light-induced photomorphogenesis. Two isoforms were specifically investigated due to their high expression during tomato de-etiolation. The multidisciplinary approach demonstrated that TFT9 expression, but not TFT6, was regulated by CKs and identified cis-regulating elements required for this response. Our study revealed >130 potential TFT6/9 interactors. Their functional annotation predicted that TFTs might regulate the activity of proteins involved notably in cell wall strengthening or primary metabolism. Several potential interactors were also predicted to be CK-responsive. For the first time, the 14-3-3 interactome linked to de-etiolation was investigated and evidenced that 14-3-3s might be involved in CK signaling pathway, cell expansion inhibition and steady-state growth rate establishment, and reprograming from heterotrophy to autotrophy. BIOLOGICAL SIGNIFICANCE: Tomato (Solanum lycopersicum L.) is one of the most important vegetables consumed all around the world and represents probably the most preferred garden crop. Regulation of hypocotyl growth by light plays an important role in the early development of a seedling, and consequently the homogeneity of the culture. The present study focuses on the importance of tomato 14-3-3/TFT proteins in this process. We provide here the first report of 14-3-3 interactome in the regulation of light-induced de-etiolation and subsequent photomorphogenesis. Our data provide new insights into light-induced de-etiolation and open new horizons for dissecting the post-transcriptional regulations.
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Affiliation(s)
- Petra Hloušková
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University in Olomouc, Šlechtitelu 27, 783 71 Olomouc, Czechia
| | - Martin Černý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czechia
| | - Nikola Kořínková
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University in Olomouc, Šlechtitelu 27, 783 71 Olomouc, Czechia
| | - Markéta Luklová
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czechia
| | - Eugenio Gómez Minguet
- Instituto de Biología Molecular y Celular de Plantas (UPV-Consejo Superior de Investigaciones Científicas), Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Břetislav Brzobohatý
- Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR and CEITEC-Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czechia
| | - Petr Galuszka
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University in Olomouc, Šlechtitelu 27, 783 71 Olomouc, Czechia
| | - Véronique Bergougnoux
- Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University in Olomouc, Šlechtitelu 27, 783 71 Olomouc, Czechia.
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Gonzalez ME, Marco F, Minguet EG, Carrasco-Sorli P, Blázquez MA, Carbonell J, Ruiz OA, Pieckenstain FL. Perturbation of spermine synthase gene expression and transcript profiling provide new insights on the role of the tetraamine spermine in Arabidopsis defense against Pseudomonas viridiflava. Plant Physiol 2011; 156:2266-77. [PMID: 21628628 PMCID: PMC3149955 DOI: 10.1104/pp.110.171413] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Accepted: 05/26/2011] [Indexed: 05/18/2023]
Abstract
The role of the tetraamine spermine in plant defense against pathogens was investigated by using the Arabidopsis (Arabidopsis thaliana)-Pseudomonas viridiflava pathosystem. The effects of perturbations of plant spermine levels on susceptibility to bacterial infection were evaluated in transgenic plants (35S::spermine synthase [SPMS]) that overexpressed the SPMS gene and accumulated spermine, as well as in spms mutants with low spermine levels. The former exhibited higher resistance to P. viridiflava than wild-type plants, while the latter were more susceptible. Exogenous supply of spermine to wild-type plants also increased disease resistance. Increased resistance provided by spermine was partly counteracted by the polyamine oxidase inhibitor SL-11061, demonstrating that the protective effect of spermine partly depends on its oxidation. In addition, global changes in gene expression resulting from perturbations of spermine levels were analyzed by transcript profiling 35S::SPMS-9 and spms-2 plants. Overexpression of 602 genes was detected in 35S::SPMS-9 plants, while 312 genes were down-regulated, as compared to the wild type. In the spms-2 line, 211 and 158 genes were up- and down-regulated, respectively. Analysis of gene ontology term enrichment demonstrated that many genes overexpressed only in 35S::SPMS-9 participate in pathogen perception and defense responses. Notably, several families of disease resistance genes, transcription factors, kinases, and nucleotide- and DNA/RNA-binding proteins were overexpressed in this line. Thus, a number of spermine-responsive genes potentially involved in resistance to P. viridiflava were identified. The obtained results support the idea that spermine contributes to plant resistance to P. viridiflava.
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Affiliation(s)
| | | | | | | | | | | | | | - Fernando Luis Pieckenstain
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús/Universidad Nacional de San Martín-Consejo Nacional de Investigaciones Científificas y Técnicas, CC 164 (B7130IWA) Chascomus, Argentina (M.E.G., O.A.R., F.L.P.); Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Facultad de Ciencias Biológicas, 46100 Burjassot, Valencia, Spain (F.M., P.C.-S.); Instituto de Biología Molecular y Celular de Plantas (Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas), 46022 Valencia, Spain (E.G.M., M.A.B., J.C.)
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Moyroud E, Minguet EG, Ott F, Yant L, Posé D, Monniaux M, Blanchet S, Bastien O, Thévenon E, Weigel D, Schmid M, Parcy F. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell 2011; 23:1293-306. [PMID: 21515819 PMCID: PMC3101549 DOI: 10.1105/tpc.111.083329] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/22/2011] [Accepted: 04/01/2011] [Indexed: 05/18/2023]
Abstract
Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.
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Affiliation(s)
- Edwige Moyroud
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Eugenio Gómez Minguet
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Felix Ott
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Levi Yant
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - David Posé
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Marie Monniaux
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Sandrine Blanchet
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Olivier Bastien
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Markus Schmid
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - François Parcy
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique, Commissariat à l’Énergie Atomique, Institut National de la Recherche Agronomique, Université Joseph Fourier Grenoble I, 38054 Grenoble, France
- Address correspondence to
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