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Azarova DS, Omelyanchuk NA, Mironova VV, Zemlyanskaya EV, Lavrekha VV. DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning. Vavilovskii Zhurnal Genet Selektsii 2023; 27:890-897. [PMID: 38213710 PMCID: PMC10777285 DOI: 10.18699/vjgb-23-103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 01/13/2024] Open
Abstract
To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool's efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.
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Affiliation(s)
- D S Azarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Omelyanchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V V Mironova
- Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, the Netherlands
| | - E V Zemlyanskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V V Lavrekha
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Tsukanov AV, Mironova VV, Levitsky VG. Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis. Front Plant Sci 2022; 13:938545. [PMID: 35968123 PMCID: PMC9373801 DOI: 10.3389/fpls.2022.938545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/05/2022] [Indexed: 05/15/2023]
Abstract
Position weight matrix (PWM) is the traditional motif model representing the transcription factor (TF) binding sites. It proposes that the positions contribute independently to TFs binding affinity, although this hypothesis does not fit the data perfectly. This explains why PWM hits are missing in a substantial fraction of ChIP-seq peaks. To study various modes of the direct binding of plant TFs, we compiled the benchmark collection of 111 ChIP-seq datasets for Arabidopsis thaliana, and applied the traditional PWM, and two alternative motif models BaMM and SiteGA, proposing the dependencies of the positions. The variation in the stringency of the recognition thresholds for the models proposed that the hits of PWM, BaMM, and SiteGA models are associated with the sites of high/medium, any, and low affinity, respectively. At the medium recognition threshold, about 60% of ChIP-seq peaks contain PWM hits consisting of conserved core consensuses, while BaMM and SiteGA provide hits for an additional 15% of peaks in which a weaker core consensus is compensated through intra-motif dependencies. The presence/absence of these dependencies in the motifs of alternative/traditional models was confirmed by the dependency logo DepLogo visualizing the position-wise partitioning of the alignments of predicted sites. We exemplify the detailed analysis of ChIP-seq profiles for plant TFs CCA1, MYC2, and SEP3. Gene ontology (GO) enrichment analysis revealed that among the three motif models, the SiteGA had the highest portions of genes with the significantly enriched GO terms among all predicted genes. We showed that both alternative motif models provide for traditional PWM greater extensions in predicted sites for TFs MYC2/SEP3 with condition/tissue specific functions, compared to those for TF CCA1 with housekeeping functions. Overall, the combined application of standard and alternative motif models is beneficial to detect various modes of the direct TF-DNA interactions in the maximal portion of ChIP-seq loci.
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Affiliation(s)
- Anton V. Tsukanov
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Victoria V. Mironova
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk, Russia
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, Netherlands
| | - Victor G. Levitsky
- Department of Systems Biology, Institute of Cytology and Genetics, Novosibirsk, Russia
- Department of Natural Science, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Victor G. Levitsky
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Shi D, Jouannet V, Agustí J, Kaul V, Levitsky V, Sanchez P, Mironova VV, Greb T. Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. Plant Cell 2021; 33:200-223. [PMID: 33582756 PMCID: PMC8136906 DOI: 10.1093/plcell/koaa019] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 05/06/2023]
Abstract
Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.
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Affiliation(s)
- Dongbo Shi
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Virginie Jouannet
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Javier Agustí
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), C/Enginyer Fausto Elio S/N. 46011 Valencia, Spain
| | - Verena Kaul
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Victor Levitsky
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Pablo Sanchez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria V Mironova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Author for correspondence:
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Savina MS, Mironova VV. PlantLayout pipeline to model tissue patterning. Vavilovskii Zhurnal Genet Selektsii 2021; 24:102-107. [PMID: 33659787 PMCID: PMC7716512 DOI: 10.18699/vj20.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To study the mechanisms underlying developmental pattern formation in a tissue, one needs to analyze the dynamics of the regulators in time and space across the tissue of a specific architecture. This problem is essential for the developmental regulators (morphogens) that distribute over the tissues anisotropically, forming there maxima and gradients and guiding cellular processes in a dose-dependent manner. Here we present the PlantLayout pipeline for MATLAB software, which facilitates the computational studies of tissue patterning. With its help, one can build a structural model of a two-dimensional tissue, embed it into a mathematical model in ODEs, perform numerical simulations, and visualize the obtained results - everything on the same platform. As a result, one can study the concentration dynamics of developmental regulators over the cell layout reconstructed from the real tissue. PlantLayout allows studying the dynamics and the output of gene networks guided by the developmental regulator in specific cells. The gene networks could be different for different cell types. One of the obstacles that PlantLayout removes semi-automatically is the determination of the cell wall orientation which is relevant when cells in the tissue have a polarity. Additionally, PlantLayout allows automatically extracting other quantitative and qualitative features of the cells and the cell walls, which might help in the modeling of a developmental pattern, such as the length and the width of the cell walls, the set of the neighboring cells, cell volume and cell perimeter. We demonstrate PlantLayout performance on the model of phytohormone auxin distribution over the plant root tip.
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Affiliation(s)
- M S Savina
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V V Mironova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Abstract
The protocol allows to define and characterize mitosis distribution patterns in the plant root meristem. The method does not require genetic markers, which makes it applicable to plants of different non-transgenic genotypes, including ecotypes, mutants, and non-model plant species. Computer analysis of the mitosis distribution in three dimensions with iRoCS Toolbox identifies statistically significant changes in proliferation activity within specific root tissues and cell lineages.
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Affiliation(s)
- Viktoriya V Lavrekha
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- LCTEB, Novosibirsk State University, Novosibirsk, Russia
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | - Victoria V Mironova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- LCTEB, Novosibirsk State University, Novosibirsk, Russia.
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Novikova DD, Cherenkov PA, Sizentsova YG, Mironova VV. metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. Genes (Basel) 2020; 11:genes11060634. [PMID: 32526881 PMCID: PMC7348973 DOI: 10.3390/genes11060634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism’s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals.
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Affiliation(s)
- Daria D. Novikova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Pavel A. Cherenkov
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
| | - Yana G. Sizentsova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, Lavrentyeva avenue 10, 630090 Novosibirsk, Russia; (D.D.N.); (Y.G.S.)
- Novosibirsk State University, 2 Pirogova Street, 630090 Novosibirsk, Russia;
- Correspondence:
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Wiebe DS, Omelyanchuk NA, Mukhin AM, Grosse I, Lashin SA, Zemlyanskaya EV, Mironova VV. Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. Genes (Basel) 2020; 11:genes11040434. [PMID: 32316383 PMCID: PMC7230499 DOI: 10.3390/genes11040434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.
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Affiliation(s)
- Daniil S. Wiebe
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Nadezhda A. Omelyanchuk
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Aleksei M. Mukhin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Sergey A. Lashin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria V. Mironova
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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8
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Savina MS, Pasternak T, Omelyanchuk NA, Novikova DD, Palme K, Mironova VV, Lavrekha VV. Cell Dynamics in WOX5-Overexpressing Root Tips: The Impact of Local Auxin Biosynthesis. Front Plant Sci 2020; 11:560169. [PMID: 33193486 PMCID: PMC7642516 DOI: 10.3389/fpls.2020.560169] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/16/2020] [Indexed: 05/18/2023]
Abstract
Root stem cell niche functioning requires the formation and maintenance of the specific "auxin-rich domain" governed by directional auxin transport and local auxin production. Auxin maximum co-localizes with the WOX5 expression domain in the quiescent center that separates mitotically active proximal and distal root meristems. Here we unravel the interconnected processes happening under WOX5 overexpression by combining in vivo experiments and mathematical modeling. We showed that WOX5-induced TAA1-mediated auxin biosynthesis is the cause, whereas auxin accumulation, PIN transporters relocation, and auxin redistribution between proximal and distal root meristems are its subsequent effects that influence the formation of the well-described phenotype with an enlarged root cap. These findings helped us to clarify the role of WOX5, which serves as a local QC-specific regulator that activates biosynthesis of non-cell-autonomous signal auxin to regulate the distal meristem functioning. The mathematical model with WOX5-mediated auxin biosynthesis and auxin-regulated cell growth, division, and detachment reproduces the columella cells dynamics in both wild type and under WOX5 dysregulation.
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Affiliation(s)
- Maria S. Savina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | | | | | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, Germany
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
- LCTEB, Novosibirsk State University, Novosibirsk, Russia
| | - Viktoriya V. Lavrekha
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia
- LCTEB, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Viktoriya V. Lavrekha,
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Pasternak T, Groot EP, Kazantsev FV, Teale W, Omelyanchuk N, Kovrizhnykh V, Palme K, Mironova VV. Salicylic Acid Affects Root Meristem Patterning via Auxin Distribution in a Concentration-Dependent Manner. Plant Physiol 2019; 180:1725-1739. [PMID: 31036755 PMCID: PMC6752920 DOI: 10.1104/pp.19.00130] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/17/2019] [Indexed: 05/18/2023]
Abstract
The phytohormone salicylic acid (SA) is well known for its induction of pathogenesis-related proteins and systemic acquired resistance; SA also has specific effects on plant growth and development. Here we analyzed the effect of SA on Arabidopsis (Arabidopsis thaliana) root development. We show that exogenous SA treatment at low (below 50 µM) and high (greater than 50 µM) concentrations affect root meristem development in two different PR1-independent ways. Low-concentration SA promoted adventitious roots and altered architecture of the root apical meristem, whereas high-concentration SA inhibited all growth processes in the root. All exposures to exogenous SA led to changes in auxin synthesis and transport. A wide range of SA treatment concentrations activated auxin synthesis, but the effect of SA on auxin transport was dose dependent. Mathematical modeling of auxin synthesis and transport predicted auxin accumulation or depletion in the root tip following low- or high-concentration SA treatments, respectively. SA-induced auxin accumulation led to the formation of more layers of columella initials, an additional cortical cell layer (middle cortex), and extra files of epidermis, cortex, and endodermis cells. Suppression of SHORT ROOT and activation of CYCLIN D6;1 mediated the changes in radial architecture of the root. We propose that low-concentration SA plays an important role in shaping root meristem structure and root system architecture.
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Affiliation(s)
- Taras Pasternak
- Institute for Biology II, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
| | - Edwin P Groot
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'An 271018, China
| | - Fedor V Kazantsev
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - William Teale
- Institute for Biology II, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
| | - Nadya Omelyanchuk
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vasilina Kovrizhnykh
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Klaus Palme
- Institute for Biology II, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
- Center for Biosystems Analysis, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany
| | - Victoria V Mironova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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Zemlyanskaya EV, Omelyanchuk NA, Ubogoeva EV, Mironova VV. Deciphering Auxin-Ethylene Crosstalk at a Systems Level. Int J Mol Sci 2018; 19:ijms19124060. [PMID: 30558241 PMCID: PMC6321013 DOI: 10.3390/ijms19124060] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 01/17/2023] Open
Abstract
The auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to ethylene are largely dependent on auxin, the key regulator of plant morphogenesis. Auxin, in turn, is capable of inducing ethylene biosynthesis and signaling, making the interaction of these hormones reciprocal. Recent studies discovered a number of molecular events underlying auxin-ethylene crosstalk. In this review, we summarize the results of fine-scale and large-scale experiments on the interactions between the auxin and ethylene pathways in Arabidopsis. We integrate knowledge on molecular crosstalk events, their tissue specificity, and associated phenotypic responses to decipher the crosstalk mechanisms at a systems level. We also discuss the prospects of applying systems biology approaches to study the mechanisms of crosstalk between plant hormones.
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Affiliation(s)
- Elena V Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Nadya A Omelyanchuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena V Ubogoeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Victoria V Mironova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
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11
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Lavrekha VV, Pasternak T, Ivanov VB, Palme K, Mironova VV. 3D analysis of mitosis distribution highlights the longitudinal zonation and diarch symmetry in proliferation activity of the Arabidopsis thaliana root meristem. Plant J 2017; 92:834-845. [PMID: 28921702 DOI: 10.1111/tpj.13720] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/26/2017] [Accepted: 09/04/2017] [Indexed: 05/13/2023]
Abstract
To date CYCB1;1 marker and cortex cell lengths have been conventionally used to determine the proliferation activity of the Arabidopsis root meristem. By creating a 3D map of mitosis distribution we showed that these markers overlooked that stele and endodermis save their potency to divide longer than the cortex and epidermis. Cessation of cell divisions is not a random process, so that mitotic activity within the endodermis and stele shows a diarch pattern. Mitotic activity of all root tissues peaked at the same distance from the quiescent center (QC); however, different tissues stopped dividing at different distances, with cells of the protophloem exiting the cell cycle first and the procambial cells being the last. The robust profile of mitotic activity in the root tip defines the longitudinal zonation in the meristem with the proliferation domain, where all cells are able to divide; and the transition domain, where the cell files cease to divide. 3D analysis of cytokinin deficient and cytokinin signaling mutants showed that their proliferation domain is similar to that of the wild type, but the transition domain is much longer. Our data suggest a strong inhibitory effect of cytokinin on anticlinal cell divisions in the stele.
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Affiliation(s)
- Viktoriya V Lavrekha
- Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia
- LCTEB, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, 630090, Russia
| | - Taras Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, 79104, Germany
| | - Victor B Ivanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Str. 35, 127276, Moscow, Russia
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies University of Freiburg, Freiburg, 79104, Germany
| | - Victoria V Mironova
- Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk, 630090, Russia
- LCTEB, Novosibirsk State University, 2 Pirogova Str., Novosibirsk, 630090, Russia
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12
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Zemlyanskaya EV, Wiebe DS, Omelyanchuk NA, Levitsky VG, Mironova VV. Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L. J Bioinform Comput Biol 2017; 14:1641009. [PMID: 27122321 DOI: 10.1142/s0219720016410092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression.
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Affiliation(s)
- Elena V Zemlyanskaya
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Daniil S Wiebe
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Nadezhda A Omelyanchuk
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Victor G Levitsky
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Victoria V Mironova
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
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13
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Hong JH, Savina M, Du J, Devendran A, Kannivadi Ramakanth K, Tian X, Sim WS, Mironova VV, Xu J. A Sacrifice-for-Survival Mechanism Protects Root Stem Cell Niche from Chilling Stress. Cell 2017. [PMID: 28648662 DOI: 10.1016/j.cell.2017.06.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Temperature has a profound influence on plant and animal development, but its effects on stem cell behavior and activity remain poorly understood. Here, we characterize the responses of the Arabidopsis root to chilling (low but above-freezing) temperature. Chilling stress at 4°C leads to DNA damage predominantly in root stem cells and their early descendants. However, only newly generated/differentiating columella stem cell daughters (CSCDs) preferentially die in a programmed manner. Inhibition of the DNA damage response in these CSCDs prevents their death but makes the stem cell niche more vulnerable to chilling stress. Mathematical modeling and experimental validation indicate that CSCD death results in the re-establishment of the auxin maximum in the quiescent center (QC) and the maintenance of functional stem cell niche activity under chilling stress. This mechanism improves the root's ability to withstand the accompanying environmental stresses and to resume growth when optimal temperatures are restored.
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Affiliation(s)
- Jing Han Hong
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Maria Savina
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk 630090, Russia
| | - Jing Du
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ajay Devendran
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Karthikbabu Kannivadi Ramakanth
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Tian
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Wei Shi Sim
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Victoria V Mironova
- Institute of Cytology and Genetics, Novosibirsk 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk 630090, Russia
| | - Jian Xu
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore.
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14
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Omelyanchuk NA, Kovrizhnykh VV, Oshchepkova EA, Pasternak T, Palme K, Mironova VV. A detailed expression map of the PIN1 auxin transporter in Arabidopsis thaliana root. BMC Plant Biol 2016; 16 Suppl 1:5. [PMID: 26821586 PMCID: PMC4895256 DOI: 10.1186/s12870-015-0685-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
BACKGROUND Theauxin efflux carrier PIN1 is a key mediator of polar auxin transport in developing plant tissues. This is why factors that are supposed to be involved in auxin distribution are frequently tested in the regulation of PIN1 expression. As a result, diverse aspects of PIN1 expression are dispersed across dozens of papers entirely devoted to other specific topics related to the auxin pathway. Integration of these puzzle pieces about PIN1 expression revealed that, along with a recurring pattern, some features of PIN1 expression varied from article to article. To determine if this uncertainty is related to the specific foci of articles or has a basis in the variability of PIN1 gene activity, we performed a comprehensive 3D analysis of PIN1 expression patterns in Arabidopsis thaliana roots. RESULTS We provide here a detailed map of PIN1 expression in the primary root, in the lateral root primordia and at the root-shoot junction. The variability in PIN1 expression pattern observed in individual roots may occur due to differences in auxin distribution between plants. To simulate this effect, we analysed PIN1 expression in the roots from wild type seedlings treated with different IAA concentrations and pin mutants. Most changes in PIN1 expression after exogenous IAA treatment and in pin mutants were also recorded in wild type but with lower frequency and intensity. Comparative studies of exogenous auxin effects on PIN1pro:GUS and PIN1pro:PIN1-GFP plants indicated that a positive auxin effect is explicit at the level of PIN1 promoter activity, whereas the inhibitory effect relates to post-transcriptional regulation. CONCLUSIONS Our results suggest that the PIN1 expression pattern in the root meristem accurately reflects changes in auxin content. This explains the variability of PIN1 expression in the individual roots and makes PIN1 a good marker for studying root meristem activity.
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Affiliation(s)
- N A Omelyanchuk
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - V V Kovrizhnykh
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - E A Oshchepkova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - T Pasternak
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis (ZBSA), BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, 79104, Germany
| | - K Palme
- Institute of Biology II/Molecular Plant Physiology, Centre for BioSystems Analysis (ZBSA), BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, 79104, Germany.
| | - V V Mironova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
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15
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Zemlyanskaya EV, Levitsky VG, Oshchepkov DY, Grosse I, Mironova VV. The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana. Front Plant Sci 2016; 7:2044. [PMID: 28119721 PMCID: PMC5220190 DOI: 10.3389/fpls.2016.02044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/21/2016] [Indexed: 05/08/2023]
Abstract
The plant hormone ethylene regulates numerous developmental processes and stress responses. Ethylene signaling proceeds via a linear pathway, which activates transcription factor (TF) EIN3, a primary transcriptional regulator of ethylene response. EIN3 influences gene expression upon binding to a specific sequence in gene promoters. This interaction, however, might be considerably affected by additional co-factors. In this work, we perform whole genome bioinformatics study to identify the impact of epigenetic factors in EIN3 functioning. The analysis of publicly available ChIP-Seq data on EIN3 binding in Arabidopsis thaliana showed bimodality of distribution of EIN3 binding regions (EBRs) in gene promoters. Besides a sharp peak in close proximity to transcription start site, which is a common binding region for a wide variety of TFs, we found an additional extended peak in the distal promoter region. We characterized all EBRs with respect to the epigenetic status appealing to previously published genome-wide map of nine chromatin states in A. thaliana. We found that the implicit distal peak was associated with a specific chromatin state (referred to as chromatin state 4 in the primary source), which was just poorly represented in the pronounced proximal peak. Intriguingly, EBRs corresponding to this chromatin state 4 were significantly associated with ethylene response, unlike the others representing the overwhelming majority of EBRs related to the explicit proximal peak. Moreover, we found that specific EIN3 binding sequences predicted with previously described model were enriched in the EBRs mapped to the chromatin state 4, but not to the rest ones. These results allow us to conclude that the interplay of genetic and epigenetic factors might cause the distinct modes of EIN3 regulation.
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Affiliation(s)
- Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
- *Correspondence: Elena V. Zemlyanskaya,
| | - Victor G. Levitsky
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
| | - Dmitry Y. Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
| | - Ivo Grosse
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
- Institute of Computer Science, Martin Luther University Halle-WittenbergHalle(Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
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16
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Mironova VV, Omelyanchuk NA, Wiebe DS, Levitsky VG. Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome. BMC Genomics 2014; 15 Suppl 12:S4. [PMID: 25563792 PMCID: PMC4331925 DOI: 10.1186/1471-2164-15-s12-s4] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence analysis of experimentally proven AuxREs, we revealed both an extended nucleotide context pattern for AuxRE itself and three distinct types of its coupling motifs (Y-patch, AuxRE-like, and ABRE-like), which together with AuxRE may form the composite elements. Computational analysis of the genome-wide distribution of the predicted AuxREs and their impact on auxin responsive gene expression allowed us to conclude that: (1) AuxREs are enriched around the transcription start site with the maximum density in 5'UTR; (2) AuxREs mediate auxin responsive up-regulation, not down-regulation. (3) Directly oriented single AuxREs and reverse multiple AuxREs are mostly associated with auxin responsiveness. In the composite AuxRE elements associated with auxin response, ABRE-like and Y-patch are 5'-flanking or overlapping AuxRE, whereas AuxRE-like motif is 3'-flanking. The specificity in location and orientation of the coupling elements suggests them as potential binding sites for ARFs partners.
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17
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Mironova VV, Omelyanchuk NA, Novoselova ES, Doroshkov AV, Kazantsev FV, Kochetov AV, Kolchanov NA, Mjolsness E, Likhoshvai VA. Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance. Ann Bot 2012; 110:349-60. [PMID: 22510326 PMCID: PMC3394645 DOI: 10.1093/aob/mcs069] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/14/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport. The PIN family of auxin transporters plays a critical role in polar auxin transport, and two mechanisms of auxin maximum formation in the RAM based on PIN-mediated auxin transport have been proposed to date: the reverse fountain and the reflected flow mechanisms. METHODS The two mechanisms are combined here in in silico studies of auxin distribution in intact roots and roots cut into two pieces in the proximal meristem region. In parallel, corresponding experiments were performed in vivo using DR5::GFP Arabidopsis plants. KEY RESULTS The reverse fountain and the reflected flow mechanism naturally cooperate for RAM patterning and maintenance in intact root. Regeneration of the RAM in decapitated roots is provided by the reflected flow mechanism. In the excised root tips local auxin biosynthesis either alone or in cooperation with the reverse fountain enables RAM maintenance. CONCLUSIONS The efficiency of a dual-mechanism model in guiding biological experiments on RAM regeneration and maintenance is demonstrated. The model also allows estimation of the concentrations of auxin and PINs in root cells during development and under various treatments. The dual-mechanism model proposed here can be a powerful tool for the study of several different aspects of auxin function in root.
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Affiliation(s)
- V V Mironova
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia.
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18
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Mironova VV, Omelyanchuk NA, Ponomarenko PM, Ponomarenko MP, Kolchanov NA. Specific/nonspecific binding of TBP to promoter DNA of the auxin response factor genes in plants correlated with ARFs function on gene transcription (activator/repressor). DOKL BIOCHEM BIOPHYS 2010; 433:191-6. [PMID: 20714854 DOI: 10.1134/s1607672910040125] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Indexed: 12/20/2022]
Affiliation(s)
- V V Mironova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, Russia
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19
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Mironova VV, Omelyanchuk NA, Yosiphon G, Fadeev SI, Kolchanov NA, Mjolsness E, Likhoshvai VA. A plausible mechanism for auxin patterning along the developing root. BMC Syst Biol 2010; 4:98. [PMID: 20663170 PMCID: PMC2921385 DOI: 10.1186/1752-0509-4-98] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 07/21/2010] [Indexed: 01/09/2023]
Abstract
Background In plant roots, auxin is critical for patterning and morphogenesis. It regulates cell elongation and division, the development and maintenance of root apical meristems, and other processes. In Arabidopsis, auxin distribution along the central root axis has several maxima: in the root tip, in the basal meristem and at the shoot/root junction. The distal maximum in the root tip maintains the stem cell niche. Proximal maxima may trigger lateral or adventitious root initiation. Results We propose a reflected flow mechanism for the formation of the auxin maximum in the root apical meristem. The mechanism is based on auxin's known activation and inhibition of expressed PIN family auxin carriers at low and high auxin levels, respectively. Simulations showed that these regulatory interactions are sufficient for self-organization of the auxin distribution pattern along the central root axis under varying conditions. The mathematical model was extended with rules for discontinuous cell dynamics so that cell divisions were also governed by auxin, and by another morphogen Division Factor which combines the actions of cytokinin and ethylene on cell division in the root. The positional information specified by the gradients of these two morphogens is able to explain root patterning along the central root axis. Conclusion We present here a plausible mechanism for auxin patterning along the developing root, that may provide for self-organization of the distal auxin maximum when the reverse fountain has not yet been formed or has been disrupted. In addition, the proximal maxima are formed under the reflected flow mechanism in response to periods of increasing auxin flow from the growing shoot. These events may predetermine lateral root initiation in a rhyzotactic pattern. Another outcome of the reflected flow mechanism - the predominance of lateral or adventitious roots in different plant species - may be based on the different efficiencies with which auxin inhibits its own transport in different species, thereby distinguishing two main types of plant root architecture: taproot vs. fibrous.
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Affiliation(s)
- Victoria V Mironova
- Institute of Cytology and Genetics, SB RAS, Lavrentyeva 10, Novosibirsk, Russia
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20
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Omel'ianchuk NA, Mironova VV, Kolchanov NA. [Genetics of plant development: integrating data from different observations and experiments in databases]. Genetika 2009; 45:1476-1492. [PMID: 20058795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Genetics of plant development as a scientific discipline integrates experimental evidence from such different fields of biology as embryology, plant anatomy, molecular biology, and genetics, and studies their relationships with ontogeny. To date, traditional publication of scientific studies in form of articles is supplemented by presenting the results of extensive genome-scale experiments in genomics, transcriptomics, proteomics, and phenomics in databases. The information burst, cased both by genome-scale studies and growth in the number of publications, requires the development of general standards of annotating data from different sources for their integration and comparison. In this review, we present classification and analysis of existing databases, in which the user can find various kinds of information essential for studying developmental genetics of plants, and discuss problems of data integration both within the informational resources and among them.
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Likhoshvaĭ VA, Omel'ianchuk NA, Mironova VV, Fadeev SI, Melsness ED, Kolchanov NA. [Mathematical model of auxin distribution in the plant root]. Ontogenez 2007; 38:446-456. [PMID: 18179024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Regulation of plant growth and development by auxin is mediated by the hormone controlled distribution and dose-dependent mechanisms of its action. A mathematical model is proposed, which described the distribution of auxin in the cells extending along the central axis of the Arabidopsis thaliana root. This model reproduces qualitatively both auxin distribution in cells of the root central axis under the normal conditions and under the conditions of decreased active transport and the recovery of auxin distribution and related meristem restoration during root regeneration after ablation of its tip. Different types of distribution of the auxin concentration over the vertical root axis are described, possible variants of root growth and lateral roots formation are proposed, and biological interpretation is given to different regimes of model behavior.
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Akberdin IR, Ozonov EA, Mironova VV, Omelyanchuk NA, Likhoshvai VA, Gorpinchenko DN, Kolchanov NA. A cellular automaton to model the development of primary shoot meristems of Arabidopsis thaliana. J Bioinform Comput Biol 2007; 5:641-50. [PMID: 17636867 DOI: 10.1142/s0219720007002862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2006] [Revised: 02/13/2007] [Accepted: 02/13/2007] [Indexed: 11/18/2022]
Abstract
Development of organisms is a very complex process in which a lot of gene networks of different cell types are integrated. Development of a cellular automaton (Ermentrout and Edelshtein-Keshet, J Theor Biol 160:97-133, 1993) that models the morphodynamics of different cell types is the first step in understanding and analysis of the regulatory mechanisms underlying the functioning of developmental gene networks. A model of a cellular automaton has been developed, which simulates the embryonic development of shoot meristem in Arabidopsis thaliana. The model adequately describes the basic stages in development of this organ in wild and mutant types.
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Affiliation(s)
- Ilya R Akberdin
- Institute of Cytology and Genetics SB RAS, Lavrentieva ave. 10 Novosibirsk, 630090, Russia.
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23
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Meshandin AG, Vaneeva LI, Agapkina NP, Mironova VV, Dargeeva TA. [The use of modified polystyrene plates in solid-phase immunoenzyme analysis for the diagnosis of infections]. Zh Mikrobiol Epidemiol Immunobiol 1993:97-100. [PMID: 8067155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The practical aspects of the theory of the adsorption of bioligands on the plastic surface have been considered and discussed. The possibility of standardizing polystyrene plates, as well as obtaining plates with the predetermined level of adsorption activity with respect to given antigens (antibodies), has been shown with the use of the patented technology for the modification of polystyrene plates. The data on the adsorption of antigens used as an experimental model (human and rabbit immunoglobulin fractions) are presented, and an increase in adsorption activity has been shown with the use of modified plates. For practical confirmation, some examples of using these plates in actual assay systems intended for the evaluation of HBsAg carriership and antibodies to HIV are given. A considerable increase (2- to 10-fold) of the signal from positive samples has been shown to occur, the signal from negative samples remaining practically unchanged.
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24
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Meshandin AG, Vaneeva LI, Agapkina NP, Mironova VV. [The use of the method of the complete advisability function for evaluating the quality and standardization of the plates in solid-phase EIA]. Zh Mikrobiol Epidemiol Immunobiol 1991:39-41. [PMID: 1882627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An attempt to use the method of the complete advisability function for the evaluation of the quality of plates and their standardization in the enzyme-linked immunosorbent assay (ELISA) has been made. Correlations have been empirically established, thus making it possible to calculate the optimum proportions of different ELISA factors: the dose of the antigen (antibody) and the time of sorption, which ensures the best ELISA results with a given type of plates.
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25
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Kuvshinov VS, Mironova VV, Bogoliubov IS. [A biopsy forceps with a needle for a flexible endoscope]. Med Tekh 1988:58-9. [PMID: 3405069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biopsy forceps with a suture needle were developed. They will enable to increase considerably the efficacy and accuracy of diagnostic procedures in early cancer and precancerous conditions, and the differentiation of malignant and benign affections of internal organs as well.
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Mironova VV, Tkach TM. [Method of ultraphonophoresis of a calcium chloride solution in the combined treatment of periodontal diseases]. Stomatologiia (Mosk) 1981; 60:35-7. [PMID: 6947520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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27
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Mironova VV. [Treatment of apical periodontitis by ultraphonophoresis]. Stomatologiia (Mosk) 1977; 56:63-5. [PMID: 270839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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28
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Mironova VV. [Experimental study of the effectiveness of ultraphonokhoresis in treating apical periodontitis]. Stomatologiia (Mosk) 1977; 56:75-8. [PMID: 269532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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