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Nicolas Mala KL, Skalak J, Zemlyanskaya E, Dolgikh V, Jedlickova V, Robert HS, Havlickova L, Panzarova K, Trtilek M, Bancroft I, Hejatko J. Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses: insights from comparative analysis of Brassica type-A response regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:6346-6368. [PMID: 39171371 PMCID: PMC11523033 DOI: 10.1093/jxb/erae335] [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: 06/06/2024] [Accepted: 08/21/2024] [Indexed: 08/23/2024]
Abstract
Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development and adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of the MSP cascade and cytokinin primary response genes, are thought to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, transcriptional data also suggest the involvement of RRA genes in stress-related responses. By employing evolutionary conservation with the well-characterized Arabidopsis thaliana RRA genes, we identified five and 38 novel putative RRA genes in Brassica oleracea and Brassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs of ARR3, ARR6, and ARR16 as singletons during the evolution of Brassicaceae. We categorized RRA genes based on the kinetics of their cytokinin-mediated up-regulation and observed both similarities and specificities in this type of response across Brassicaceae species. Using bioinformatic analysis and experimental data demonstrating the cytokinin and abiotic stress responsiveness of the A. thaliana-derived TCSv2 reporter, we unveil the mechanistic conservation of cytokinin- and stress-mediated up-regulation of RRA genes in B. rapa and B. napus. Notably, we identify partial cytokinin dependency of cold stress-induced RRA transcription, thus further demonstrating the role of cytokinin signaling in crop adaptive responses.
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Affiliation(s)
- Katrina Leslie Nicolas Mala
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Jan Skalak
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Elena Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Vladislav Dolgikh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Veronika Jedlickova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | - Helene S Robert
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
| | | | - Klara Panzarova
- PSI (Photon Systems Instruments), Ltd, Drásov, 66424 Drásov, Czech Republic
| | - Martin Trtilek
- PSI (Photon Systems Instruments), Ltd, Drásov, 66424 Drásov, Czech Republic
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
| | - Jan Hejatko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A2, 625 00 Brno, Czech Republic
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Saha SR, Islam SMS, Itoh K. Identification of abiotic stress-responsive genes: a genome-wide analysis of the cytokinin response regulator gene family in rice. Genes Genet Syst 2024; 99:n/a. [PMID: 38945898 DOI: 10.1266/ggs.24-00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
Response regulators (RRs) are implicated in various developmental processes as well as environmental responses by acting as either positive or negative regulators, and are crucial components of cytokinin signaling in plants. We characterized 36 RRs in rice (Oryza sativa L.; Os) using in silico analysis of publicly available data. A comprehensive analysis of OsRR family members covered their physicochemical properties, chromosomal distribution, subcellular localization, phylogeny, gene structure, distribution of conserved motifs and domains, and gene duplication events. Gene Ontology analysis indicated that 22 OsRR genes contribute mainly to the cytokinin response and signal transduction. Predicted cis-elements in RR promoter sequences related to phytohormones and abiotic stresses indicated that RRs are involved in hormonal and environmental responses, supporting previous studies. MicroRNA (miRNA) target analysis showed that 148 miRNAs target 29 OsRR genes. In some cases, multiple RRs are targets of the same miRNA group, and may be controlled by common stimulus responses. Based on the analysis of publicly available gene expression data, OsRR4, OsRR6, OsRR9, OsRR10, OsRR22, OsPRR73 and OsPRR95 were found to be involved in responses to abiotic stresses. Using quantitative reverse transcription polymerase chain reaction we confirmed that six of these RRs, namely OsRR4, OsRR6, OsRR9, OsRR10, OsRR22 and OsPRR73, are involved in the response to salinity, osmotic, alkaline and wounding stresses, and can potentially be used as models to understand molecular mechanisms underlying stress responsiveness.
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Affiliation(s)
- Setu Rani Saha
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University
| | | | - Kimiko Itoh
- Institute of Science and Technology, Niigata University
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Shi Y, Ding G, Shen H, Li Z, Li H, Xiao G. Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice. FRONTIERS IN PLANT SCIENCE 2024; 14:1309802. [PMID: 38273943 PMCID: PMC10809405 DOI: 10.3389/fpls.2023.1309802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Introduction As one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown. Results In present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter. Discussion Collectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.
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Affiliation(s)
- Yanping Shi
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Guohua Ding
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Haitao Shen
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Zihan Li
- Geosystems Research Institute, Mississippi State University, Starkville, MS, United States
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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