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Sadaqat M, Fatima K, Azeem F, Shaheen T, Rahman MU, Ali T, Al-Megrin WAI, Tahir Ul Qamar M. Computational analysis and expression profiling of two-component system (TCS) gene family members in mango ( Mangifera indica) indicated their roles in stress response. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24055. [PMID: 38870341 DOI: 10.1071/fp24055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/19/2024] [Indexed: 06/15/2024]
Abstract
The two-component system (TCS) gene family is among the most important signal transduction families in plants and is involved in the regulation of various abiotic stresses, cell growth and division. To understand the role of TCS genes in mango (Mangifera indica ), a comprehensive analysis of TCS gene family was carried out in mango leading to identification of 65 MiTCS genes. Phylogenetic analysis divided MiTCSs into three groups (histidine kinases, histidine-containing phosphotransfer proteins, and response regulators) and 11 subgroups. One tandem duplication and 23 pairs of segmental duplicates were found within the MiTCSs . Promoter analysis revealed that MiTCSs contain a large number of cis -elements associated with environmental stresses, hormone response, light signalling, and plant development. Gene ontology analysis showed their involvement in various biological processes and molecular functions, particularly signal transduction. Protein-protein interaction analysis showed that MiTCS proteins interacted with each other. The expression pattern in various tissues and under many stresses (drought, cold, and disease) showed that expression levels varied among various genes in different conditions. MiTCSs 3D structure predictions showed structural conservation among members of the same groups. This information can be further used to develop improved cultivars and will serve as a foundation for gaining more functional insights into the TCS gene family.
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Affiliation(s)
- Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Farrukh Azeem
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Tayyaba Shaheen
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Mahmood-Ur- Rahman
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Tehreem Ali
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Wafa Abdullah I Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
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Hornai EML, Aycan M, Mitsui T. The Promising B-Type Response Regulator hst1 Gene Provides Multiple High Temperature and Drought Stress Tolerance in Rice. Int J Mol Sci 2024; 25:2385. [PMID: 38397061 PMCID: PMC10889171 DOI: 10.3390/ijms25042385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
High temperatures, drought, and salt stresses severely inhibit plant growth and production due to the effects of climate change. The Arabidopsis ARR1, ARR10, and ARR12 genes were identified as negative salt and drought stress regulators. However, in rice, the tolerance capacity of the hst1 gene, which is orthologous to the ARR1, ARR10, and ARR12 genes, to drought and multiple high temperature and drought stresses remains unknown. At the seedling and reproductive stages, we investigated the drought (DS) high temperature (HT) and multiple high temperature and drought stress (HT+DS) tolerance capacity of the YNU31-2-4 (YNU) genotype, which carries the hst1 gene, and its nearest genomic relative Sister Line (SL), which has a 99% identical genome without the hst1 gene. At the seedling stage, YNU demonstrated greater growth, photosynthesis, antioxidant enzyme activity, and decreased ROS accumulation under multiple HT+DS conditions. The YNU genotype also demonstrated improved yield potential and grain quality due to higher antioxidant enzyme activity and lower ROS generation throughout the reproductive stage under multiple HT+DS settings. Furthermore, for the first time, we discovered that the B-type response regulator hst1 gene controls ROS generation and antioxidant enzyme activities by regulating upstream and downstream genes to overcome yield reduction under multiple high temperatures and drought stress. This insight will help us to better understand the mechanisms of high temperature and drought stress tolerance in rice, as well as the evolution of tolerant crops that can survive increased salinity to provide food security during climate change.
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Affiliation(s)
- Ermelinda Maria Lopes Hornai
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- National Division of Research and Statistics, Timor-Leste Ministry of Agriculture, Fisheries and Forest, Dili 626, Timor-Leste
| | - Murat Aycan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
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Rieger J, Fitz M, Fischer SM, Wallmeroth N, Flores-Romero H, Fischer NM, Brand LH, García-Sáez AJ, Berendzen KW, Mira-Rodado V. Exploring the Binding Affinity of the ARR2 GARP DNA Binding Domain via Comparative Methods. Genes (Basel) 2023; 14:1638. [PMID: 37628689 PMCID: PMC10454580 DOI: 10.3390/genes14081638] [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] [Received: 07/19/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Plants have evolved signaling mechanisms such as the multi-step phosphorelay (MSP) to respond to different internal and external stimuli. MSP responses often result in gene transcription regulation that is modulated through transcription factors such as B-type Arabidopsis response regulator (ARR) proteins. Among these proteins, ARR2 is a key component that is expressed ubiquitously and is involved in many aspects of plant development. Although it has been noted that B-type ARRs bind to their cognate genes through a DNA-binding domain termed the GARP domain, little is known about the structure and function of this type of DNA-binding domain; thus, how ARRs bind to DNA at a structural level is still poorly understood. In order to understand how the MSP functions in planta, it is crucial to unravel both the kinetics as well as the structural identity of the components involved in such interactions. For this reason, this work focusses on resolving how the GARP domain of ARR2 (GARP2) binds to the promoter region of ARR5, one of its native target genes in cytokinin signaling. We have established that GARP2 specifically binds to the ARR5 promoter with three different bi-molecular interaction systems-qDPI-ELISA, FCS, and MST-and we also determined the KD of this interaction. In addition, structural modeling of the GARP2 domain confirms that GARP2 entails a HTH motif, and that protein-DNA interaction most likely occurs via the α3-helix and the N-terminal arm of this domain since mutations in this region hinder ARR2's ability to activate transcription.
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Affiliation(s)
- Janine Rieger
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Michael Fitz
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Stefan Markus Fischer
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Niklas Wallmeroth
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Hector Flores-Romero
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | - Nina Monika Fischer
- Institute for Bioinformatics and Medical Informatics, Tübingen University, 72076 Tübingen, Germany
| | - Luise Helene Brand
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
| | - Ana J. García-Sáez
- Interfaculty Institute of Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
- CECAD Research Center, Institute of Genetics, Cologne University, 51069 Cologne, Germany
| | | | - Virtudes Mira-Rodado
- Center for Plant Molecular Biology (ZMBP), Tübingen University, 72076 Tübingen, Germany
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Sadaqat M, Umer B, Attia KA, Abdelkhalik AF, Azeem F, Javed MR, Fatima K, Zameer R, Nadeem M, Tanveer MH, Sun S, Ercisli S, Nawaz MA. Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress. Front Genet 2023; 14:1142544. [PMID: 37323660 PMCID: PMC10267837 DOI: 10.3389/fgene.2023.1142544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023] Open
Abstract
The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.
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Affiliation(s)
- Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Basit Umer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kotb A. Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amr F. Abdelkhalik
- Biotechnology School, Nile University, Giza, Egypt
- Rice Biotechnology Lab, Rice Research and Training Center, Field Crops Research Institute, ARC, Kafrelshikh, Egypt
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Roshan Zameer
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Majid Nadeem
- Wheat Research Institute, Ayub Agriculture Research Institute, Faisalabad, Pakistan
| | | | - Sangmi Sun
- Department of Biotechnology, Chonnam National University, Yesosu Campus, Yesosu Si, Republic of Korea
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Türkiye
- HGF Agro, Ata Teknokent, Erzurum, Türkiye
| | - Muhammad Amjad Nawaz
- Advanced Engineering School (Agrobiotek), Tomsk State University, Tomsk, Russia
- Center for Research in the Field of Materials and Technologies, Tomsk State University, Tomsk, Russia
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Liu H, Chen R, Li H, Lin J, Wang Y, Han M, Wang T, Wang H, Chen Q, Chen F, Chu P, Liang C, Ren C, Zhang Y, Yang F, Sheng Y, Wei J, Wu X, Yu G. Genome-wide identification and expression analysis of SlRR genes in response to abiotic stress in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:322-333. [PMID: 36457231 DOI: 10.1111/plb.13494] [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: 04/30/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The cytokinin two-component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive. In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type-A, type-B and type-C). Various stress-responsive cis-elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO3 treatments was further investigated by qRT-PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress. We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses.
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Affiliation(s)
- H Liu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - R Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Li
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Lin
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - M Han
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - T Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Q Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - P Chu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Liang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Ren
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Zhang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Yang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Sheng
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Wei
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - X Wu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - G Yu
- Heilongjiang Bayi Agricultural University, Daqing, China
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Integrated Transcriptome and Metabolome Analysis Reveals Phenylpropanoid Biosynthesis and Phytohormone Signaling Contribute to " Candidatus Liberibacter asiaticus" Accumulation in Citrus Fruit Piths (Fluffy Albedo). Int J Mol Sci 2022; 23:ijms232415648. [PMID: 36555287 PMCID: PMC9779719 DOI: 10.3390/ijms232415648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
"Candidatus Liberibacter asiaticus" (CLas) is a phloem-restricted α-proteobacterium that is associated with citrus huanglongbing (HLB), which is the most destructive disease that affects all varieties of citrus. Although midrib is usually used as a material for CLas detection, we recently found that the bacterium was enriched in fruits, especially in the fruit pith. However, no study has revealed the molecular basis of these two parts in responding to CLas infection. Therefore, we performed transcriptome and UHPLC-MS-based targeted and untargeted metabolomics analyses in order to organize the essential genes and metabolites that are involved. Transcriptome and metabolome characterized 4834 differentially expressed genes (DEGs) and 383 differentially accumulated metabolites (DAMs) between the two materials, wherein 179 DEGs and 44 DAMs were affected by HLB in both of the tissues, involving the pathways of phenylpropanoid biosynthesis, phytohormone signaling transduction, starch and sucrose metabolism, and photosynthesis. Notably, we discovered that the gene expression that is related to beta-glucosidase and endoglucanase was up-regulated in fruits. In addition, defense-related gene expression and metabolite accumulation were significantly down-regulated in infected fruits. Taken together, the decreased amount of jasmonic acid, coupled with the reduced accumulation of phenylpropanoid and the increased proliferation of indole-3-acetic acid, salicylic acid, and abscisic acid, compared to leaf midribs, may contribute largely to the enrichment of CLas in fruit piths, resulting in disorders of photosynthesis and starch and sucrose metabolism.
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Lee D, Hua L, Khoshravesh R, Giuliani R, Kumar I, Cousins A, Sage TL, Hibberd JM, Brutnell TP. Engineering chloroplast development in rice through cell-specific control of endogenous genetic circuits. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2291-2303. [PMID: 34328250 PMCID: PMC8541780 DOI: 10.1111/pbi.13660] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
The engineering of C4 photosynthetic activity into the C3 plant rice has the potential to nearly double rice yields. To engineer a two-cell photosynthetic system in rice, the rice bundle sheath (BS) must be rewired to enhance photosynthetic capacity. Here, we show that BS chloroplast biogenesis is enhanced when the transcriptional activator, Oryza sativa Cytokinin GATA transcription factor 1 (OsCGA1), is driven by a vascular specific promoter. Ectopic expression of OsCGA1 resulted in increased BS chloroplast planar area and increased expression of photosynthesis-associated nuclear genes (PhANG), required for the biogenesis of photosynthetically active chloroplasts in BS cells of rice. A further refinement using a DNAse dead Cas9 (dCas9) activation module driven by the same cell-type specific promoter, directed enhanced chloroplast development of the BS cells when gRNA sequences were delivered by the dCas9 module to the promoter of the endogenous OsCGA1 gene. Single gRNA expression was sufficient to mediate the transactivation of both the endogenous gene and a transgenic GUS reporter fused with OsCGA1 promoter. Our results illustrate the potential for tissue-specific dCas9-activation and the co-regulation of genes needed for multistep engineering of C4 rice.
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Affiliation(s)
| | - Lei Hua
- Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Roxana Khoshravesh
- Department of Ecology and Evolutionary Biologythe University of TorontoTorontoONCanada
- Department of Biologythe University of New MexicoAlbuquerqueNMUSA
| | - Rita Giuliani
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | | | - Asaph Cousins
- School of Biological SciencesWashington State UniversityPullmanWAUSA
| | - Tammy L. Sage
- Department of Ecology and Evolutionary Biologythe University of TorontoTorontoONCanada
| | | | - Thomas P. Brutnell
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Joint Laboratory for Photosynthesis Enhancement and C4 Rice DevelopmentBiotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
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Varkonyi-Gasic E, Wang T, Cooney J, Jeon S, Voogd C, Douglas MJ, Pilkington SM, Akagi T, Allan AC. Shy Girl, a kiwifruit suppressor of feminization, restricts gynoecium development via regulation of cytokinin metabolism and signalling. THE NEW PHYTOLOGIST 2021; 230:1461-1475. [PMID: 33503269 DOI: 10.1111/nph.17234] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Kiwifruit (Actinidia chinensis) is a dioecious, long-living woody perennial vine. Reduced generation time and induction of hermaphroditism can accelerate crop improvement and facilitate alternative farming for better food security in the face of climate change. Previous studies identified that CENTRORADIALIS genes CEN and CEN4 act to repress flowering, whilst the male-specific Shy Girl (SyGl) gene with homology to type-C cytokinin response regulators could repress gynoecium development in model plants. Here we use CRISPR/Cas9 to mutagenize CEN, CEN4 and SyGl in the male kiwifruit A. chinensis 'Bruce'. Biallelic mutations of CEN and CEN4 generated rapid-flowering male plants, and simultaneous targeting of CEN4 and SyGl gave rise to rapid-flowering hermaphrodites with restored gynoecial function and viable pollen, providing functional evidence for the role of SyGl in suppression of feminization. Analysis of ovary tissues identified genes that contribute to carpel development and revealed that SyGl affected both cytokinin profiles and the expression of genes involved in cytokinin metabolism and signalling. The plant lines generated by CEN4/SyGl knockout could self-pollinate and produce fast-flowering offspring. These results establish that SyGI acts as the suppressor of feminization in kiwifruit and demonstrate the potential for accelerated breeding in an outcrossing horticultural woody perennial.
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Affiliation(s)
- Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Tianchi Wang
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Janine Cooney
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hamilton, 3240, New Zealand
| | - Subin Jeon
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Charlotte Voogd
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Mikaela J Douglas
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Sarah M Pilkington
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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The genetic framework of shoot regeneration in Arabidopsis comprises master regulators and conditional fine-tuning factors. Commun Biol 2020; 3:549. [PMID: 33009513 PMCID: PMC7532540 DOI: 10.1038/s42003-020-01274-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Clonal propagation and genetic engineering of plants requires regeneration, but many species are recalcitrant and there is large variability in explant responses. Here, we perform a genome-wide association study using 190 natural Arabidopsis accessions to dissect the genetics of shoot regeneration from root explants and several related in vitro traits. Strong variation is found in the recorded phenotypes and association mapping pinpoints a myriad of quantitative trait genes, including prior candidates and potential novel regeneration determinants. As most of these genes are trait- and protocol-specific, we propose a model wherein shoot regeneration is governed by many conditional fine-tuning factors and a few universal master regulators such as WUSCHEL, whose transcript levels correlate with natural variation in regenerated shoot numbers. Potentially novel genes in this last category are AT3G09925, SUP, EDA40 and DOF4.4. We urge future research in the field to consider multiple conditions and genetic backgrounds. Robin Lardon et al. report a genome-wide association study of shoot regeneration in Arabidopsis under 2 different in vitro incubation conditions. They find wide variation in regeneration phenotypes, attributable to allelic variants in key developmental genes, and show that genetic association patterns differ depending on environmental factors.
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10
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Huo R, Liu Z, Yu X, Li Z. The Interaction Network and Signaling Specificity of Two-Component System in Arabidopsis. Int J Mol Sci 2020; 21:ijms21144898. [PMID: 32664520 PMCID: PMC7402358 DOI: 10.3390/ijms21144898] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 01/25/2023] Open
Abstract
Two-component systems (TCS) in plants have evolved into a more complicated multi-step phosphorelay (MSP) pathway, which employs histidine kinases (HKs), histidine-containing phosphotransfer proteins (HPts), and response regulators (RRs) to regulate various aspects of plant growth and development. How plants perceive the external signals, then integrate and transduce the secondary signals specifically to the desired destination, is a fundamental characteristic of the MSP signaling network. The TCS elements involved in the MSP pathway and molecular mechanisms of signal transduction have been best understood in the model plant Arabidopsis thaliana. In this review, we focus on updated knowledge on TCS signal transduction in Arabidopsis. We first present a brief description of the TCS elements; then, the protein–protein interaction network is established. Finally, we discuss the possible molecular mechanisms involved in the specificity of the MSP signaling at the mRNA and protein levels.
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Affiliation(s)
- Ruxue Huo
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China;
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China
| | - Zhenning Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi 276000, China
- Correspondence: (Z.L.); (Z.L.)
| | - Xiaolin Yu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China;
- Correspondence: (Z.L.); (Z.L.)
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Cronk Q, Soolanayakanahally R, Bräutigam K. Gene expression trajectories during male and female reproductive development in balsam poplar (Populus balsamifera L.). Sci Rep 2020; 10:8413. [PMID: 32439903 PMCID: PMC7242425 DOI: 10.1038/s41598-020-64938-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Plant reproductive development from the first appearance of reproductively committed axes through to floral maturation requires massive and rapid remarshalling of gene expression. In dioecious species such as poplar this is further complicated by divergent male and female developmental programs. We used seven time points in male and female balsam poplar (Populus balsamifera L.) buds and catkins representing the full annual flowering cycle, to elucidate the effects of time and sex on gene expression during reproductive development. Time (developmental stage) is dominant in patterning gene expression with the effect of sex nested within this. Here, we find (1) evidence for five successive waves of alterations to the chromatin landscape which may be important in setting the overall reproductive trajectory, regardless of sex. (2) Each individual developmental stage is further characterized by marked sex-differential gene expression. (3) Consistent sexually differentiated gene expression regardless of developmental stage reveal candidates for high-level regulators of sex and include the female-specific poplar ARR17 homologue. There is also consistent male-biased expression of the MADS-box genes PISTILLATA and APETALA3. Our work provides insights into expression trajectories shaping reproductive development, its potential underlying mechanisms, and sex-specific translation of the genome information into reproductive structures in balsam poplar.
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Affiliation(s)
- Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, SK, S0G 2K0, Canada
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L 1C6, Canada.
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Kroll CK, Brenner WG. Cytokinin Signaling Downstream of the His-Asp Phosphorelay Network: Cytokinin-Regulated Genes and Their Functions. FRONTIERS IN PLANT SCIENCE 2020; 11:604489. [PMID: 33329676 PMCID: PMC7718014 DOI: 10.3389/fpls.2020.604489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/26/2020] [Indexed: 05/17/2023]
Abstract
The plant hormone cytokinin, existing in several molecular forms, is perceived by membrane-localized histidine kinases. The signal is transduced to transcription factors of the type-B response regulator family localized in the nucleus by a multi-step histidine-aspartate phosphorelay network employing histidine phosphotransmitters as shuttle proteins across the nuclear envelope. The type-B response regulators activate a number of primary response genes, some of which trigger in turn further signaling events and the expression of secondary response genes. Most genes activated in both rounds of transcription were identified with high confidence using different transcriptomic toolkits and meta analyses of multiple individual published datasets. In this review, we attempt to summarize the existing knowledge about the primary and secondary cytokinin response genes in order to try connecting gene expression with the multitude of effects that cytokinin exerts within the plant body and throughout the lifespan of a plant.
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New Insights into Multistep-Phosphorelay (MSP)/ Two-Component System (TCS) Regulation: Are Plants and Bacteria that Different? PLANTS 2019; 8:plants8120590. [PMID: 31835810 PMCID: PMC6963811 DOI: 10.3390/plants8120590] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/27/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022]
Abstract
The Arabidopsis multistep-phosphorelay (MSP) is a signaling mechanism based on a phosphorelay that involves three different types of proteins: Histidine kinases, phosphotransfer proteins, and response regulators. Its bacterial equivalent, the two-component system (TCS), is the most predominant device for signal transduction in prokaryotes. The TCS has been extensively studied and is thus generally well-understood. In contrast, the MSP in plants was first described in 1993. Although great advances have been made, MSP is far from being completely comprehended. Focusing on the model organism Arabidopsis thaliana, this review summarized recent studies that have revealed many similarities with bacterial TCSs regarding how TCS/MSP signaling is regulated by protein phosphorylation and dephosphorylation, protein degradation, and dimerization. Thus, comparison with better-understood bacterial systems might be relevant for an improved study of the Arabidopsis MSP.
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