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Pahal S, Srivastava H, Saxena S, Tribhuvan KU, Kaila T, Sharma S, Grewal S, Singh NK, Gaikwad K. Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.). Genes Genomics 2024; 46:65-94. [PMID: 37985548 DOI: 10.1007/s13258-023-01460-z] [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: 04/26/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity. OBJECTIVE Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea. METHODS The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs. RESULTS 1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response. CONCLUSION In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.
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Affiliation(s)
- Suman Pahal
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | | | - Swati Saxena
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sapna Grewal
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India.
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.
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Jameson PE. Cytokinin Translocation to, and Biosynthesis and Metabolism within, Cereal and Legume Seeds: Looking Back to Inform the Future. Metabolites 2023; 13:1076. [PMID: 37887400 PMCID: PMC10609209 DOI: 10.3390/metabo13101076] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Early in the history of cytokinins, it was clear that Zea mays seeds contained not just trans-zeatin, but its nucleosides and nucleotides. Subsequently, both pods and seeds of legumes and cereal grains have been shown to contain a complex of cytokinin forms. Relative to the very high quantities of cytokinin detected in developing seeds, only a limited amount appears to have been translocated from the parent plant. Translocation experiments, and the detection of high levels of endogenous cytokinin in the maternal seed coat tissues of legumes, indicates that cytokinin does not readily cross the maternal/filial boundary, indicating that the filial tissues are autonomous for cytokinin biosynthesis. Within the seed, trans-zeatin plays a key role in sink establishment and it may also contribute to sink strength. The roles, if any, of the other biologically active forms of cytokinin (cis-zeatin, dihydrozeatin and isopentenyladenine) remain to be elucidated. The recent identification of genes coding for the enzyme that leads to the biosynthesis of trans-zeatin in rice (OsCYP735A3 and 4), and the identification of a gene coding for an enzyme (CPN1) that converts trans-zeatin riboside to trans-zeatin in the apoplast, further cements the key role played by trans-zeatin in plants.
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Affiliation(s)
- Paula E Jameson
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
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Fatima K, Sadaqat M, Azeem F, Rao MJ, Albekairi NA, Alshammari A, Tahir ul Qamar M. Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp . revealed their role in multiple stresses. Front Genet 2023; 14:1252020. [PMID: 37799143 PMCID: PMC10547876 DOI: 10.3389/fgene.2023.1252020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.
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Affiliation(s)
- Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Farrukh Azeem
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
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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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Cervantes-Pérez SA, Thibivilliers S, Laffont C, Farmer AD, Frugier F, Libault M. Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume. MOLECULAR PLANT 2022; 15:1868-1888. [PMID: 36321199 DOI: 10.1016/j.molp.2022.10.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Medicago truncatula is a model legume species that has been studied for decades to understand the symbiotic relationship between legumes and soil bacteria collectively named rhizobia. This symbiosis called nodulation is initiated in roots with the infection of root hair cells by the bacteria, as well as the initiation of nodule primordia from root cortical, endodermal, and pericycle cells, leading to the development of a new root organ, the nodule, where bacteria fix and assimilate the atmospheric dinitrogen for the benefit of the plant. Here, we report the isolation and use of the nuclei from mock and rhizobia-inoculated roots for the single nuclei RNA-seq (sNucRNA-seq) profiling to gain a deeper understanding of early responses to rhizobial infection in Medicago roots. A gene expression map of the Medicago root was generated, comprising 25 clusters, which were annotated as specific cell types using 119 Medicago marker genes and orthologs to Arabidopsis cell-type marker genes. A focus on root hair, cortex, endodermis, and pericycle cell types, showing the strongest differential regulation in response to a short-term (48 h) rhizobium inoculation, revealed not only known genes and functional pathways, validating the sNucRNA-seq approach, but also numerous novel genes and pathways, allowing a comprehensive analysis of early root symbiotic responses at a cell type-specific level.
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Affiliation(s)
- Sergio Alan Cervantes-Pérez
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Paris-Cité, Université d'Evry, 91190 Gif-sur-Yvette, France
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68503, USA; Single Cell Genomics Core Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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6
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Sauviac L, Rémy A, Huault E, Dalmasso M, Kazmierczak T, Jardinaud MF, Legrand L, Moreau C, Ruiz B, Cazalé AC, Valière S, Gourion B, Dupont L, Gruber V, Boncompagni E, Meilhoc E, Frendo P, Frugier F, Bruand C. A dual legume-rhizobium transcriptome of symbiotic nodule senescence reveals coordinated plant and bacterial responses. PLANT, CELL & ENVIRONMENT 2022; 45:3100-3121. [PMID: 35781677 DOI: 10.1111/pce.14389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Senescence determines plant organ lifespan depending on aging and environmental cues. During the endosymbiotic interaction with rhizobia, legume plants develop a specific organ, the root nodule, which houses nitrogen (N)-fixing bacteria. Unlike earlier processes of the legume-rhizobium interaction (nodule formation, N fixation), mechanisms controlling nodule senescence remain poorly understood. To identify nodule senescence-associated genes, we performed a dual plant-bacteria RNA sequencing approach on Medicago truncatula-Sinorhizobium meliloti nodules having initiated senescence either naturally (aging) or following an environmental trigger (nitrate treatment or salt stress). The resulting data allowed the identification of hundreds of plant and bacterial genes differentially regulated during nodule senescence, thus providing an unprecedented comprehensive resource of new candidate genes associated with this process. Remarkably, several plant and bacterial genes related to the cell cycle and stress responses were regulated in senescent nodules, including the rhizobial RpoE2-dependent general stress response. Analysis of selected core nodule senescence plant genes allowed showing that MtNAC969 and MtS40, both homologous to leaf senescence-associated genes, negatively regulate the transition between N fixation and senescence. In contrast, overexpression of a gene involved in the biosynthesis of cytokinins, well-known negative regulators of leaf senescence, may promote the transition from N fixation to senescence in nodules.
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Affiliation(s)
- Laurent Sauviac
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Antoine Rémy
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Emeline Huault
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | | | - Théophile Kazmierczak
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Marie-Françoise Jardinaud
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Ludovic Legrand
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Corentin Moreau
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Anne-Claire Cazalé
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | | | - Benjamin Gourion
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | | | - Véronique Gruber
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | | | - Eliane Meilhoc
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
| | - Pierre Frendo
- Université Côte d'Azur, INRAE, CNRS, ISA, Nice, France
| | - Florian Frugier
- Institute of Plant Sciences-Paris Saclay (IPS2), Paris-Saclay University, CNRS, INRAE, Université de Paris, Gif-sur-Yvette, France
| | - Claude Bruand
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), Université de Toulouse, INRAE, CNRS, INPT-ENSAT, INSA, Castanet-Tolosan, France
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Tran LH, Urbanowicz A, Jasiński M, Jaskolski M, Ruszkowski M. 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2021; 12:756341. [PMID: 34630499 PMCID: PMC8498639 DOI: 10.3389/fpls.2021.756341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Cytokinins are phytohormones regulating many biological processes that are vital to plants. CYTOKININ RESPONSE1 (CRE1), the main cytokinin receptor, has a modular architecture composed of a cytokinin-binding CHASE (Cyclases/Histidine kinases Associated Sensory Extracellular) domain, followed by a transmembrane fragment, an intracellular histidine kinase (HK) domain, and a receiver domain (REC). Perception of cytokinin signaling involves (i) a hormone molecule binding to the CHASE domain, (ii) CRE1 autophosphorylation at a conserved His residue in the HK domain, followed by a phosphorelay to (iii) a conserved Asp residue in the REC domain, (iv) a histidine-containing phosphotransfer protein (HPt), and (v) a response regulator (RR). This work focuses on the crystal structures of the REC domain of CRE1 from the model plant Arabidopsis thaliana and from the model legume Medicago truncatula. Both REC domains form tight 3D-domain-swapped dimers. Dimerization of the REC domain agrees with the quaternary assembly of the entire CRE1 but is incompatible with a model of its complex with HPt, suggesting that a considerable conformational change should occur to enable the signal transduction. Indeed, phosphorylation of the REC domain can change the HPt-binding properties of CRE1, as shown by functional studies.
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Affiliation(s)
- Linh H. Tran
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Anna Urbanowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Jasiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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Aremu AO, Plačková L, Egbewale SO, Doležal K, Magadlela A. Soil nutrient status of KwaZulu-Natal savanna and grassland biomes causes variation in cytokinin functional groups and their levels in above-ground and underground parts of three legumes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1337-1351. [PMID: 34220044 PMCID: PMC8212235 DOI: 10.1007/s12298-021-01021-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/30/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Cytokinins (CKs) are involved in several developmental stages in the life-cycle of plants. The CK content in plants and their respective organs are susceptible to changes under different environmental conditions. In the current study, we profiled the CK content in the above and underground organs of three legumes (Lessertia frutescens, Mucuna pruriens and Pisum sativum) grown in soils collected from four locations (Ashburton, Bergville, Hluhluwe and Izingolweni) in KwaZulu-Natal province, South Africa. The quantified CK contents in the three legumes were categorized on the basis of their side chains (isoprenoid, aromatic and furfural) and modifications (e.g. free bases and glucosides). Legume and soil types as well as their interaction significantly influenced the concentrations of CKs. Lessertia frutescens, Mucuna pruriens and Pisum sativum had CK content that ranged from 124-653, 170-670 and 69-595 pmol/g DW, respectively. Substantial quantity (> 600 pmol/g DW) of CK were observed in plants grown in Bergville (above-ground part of Lessertia frutescens) and Izingolweni (underground part of Mucuna pruriens) soils. A total of 28 CK derivatives observed in the legumes comprised of isoprenoid (22), aromatic (5) and furfural (1) side-chain CKs. However, the 16 CK derivatives in Mucuna pruriens were isoprenoid-type based on the side-chain. Generally, a higher ratio of cis-zeatin (cZ) relative to the trans-zeatin (tZ) was evident in the above-ground part of Lessertia frutescens and Pisum sativum for the four soil treatments. In terms of functional and physiological importance of the CKs, the free bases (active form) and ribosides (translocation form) were the most abundant CK in Lessertia frutescens and Pisum sativum. However, N-glucoside, a deactivation/detoxicification product was the most dominant CK in Mucuna pruriens from Hluhluwe and Izingolweni soils. The total CKs in the underground parts of the legumes had a positive significant correlation with the total phosphorus and nitrogen content in the plant as well as the soil nitrogen. Overall, the CK profiles of the legumes were strongly influenced by the soil types. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01021-2.
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Affiliation(s)
- Adeyemi Oladapo Aremu
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000 South Africa
- Indigenous Knowledge Systems (IKS) Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2790 South Africa
| | - Lenka Plačková
- Department of Chemical Biology, Faculty of Science, Palacký University, Slechtitelu 27, 783 71 Olomouc-Holice, Czech Republic
| | - Samson Olufemi Egbewale
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000 South Africa
| | - Karel Doležal
- Department of Chemical Biology, Faculty of Science, Palacký University, Slechtitelu 27, 783 71 Olomouc-Holice, Czech Republic
| | - Anathi Magadlela
- School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban, 4000 South Africa
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Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore? Int J Mol Sci 2021; 22:ijms22094588. [PMID: 33925559 PMCID: PMC8123782 DOI: 10.3390/ijms22094588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.
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Vaughan-Hirsch J, Tallerday EJ, Burr CA, Hodgens C, Boeshore SL, Beaver K, Melling A, Sari K, Kerr ID, Šimura J, Ljung K, Xu D, Liang W, Bhosale R, Schaller GE, Bishopp A, Kieber JJ. Function of the pseudo phosphotransfer proteins has diverged between rice and Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:159-173. [PMID: 33421204 DOI: 10.1111/tpj.15156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
The phytohormone cytokinin plays a significant role in nearly all aspects of plant growth and development. Cytokinin signaling has primarily been studied in the dicot model Arabidopsis, with relatively little work done in monocots, which include rice (Oryza sativa) and other cereals of agronomic importance. The cytokinin signaling pathway is a phosphorelay comprised of the histidine kinase receptors, the authentic histidine phosphotransfer proteins (AHPs) and type-B response regulators (RRs). Two negative regulators of cytokinin signaling have been identified: the type-A RRs, which are cytokinin primary response genes, and the pseudo histidine phosphotransfer proteins (PHPs), which lack the His residue required for phosphorelay. Here, we describe the role of the rice PHP genes. Phylogenic analysis indicates that the PHPs are generally first found in the genomes of gymnosperms and that they arose independently in monocots and dicots. Consistent with this, the three rice PHPs fail to complement an Arabidopsis php mutant (aphp1/ahp6). Disruption of the three rice PHPs results in a molecular phenotype consistent with these elements acting as negative regulators of cytokinin signaling, including the induction of a number of type-A RR and cytokinin oxidase genes. The triple php mutant affects multiple aspects of rice growth and development, including shoot morphology, panicle architecture, and seed fill. In contrast to Arabidopsis, disruption of the rice PHPs does not affect root vascular patterning, suggesting that while many aspects of key signaling networks are conserved between monocots and dicots, the roles of at least some cytokinin signaling elements are distinct.
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Affiliation(s)
| | - Emily J Tallerday
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Christian A Burr
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Charlie Hodgens
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Samantha L Boeshore
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kevin Beaver
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Allison Melling
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kartika Sari
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
- FKIP, Universitas Muhammadiyah Metro, Lampung, 34111, Indonesia
| | - Ian D Kerr
- University of Nottingham, Loughborough, NG7 2UH, UK
| | - Jan Šimura
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), Umeå, 901 83, Sweden
| | - Dawei Xu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanqi Liang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rahul Bhosale
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - G Eric Schaller
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
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Hnatuszko-Konka K, Gerszberg A, Weremczuk-Jeżyna I, Grzegorczyk-Karolak I. Cytokinin Signaling and De Novo Shoot Organogenesis. Genes (Basel) 2021; 12:265. [PMID: 33673064 PMCID: PMC7917986 DOI: 10.3390/genes12020265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/16/2022] Open
Abstract
The ability to restore or replace injured tissues can be undoubtedly named among the most spectacular achievements of plant organisms. One of such regeneration pathways is organogenesis, the formation of individual organs from nonmeristematic tissue sections. The process can be triggered in vitro by incubation on medium supplemented with phytohormones. Cytokinins are a class of phytohormones demonstrating pleiotropic effects and a powerful network of molecular interactions. The present study reviews existing knowledge on the possible sequence of molecular and genetic events behind de novo shoot organogenesis initiated by cytokinins. Overall, the review aims to collect reactions encompassed by cytokinin primary responses, starting from phytohormone perception by the dedicated receptors, to transcriptional reprogramming of cell fate by the last module of multistep-phosphorelays. It also includes a brief reminder of other control mechanisms, such as epigenetic reprogramming.
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Affiliation(s)
- Katarzyna Hnatuszko-Konka
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Aneta Gerszberg
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland;
| | - Izabela Weremczuk-Jeżyna
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
| | - Izabela Grzegorczyk-Karolak
- Department of Biology and Pharmaceutical Botany, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland; (I.W.-J.); (I.G.-K.)
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Tan S, Sanchez M, Laffont C, Boivin S, Le Signor C, Thompson R, Frugier F, Brault M. A Cytokinin Signaling Type-B Response Regulator Transcription Factor Acting in Early Nodulation. PLANT PHYSIOLOGY 2020; 183:1319-1330. [PMID: 32376762 PMCID: PMC7333713 DOI: 10.1104/pp.19.01383] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/27/2020] [Indexed: 05/06/2023]
Abstract
Nitrogen-fixing root nodulation in legumes challenged with nitrogen-limiting conditions requires infection of the root hairs by soil symbiotic bacteria, collectively referred to as rhizobia, and the initiation of cell divisions in the root cortex. Cytokinin hormones are critical for early nodulation to coordinate root nodule organogenesis and the progression of bacterial infections. Cytokinin signaling involves regulation of the expression of cytokinin primary response genes by type-B response regulator (RRB) transcription factors. RNA interference or mutation of MtRRB3, the RRB-encoding gene most strongly expressed in Medicago truncatula roots and nodules, significantly decreased the number of nodules formed, indicating a function of this RRB in nodulation initiation. Fewer infection events were also observed in rrb3 mutant roots associated with a reduced Nod factor induction of the Early Nodulin 11 (MtENOD11) infection marker, and of the cytokinin-regulated Nodulation Signaling Pathway 2 (Mt NSP2) gene. Rhizobial infections correlate with an expansion of the nuclear area, suggesting the activation of endoreduplication cycles linked to the cytokinin-regulated Cell Cycle Switch 52A (Mt CCS52A) gene. Although no significant difference in nucleus size and endoreduplication were detected in rhizobia-infected rrb3 mutant roots, expression of the MtCCS52A endoreduplication marker was reduced. As the MtRRB3 expression pattern overlaps with those of MtNSP2 and MtCCS52A in roots and nodule primordia, chromatin immunoprecipitation-quantitative PCR and protoplast trans-activation assays were used to show that MtRRB3 can interact with and trans-activate MtNSP2 and MtCCS52A promoters. Overall, we highlight that the MtRRB3 cytokinin signaling transcription factor coordinates the expression of key early nodulation genes.
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Affiliation(s)
- Sovanna Tan
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Diderot, INRA, Université d'Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Myriam Sanchez
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Carole Laffont
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Diderot, INRA, Université d'Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Stéphane Boivin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Diderot, INRA, Université d'Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Richard Thompson
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Florian Frugier
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Diderot, INRA, Université d'Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Mathias Brault
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-Diderot, INRA, Université d'Evry, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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Héricourt F, Larcher M, Chefdor F, Koudounas K, Carqueijeiro I, Lemos Cruz P, Courdavault V, Tanigawa M, Maeda T, Depierreux C, Lamblin F, Glévarec G, Carpin S. New Insight into HPts as Hubs in Poplar Cytokinin and Osmosensing Multistep Phosphorelays: Cytokinin Pathway Uses Specific HPts. PLANTS 2019; 8:plants8120591. [PMID: 31835814 PMCID: PMC6963366 DOI: 10.3390/plants8120591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 02/02/2023]
Abstract
We have previously identified proteins in poplar which belong to an osmosensing (OS) signaling pathway, called a multistep phosphorelay (MSP). The MSP comprises histidine-aspartate kinases (HK), which act as membrane receptors; histidine phosphotransfer (HPt) proteins, which act as phosphorelay proteins; and response regulators (RR), some of which act as transcription factors. In this study, we identified the HK proteins homologous to the Arabidopsis cytokinin (CK) receptors, which are first partners in the poplar cytokinin MSP, and focused on specificity of these two MSPs (CK and OS), which seem to share the same pool of HPt proteins. Firstly, we isolated five CK HKs from poplar which are homologous to Arabidopsis AHK2, AHK3, and AHK4, namely, HK2, HK3a, HK3b, HK4a, HK4b. These HKs were shown to be functional kinases, as observed in a functional complementation of a yeast HK deleted strain. Moreover, one of these HKs, HK4a, was shown to have kinase activity dependent on the presence of CK. Exhaustive interaction tests between these five CK HKs and the 10 HPts characterized in poplar were performed using two-hybrid and BiFC experiments. The resulting partnership was compared to that previously identified between putative osmosensors HK1a/1b and HPt proteins. Finally, in planta coexpression analysis of genes encoding these potential partners revealed that almost all HPts are coexpressed with CK HKs in four different poplar organs. Overall, these results allowed us to unravel the common and specific partnerships existing between OS and CK MSP in Populus.
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Affiliation(s)
- François Héricourt
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Mélanie Larcher
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Françoise Chefdor
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Konstantinos Koudounas
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Inês Carqueijeiro
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Pamela Lemos Cruz
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Vincent Courdavault
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Mirai Tanigawa
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Christiane Depierreux
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Frédéric Lamblin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Gaëlle Glévarec
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Sabine Carpin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
- Correspondence: ; Tel.: +33-2-3849-4804
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