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Krasensky-Wrzaczek J, Wrzaczek M. New kids on the block-cysteine-rich receptor-like kinases in pattern-triggered immunity. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102619. [PMID: 39178641 DOI: 10.1016/j.pbi.2024.102619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/26/2024]
Abstract
Plant-specific receptor-like protein kinases (RLKs) are essential for pathogen recognition during pattern-triggered immunity. Together with coreceptors and associated proteins, they act as bona fide immune receptors, perceiving a variety of microbe-associated molecular patterns or damage-associated molecular patterns. The cysteine-rich receptor-like kinases (CRKs) form one of the biggest subgroups of RLKs, but so far, their ligands have not been identified. It has been shown that CRKs play important roles in plant immunity and defense responses as well as in response to abiotic stimuli and in control of plant development. However, molecular information on how CRKs integrate with the known framework of signaling components controlling early defense responses remains enigmatic.
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Affiliation(s)
- Julia Krasensky-Wrzaczek
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Michael Wrzaczek
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 370 05 České Budějovice, Czech Republic.
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2
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Shen L, Xia X, Zhang L, Yang S, Yang X. SmWRKY11 acts as a positive regulator in eggplant response to salt stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108209. [PMID: 38006793 DOI: 10.1016/j.plaphy.2023.108209] [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: 09/11/2023] [Revised: 10/31/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023]
Abstract
Salt stress is one of the most threatening abiotic stresses to plants, which can seriously affect plant growth, development, reproduction, and yield. However, the mechanisms of plant against salt stress largely remain unclear. Herein, SmWRKY11, an assumed WRKY transcription factor, was functionally characterized in eggplant against salt stress. SmWRKY11 was significantly up-regulated by salt, dehydration stress, and ABA treatment. SmWRKY11 located in the nucleus, and the Plant_zn_clust conserved domain exhibited transcriptional activation activity. Silencing of SmWRKY11 enhanced the susceptibility of eggplant to salt stress, accompanied by significantly down-regulation of transcript expression levels of salt stress defense-related genes SmNCED1, SmGSTU10, and positive regulator of salt stress response SmERF1 as well as increase of hydrogen peroxide (H2O2) content and decrease of the enzyme activities of catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX). In addition, silencing of SmERF1 also could significantly down-regulate SmWRKY11 expression in eggplant response to salt stress. By luciferase reporter assay and chromatin immunoprecipitation PCR assay, SmERF1 expression was found to be indirectly activated by SmWRKY11. These data indicate that SmWRKY11 acts as a positive regulator by forming positive feedback loop with SmERF1 via an indirect regulatory manner in eggplant response to salt stress.
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Affiliation(s)
- Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
| | - Longhao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
| | - Shixin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China.
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3
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Gandhi A, Oelmüller R. Emerging Roles of Receptor-like Protein Kinases in Plant Response to Abiotic Stresses. Int J Mol Sci 2023; 24:14762. [PMID: 37834209 PMCID: PMC10573068 DOI: 10.3390/ijms241914762] [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: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The productivity of plants is hindered by unfavorable conditions. To perceive stress signals and to transduce these signals to intracellular responses, plants rely on membrane-bound receptor-like kinases (RLKs). These play a pivotal role in signaling events governing growth, reproduction, hormone perception, and defense responses against biotic stresses; however, their involvement in abiotic stress responses is poorly documented. Plant RLKs harbor an N-terminal extracellular domain, a transmembrane domain, and a C-terminal intracellular kinase domain. The ectodomains of these RLKs are quite diverse, aiding their responses to various stimuli. We summarize here the sub-classes of RLKs based on their domain structure and discuss the available information on their specific role in abiotic stress adaptation. Furthermore, the current state of knowledge on RLKs and their significance in abiotic stress responses is highlighted in this review, shedding light on their role in influencing plant-environment interactions and opening up possibilities for novel approaches to engineer stress-tolerant crop varieties.
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Affiliation(s)
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany;
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4
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Hurst CH, Turnbull D, Xhelilaj K, Myles S, Pflughaupt RL, Kopischke M, Davies P, Jones S, Robatzek S, Zipfel C, Gronnier J, Hemsley PA. S-acylation stabilizes ligand-induced receptor kinase complex formation during plant pattern-triggered immune signaling. Curr Biol 2023; 33:1588-1596.e6. [PMID: 36924767 DOI: 10.1016/j.cub.2023.02.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023]
Abstract
Plant receptor kinases are key transducers of extracellular stimuli, such as the presence of beneficial or pathogenic microbes or secreted signaling molecules. Receptor kinases are regulated by numerous post-translational modifications.1,2,3 Here, using the immune receptor kinases FLS24 and EFR,5 we show that S-acylation at a cysteine conserved in all plant receptor kinases is crucial for function. S-acylation involves the addition of long-chain fatty acids to cysteine residues within proteins, altering their biochemical properties and behavior within the membrane environment.6 We observe S-acylation of FLS2 at C-terminal kinase domain cysteine residues within minutes following the perception of its ligand, flg22, in a BAK1 co-receptor and PUB12/13 ubiquitin ligase-dependent manner. We demonstrate that S-acylation is essential for FLS2-mediated immune signaling and resistance to bacterial infection. Similarly, mutating the corresponding conserved cysteine residue in EFR suppressed elf18-triggered signaling. Analysis of unstimulated and activated FLS2-containing complexes using microscopy, detergents, and native membrane DIBMA nanodiscs indicates that S-acylation stabilizes, and promotes retention of, activated receptor kinase complexes at the plasma membrane to increase signaling efficiency.
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Affiliation(s)
- Charlotte H Hurst
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Dionne Turnbull
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Kaltra Xhelilaj
- ZMBP Universität Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Sally Myles
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robin L Pflughaupt
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Michaela Kopischke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Susan Jones
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Julien Gronnier
- ZMBP Universität Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany; Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Piers A Hemsley
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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5
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Liu Y, Yang H, Wen F, Bao L, Zhao Z, Zhong Z. Chitooligosaccharide-induced plant stress resistance. Carbohydr Polym 2023; 302:120344. [PMID: 36604042 DOI: 10.1016/j.carbpol.2022.120344] [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: 05/31/2022] [Revised: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
In nature, the production of plant stress resistance traits is often induced by extreme environmental conditions. Under extreme conditions, plants can be irreversibly damaged. Intervention with phytostimulants, however, can improve plant stress resistance without causing damage to the plants themselves, hence maintaining the production. For example, exogenous substances such as proteins and polysaccharides can be used effectively as phytostimulants. Chitooligosaccharide, a plant stimulant, can promote seed germination and plant growth and development, and improve plant photosynthesis. In this review, we summarize progress in the research of chitooligosaccharide-induced plant stress resistance. The mechanism and related experiments of chitooligosaccharide-induced resistance to pathogen, drought, low-temperature, saline-alkali, and other stresses are classified and discussed. In addition, we put forward the challenges confronted by chitooligosaccharide-induced plant stress resistance and the future research concept that requires multidisciplinary cooperation, which could provide data for the in-depth study of the effect of chitooligosaccharide on plants.
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Affiliation(s)
- Yao Liu
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Hehe Yang
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Fang Wen
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Liangliang Bao
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Zhao
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhimei Zhong
- College of Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resource, Hohhot 010018, China; Key Laboratory of Agricultural Ecological Security and Green Development at Universities of Inner Mongolia Autonomous Region, Hohhot 010018, China.
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6
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Gutiérrez N, Pégard M, Balko C, Torres AM. Genome-wide association analysis for drought tolerance and associated traits in faba bean ( Vicia faba L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1091875. [PMID: 36818887 PMCID: PMC9928957 DOI: 10.3389/fpls.2023.1091875] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Faba bean (Vicia faba L.) is an important high protein legume adapted to diverse climatic conditions with multiple benefits for the overall sustainability of the cropping systems. Plant-based protein demand is being expanded and faba bean is a good candidate to cover this need. However, the crop is very sensitive to abiotic stresses, especially drought, which severely affects faba bean yield and development worldwide. Therefore, identifying genes associated with drought stress tolerance is a major challenge in faba bean breeding. Although the faba bean response to drought stress has been widely studied, the molecular approaches to improve drought tolerance in this crop are still limited. Here we built on recent genomic advances such as the development of the first high-density SNP genotyping array, to conduct a genome-wide association study (GWAS) using thousands of genetic polymorphisms throughout the entire faba bean genome. A worldwide collection of 100 faba bean accessions was grown under control and drought conditions and 10 morphological, phenological and physiological traits were evaluated to identify single nucleotide polymorphism (SNP) markers associated with drought tolerance. We identified 29 SNP markers significantly correlated with these traits under drought stress conditions. The flanking sequences were blasted to the Medicago truncatula reference genomes in order to annotate potential candidate genes underlying the causal variants. Three of the SNPs for chlorophyll content after the stress, correspond to uncharacterized proteins indicating the presence of novel genes associated with drought tolerance in faba bean. The significance of stress-inducible signal transducers provides valuable information on the possible mechanisms underlying the faba bean response to drought stress, thus providing a foundation for future marker-assisted breeding in the crop.
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Affiliation(s)
- Natalia Gutiérrez
- Área de Mejora y Biotecnología, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, Córdoba, Spain
| | - Marie Pégard
- INRAE P3F, 86600 Lusignan, France, INRA, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | - Christiane Balko
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Ana M. Torres
- Área de Mejora y Biotecnología, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Centro Alameda del Obispo, Córdoba, Spain
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7
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Liu H, Li X, Cai J, Jiang L, Zhang X, Wu D, Wang L, Yang A, Guo C, Chen J, Pu W, Yu F. A screening of inhibitors targeting the receptor kinase FERONIA reveals small molecules that enhance plant root immunity. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:63-77. [PMID: 36121304 PMCID: PMC9829398 DOI: 10.1111/pbi.13925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/24/2022] [Accepted: 09/08/2022] [Indexed: 05/14/2023]
Abstract
Receptor-like kinases (RLKs) constitute the largest receptor family involved in the regulation of plant immunity and growth, but small-molecule inhibitors that target RLKs to improve agronomic traits remain unexplored. The RLK member FERONIA (FER) negatively regulates plant resistance to certain soil-borne diseases that are difficult to control and cause huge losses in crop yields and economy. Here, we identified 33 highly effective FER kinase inhibitors from 1494 small molecules by monitoring FER autophosphorylation in vitro. Four representative inhibitors (reversine, cenisertib, staurosporine and lavendustin A) inhibited the kinase activity of FER and its homologues in several crops by targeting the conserved ATP pocket in the kinase structure. FER contributes to the physiological impact of representative inhibitors in plants. The treatment of roots with reversine, staurosporine and lavendustin A enhanced innate immunity in plant roots and thus alleviated soil-borne diseases in tobacco, tomato and rice without growth penalties. Consistently, RNA sequencing assays showed that lavendustin A and reversine exert profound impacts on immunity-related gene expression. Our results will set a new milestone in the development of the plant RLK kinase regulation theory and provide a novel strategy for the prevention and control of plant soil-borne diseases without growth penalties.
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Affiliation(s)
- Hong‐Bin Liu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
| | - Xiaoxu Li
- Technology CenterChina Tobacco Hunan Industrial Co., Ltd.ChangshaChina
| | - Jun Cai
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
| | - Ling‐Li Jiang
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
| | - Xin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Dousheng Wu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
| | - Lifeng Wang
- State key Laboratory of Hybrid Rice, Hunan Agricultural Biotechnology Research InstituteHunan Academy of Agricultural SciencesChangshaChina
| | - Aiguo Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Cun Guo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Jia Chen
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
| | - Wenxuan Pu
- Technology CenterChina Tobacco Hunan Industrial Co., Ltd.ChangshaChina
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and ChemometricsCollege of Biology, Hunan UniversityChangshaChina
- Yuelushan LaboratoryChangshaChina
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8
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Sun X, Xiang Y, Dou N, Zhang H, Pei S, Franco AV, Menon M, Monier B, Ferebee T, Liu T, Liu S, Gao Y, Wang J, Terzaghi W, Yan J, Hearne S, Li L, Li F, Dai M. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol 2023; 41:120-127. [PMID: 36229611 DOI: 10.1038/s41587-022-01470-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/02/2022] [Indexed: 01/21/2023]
Abstract
The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. Here we carried out genome-wide profiling of the small RNA (sRNA) transcriptome (sRNAome) and transcriptome landscapes of a global maize diversity panel under dry and wet conditions and uncover dozens of environment-specific regulatory hotspots. Transgenic and molecular studies of Drought-Related Environment-specific Super eQTL Hotspot on chromosome 8 (DRESH8) and ZmMYBR38, a target of DRESH8-derived small interfering RNAs, revealed a transposable element-mediated inverted repeats (TE-IR)-derived sRNA- and gene-regulatory network that balances plant drought tolerance with yield-related traits. A genome-wide scan revealed that TE-IRs associate with drought response and yield-related traits that were positively selected and expanded during maize domestication. These results indicate that TE-IR-mediated posttranscriptional regulation is a key molecular mechanism underlying the tradeoff between crop environmental adaptation and yield-related traits, providing potential genomic targets for the breeding of crops with greater stress tolerance but uncompromised yield.
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Affiliation(s)
- Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanli Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Nannan Dou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Surui Pei
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Arcadio Valdes Franco
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Mitra Menon
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, Davis, CA, USA
| | - Brandon Monier
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Taylor Ferebee
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Tao Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Sanyang Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Yuchi Gao
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Jubin Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | | | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Sarah Hearne
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, Texcoco, Mexico
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Feng Li
- Hubei Hongshan Laboratory, Wuhan, China.
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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9
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Transcriptomic Analysis Provides Insight into the ROS Scavenging System and Regulatory Mechanisms in Atriplex canescens Response to Salinity. Int J Mol Sci 2022; 24:ijms24010242. [PMID: 36613685 PMCID: PMC9820716 DOI: 10.3390/ijms24010242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Atriplex canescens is a representative halophyte with excellent tolerance to salt. Previous studies have revealed certain physiological mechanisms and detected functional genes associated with salt tolerance. However, knowledge on the ROS scavenging system and regulatory mechanisms in this species when adapting to salinity is limited. Therefore, this study further analyzed the transcriptional changes in genes related to the ROS scavenging system and important regulatory mechanisms in A. canescens under saline conditions using our previous RNA sequencing data. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation revealed that the differentially expressed genes (DEGs) were highly enriched in signal transduction- and reactive oxygen species-related biological processes, including "response to oxidative stress", "oxidoreductase activity", "protein kinase activity", "transcription factor activity", and "plant hormone signal transduction". Further analyses suggested that the transcription abundance of many genes involved in SOD, the AsA-GSH cycle, the GPX pathway, PrxR/Trx, and the flavonoid biosynthesis pathway were obviously enhanced. These pathways are favorable for scavenging excessive ROS induced by salt and maintaining the integrity of the cell membrane. Meanwhile, many vital transcription factor genes (WRKY, MYB, ZF, HSF, DREB, and NAC) exhibited increased transcripts, which is conducive to dealing with saline conditions by regulating downstream salt-responsive genes. Furthermore, a larger number of genes encoding protein kinases (RLK, CDPK, MAPK, and CTR1) were significantly induced by saline conditions, which is beneficial to the reception/transduction of salt-related signals. This study describes the abundant genetic resources for enhancing the salt tolerance in salt-sensitive plants, especially in forages and crops.
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10
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Ercoli MF, Ramos PZ, Jain R, Pilotte J, Dong OX, Thompson T, Wells CI, Elkins JM, Edwards AM, Couñago RM, Drewry DH, Ronald PC. An open source plant kinase chemogenomics set. PLANT DIRECT 2022; 6:e460. [PMID: 36447653 PMCID: PMC9694430 DOI: 10.1002/pld3.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.
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Affiliation(s)
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - Rashmi Jain
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Joseph Pilotte
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Ty Thompson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Carrow I. Wells
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Jonathan M. Elkins
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
- Centre for Medicines DiscoveryUniversity of OxfordOxfordUK
| | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - David H. Drewry
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
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11
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Wang HL, Yang Q, Tan S, Wang T, Zhang Y, Yang Y, Yin W, Xia X, Guo H, Li Z. Regulation of cytokinin biosynthesis using PtRD26 pro -IPT module improves drought tolerance through PtARR10-PtYUC4/5-mediated reactive oxygen species removal in Populus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:771-786. [PMID: 34990062 DOI: 10.1111/jipb.13218] [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: 11/24/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Drought is a critical environmental factor which constrains plant survival and growth. Genetic engineering provides a credible strategy to improve drought tolerance of plants. Here, we generated transgenic poplar lines expressing the isopentenyl transferase gene (IPT) under the driver of PtRD26 promoter (PtRD26pro -IPT). PtRD26 is a senescence and drought-inducible NAC transcription factor. PtRD26pro -IPT plants displayed multiple phenotypes, including improved growth and drought tolerance. Transcriptome analysis revealed that auxin biosynthesis pathway was activated in the PtRD26pro -IPT plants, leading to an increase in auxin contents. Biochemical analysis revealed that ARABIDOPSIS RESPONSE REGULATOR10 (PtARR10), one of the type-B ARR transcription factors in the cytokinin pathway, was induced in PtRD26pro -IPT plants and directly regulated the transcripts of YUCCA4 (PtYUC4) and YUCCA5 (PtYUC5), two enzymes in the auxin biosynthesis pathway. Overexpression of PtYUC4 enhanced drought tolerance, while simultaneous silencing of PtYUC4/5 evidently attenuated the drought tolerance of PtRD26pro -IPT plants. Intriguingly, PtYUC4/5 displayed a conserved thioredoxin reductase activity that is required for drought tolerance by deterring reactive oxygen species accumulation. Our work reveals the molecular basis of cytokinin and auxin interactions in response to environmental stresses, and shed light on the improvement of drought tolerance without a growth penalty in trees by molecular breeding.
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Affiliation(s)
- Hou-Ling Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qi Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuya Tan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ting Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Zhang
- Department of Biology, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Yanli Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongwei Guo
- Department of Biology, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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12
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Demirjian C, Razavi N, Desaint H, Lonjon F, Genin S, Roux F, Berthomé R, Vailleau F. Study of natural diversity in response to a key pathogenicity regulator of Ralstonia solanacearum reveals new susceptibility genes in Arabidopsis thaliana. MOLECULAR PLANT PATHOLOGY 2022; 23:321-338. [PMID: 34939305 PMCID: PMC8828461 DOI: 10.1111/mpp.13135] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/25/2021] [Accepted: 08/10/2021] [Indexed: 06/12/2023]
Abstract
Ralstonia solanacearum gram-negative phytopathogenic bacterium exerts its virulence through a type III secretion system (T3SS) that translocates type III effectors (T3Es) directly into the host cells. T3E secretion is finely controlled at the posttranslational level by helper proteins, T3SS control proteins, and type III chaperones. The HpaP protein, one of the type III secretion substrate specificity switch (T3S4) proteins, was previously highlighted as a virulence factor on Arabidopsis thaliana Col-0 accession. In this study, we set up a genome-wide association analysis to explore the natural diversity of response to the hpaP mutant of two A. thaliana mapping populations: a worldwide collection and a local population. Quantitative genetic variation revealed different genetic architectures in both mapping populations, with a global delayed response to the hpaP mutant compared to the GMI1000 wild-type strain. We have identified several quantitative trait loci (QTLs) associated with the hpaP mutant inoculation. The genes underlying these QTLs are involved in different and specific biological processes, some of which were demonstrated important for R. solanacearum virulence. We focused our study on four candidate genes, RKL1, IRE3, RACK1B, and PEX3, identified using the worldwide collection, and validated three of them as susceptibility factors. Our findings demonstrate that the study of the natural diversity of plant response to a R. solanacearum mutant in a key regulator of virulence is an original and powerful strategy to identify genes directly or indirectly targeted by the pathogen.
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Affiliation(s)
| | - Narjes Razavi
- LIPME, Université de ToulouseINRAECNRSCastanet‐TolosanFrance
| | - Henri Desaint
- LIPME, Université de ToulouseINRAECNRSCastanet‐TolosanFrance
- SYNGENTA SeedsSarriansFrance
| | - Fabien Lonjon
- LIPME, Université de ToulouseINRAECNRSCastanet‐TolosanFrance
- Present address:
Department of Cell & Systems BiologyUniversity of TorontoTorontoOntarioCanada
| | - Stéphane Genin
- LIPME, Université de ToulouseINRAECNRSCastanet‐TolosanFrance
| | - Fabrice Roux
- LIPME, Université de ToulouseINRAECNRSCastanet‐TolosanFrance
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13
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Kumar J, Gupta DS, Kesari R, Verma R, Murugesan S, Basu PS, Soren KR, Gupta S, Singh NP. Comprehensive RNAseq analysis for identification of genes expressed under heat stress in lentil. PHYSIOLOGIA PLANTARUM 2021; 173:1785-1807. [PMID: 33829491 DOI: 10.1111/ppl.13419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Lentils are highly sensitive to abrupt increases in temperature during the mid to late reproductive stages, leading to severe biomass and seed yield reduction. Therefore, we carried out an RNAseq analysis between IG4258 (heat tolerant) and IG3973 (heat sensitive) lentil genotypes at the reproductive stage under both normal and heat stress conditions in the field. It resulted in 209,549 assembled transcripts and among these 161,809 transcripts had coding regions, of which 94,437 transcripts were annotated. The differential gene expression analysis showed upregulation of 678 transcripts and downregulation of 680 transcripts between the tolerant and sensitive genotypes at the early reproductive stage. While 76 transcripts were upregulated and 47 transcripts were downregulated at the late reproductive stage under heat stress conditions. The validation of 12 up-or downregulated transcripts through RT-PCR corresponded well with the expression analysis data of RNAseq, with a correlation of R2 = 0.89. Among these transcripts, the DN364_c1_g1_i9 and DN2218_c0_g1_i5 transcripts encoded enzymes involved in the tryptophan pathway, indicating that tryptophan biosynthesis plays a role under heat stress in lentil. Moreover, KEGG pathways enrichment analysis identified transcripts associated with genes encoding proteins/regulating factors related to different metabolic pathways including signal transduction, fatty acid biosynthesis, rRNA processing, ribosome biogenesis, gibberellin (GA) biosynthesis, and riboflavin biosynthesis. This analysis also identified 6852 genic-SSRs leading to the development of 4968 SSR primers that are potential genomic resources for molecular mapping of heat-tolerant genes in lentil.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ravi Kesari
- Department of Plant Breeding and Genetics, Bhola Paswan Shastri Agricultural College, Purnea, India
| | - Renu Verma
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - Partha Sarathi Basu
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Khela Ram Soren
- Division of Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sanjeev Gupta
- All India Co-ordinated Research Project on MULLaRP, ICAR-Indian Institute of Pulses Research, Kanpur, India
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14
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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15
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Zhang F, Wu J, Sade N, Wu S, Egbaria A, Fernie AR, Yan J, Qin F, Chen W, Brotman Y, Dai M. Genomic basis underlying the metabolome-mediated drought adaptation of maize. Genome Biol 2021; 22:260. [PMID: 34488839 PMCID: PMC8420056 DOI: 10.1186/s13059-021-02481-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underlying crop environmental stress adaptation remains elusive. Results Here, we perform non-targeted metabolic profiling of leaves for 385 maize natural inbred lines grown under well-watered as well as drought-stressed conditions. A total of 3890 metabolites are identified and 1035 of these are differentially produced between well-watered and drought-stressed conditions, representing effective indicators of maize drought response and tolerance. Genetic dissections reveal the associations between these metabolites and thousands of single-nucleotide polymorphisms (SNPs), which represented 3415 metabolite quantitative trait loci (mQTLs) and 2589 candidate genes. 78.6% of mQTLs (2684/3415) are novel drought-responsive QTLs. The regulatory variants that control the expression of the candidate genes are revealed by expression QTL (eQTL) analysis of the transcriptomes of leaves from 197 maize natural inbred lines. Integrated metabolic and transcriptomic assays identify dozens of environment-specific hub genes and their gene-metabolite regulatory networks. Comprehensive genetic and molecular studies reveal the roles and mechanisms of two hub genes, Bx12 and ZmGLK44, in regulating maize metabolite biosynthesis and drought tolerance. Conclusion Our studies reveal the first population-level metabolomes in crop drought response and uncover the natural variations and genetic control of these metabolomes underlying crop drought adaptation, demonstrating that multi-omics is a powerful strategy to dissect the genetic mechanisms of crop complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02481-1.
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Affiliation(s)
- Fei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Jinfeng Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aiman Egbaria
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Feng Qin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany. .,Department of Life Sciences, Ben-Gurion University of the Negev, 8410501, Beersheba, Israel.
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan laboratory, Wuhan, 430070, China.
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16
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Schumacher C, Thümecke S, Schilling F, Köhl K, Kopka J, Sprenger H, Hincha DK, Walther D, Seddig S, Peters R, Zuther E, Haas M, Horn R. Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato ( Solanum tuberosum L.). Int J Mol Sci 2021; 22:ijms22116123. [PMID: 34200118 PMCID: PMC8201130 DOI: 10.3390/ijms22116123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Drought represents a major abiotic stress factor negatively affecting growth, yield and tuber quality of potatoes. Quantitative trait locus (QTL) analyses were performed in cultivated potatoes for drought tolerance index DRYM (deviation of relative starch yield from the experimental median), tuber starch content, tuber starch yield, tuber fresh weight, selected transcripts and metabolites under control and drought stress conditions. Eight genomic regions of major interest for drought tolerance were identified, three representing standalone DRYM QTL. Candidate genes, e.g., from signaling pathways for ethylene, abscisic acid and brassinosteroids, and genes encoding cell wall remodeling enzymes were identified within DRYM QTL. Co-localizations of DRYM QTL and QTL for tuber starch content, tuber starch yield and tuber fresh weight with underlying genes of the carbohydrate metabolism were observed. Overlaps of DRYM QTL with metabolite QTL for ribitol or galactinol may indicate trade-offs between starch and compatible solute biosynthesis. Expression QTL confirmed the drought stress relevance of selected transcripts by overlaps with DRYM QTL. Bulked segregant analyses combined with next-generation sequencing (BSAseq) were used to identify mutations in genes under the DRYM QTL on linkage group 3. Future analyses of identified genes for drought tolerance will give a better insight into drought tolerance in potatoes.
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Affiliation(s)
- Christina Schumacher
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Susanne Thümecke
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Florian Schilling
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Dirk Karl Hincha
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Sylvia Seddig
- Institute for Resistance Research and Stress Tolerance, Julius-Kühn Institut, Federal Research Centre for Cultivated Plants, Rudolf-Schick-Platz 3, 18190 Sanitz, Germany;
| | - Rolf Peters
- Landwirtschaftskammer Niedersachsen, Dethlingen 14, 29633 Munster, Germany;
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Manuela Haas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; (K.K.); (J.K.); (H.S.); (D.K.H.); (D.W.); (E.Z.); (M.H.)
| | - Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (C.S.); (S.T.); (F.S.)
- Correspondence:
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17
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Kim M, Jeong S, Lim CW, Lee SC. Mitogen-Activated Protein Kinase CaDIMK1 Functions as a Positive Regulator of Drought Stress Response and Abscisic Acid Signaling in Capsicum annuum. FRONTIERS IN PLANT SCIENCE 2021; 12:646707. [PMID: 33995446 PMCID: PMC8116957 DOI: 10.3389/fpls.2021.646707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Protein phosphorylation by kinase is an important mechanism for adapting to drought stress conditions. Here, we isolated the CaDIMK1 (Capsicum annuum drought-induced MAP kinase 1) from dehydrated pepper leaf tissue and functionally characterized it. Subcellular localization analysis revealed that the CaDIMK1 protein was localized in the cytoplasm and nucleus. CaDIMK1-silenced pepper plants exhibited drought-susceptible phenotypes that were characterized by increased transpiration rates, low leaf temperatures, and decreased stomatal closure. In contrast, CaDIMK1-overexpressing (OX) transgenic Arabidopsis plants were hypersensitive to abscisic acid (ABA) from germination to adult growth stages. Furthermore, the CaDIMK1-OX plants were tolerant to drought stress. The transcript levels of several stress-related genes were high in CaDIMK1-OX plants than in wild-type plants. Taken together, our data demonstrate that CaDIMK1 acts as a positive modulator of drought tolerance and ABA signal transduction in pepper plants.
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18
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Modulation of photosynthesis and other proteins during water-stress. Mol Biol Rep 2021; 48:3681-3693. [PMID: 33856605 DOI: 10.1007/s11033-021-06329-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/31/2021] [Indexed: 10/25/2022]
Abstract
Protein changes under drought or water stress conditions have been widely investigated. These investigations have given us enormous understanding of how drought is manifested in plants and how plants respond and adopt to such conditions. Chlorophyll fluoroescence, gas exchange, OMICS, biochemical and molecular analyses have shed light on regulation of physiology and photosynthesis of plants under drought. Use of proteomics has greatly increased the repertoire of drought-associated proteins which nevertheless, need to be investigated for their mechanistic and functional roles. Roles of such proteins have been succinctly discussed in various review articles, however more information on their functional role in countering drought is needed. In this review, recent developments in the field, alterations in the abundance of plant proteins in response to drought, monitored through numerous proteomic and immuno-blot analyses, and how these could affect plants growth and development, are discussed.
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19
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Shao A, Wang W, Fan S, Xu X, Yin Y, Erick A, Li X, Wang G, Wang H, Fu J. Comprehensive transcriptional analysis reveals salt stress-regulated key pathways, hub genes and time-specific responsive gene categories in common bermudagrass (Cynodon dactylon (L.) Pers.) roots. BMC PLANT BIOLOGY 2021; 21:175. [PMID: 33838660 PMCID: PMC8035780 DOI: 10.1186/s12870-021-02939-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 03/25/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Despite its good salt-tolerance level, key genes and pathways involved with temporal salt response of common bermudagrass (Cynodon dactylon (L.) Pers.) have not been explored. Therefore, in this study, to understand the underlying regulatory mechanism following the different period of salt exposure, a comprehensive transcriptome analysis of the bermudagrass roots was conducted. RESULTS The transcripts regulated after 1 h, 6 h, or 24 h of hydroponic exposure to 200 mM NaCl in the roots of bermudagrass were investigated. Dataset series analysis revealed 16 distinct temporal salt-responsive expression profiles. Enrichment analysis identified potentially important salt responsive genes belonging to specific categories, such as hormonal metabolism, secondary metabolism, misc., cell wall, transcription factors and genes encoded a series of transporters. Weighted gene co-expression network analysis (WGCNA) revealed that lavenderblush2 and brown4 modules were significantly positively correlated with the proline content and peroxidase activity and hub genes within these two modules were further determined. Besides, after 1 h of salt treatment, genes belonging to categories such as signalling receptor kinase, transcription factors, tetrapyrrole synthesis and lipid metabolism were immediately and exclusively up-enriched compared to the subsequent time points, which indicated fast-acting and immediate physiological responses. Genes involved in secondary metabolite biosynthesis such as simple phenols, glucosinolates, isoflavones and tocopherol biosynthesis were exclusively up-regulated after 24 h of salt treatment, suggesting a slightly slower reaction of metabolic adjustment. CONCLUSION Here, we revealed salt-responsive genes belonging to categories that were commonly or differentially expressed in short-term salt stress, suggesting possible adaptive salt response mechanisms in roots. Also, the distinctive salt-response pathways and potential salt-tolerant hub genes investigated can provide useful future references to explore the molecular mechanisms of bermudagrass.
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Affiliation(s)
- An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Amombo Erick
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Guangyang Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Hongli Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, People's Republic of China.
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20
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Xi L, Schulze WX, Wu XN. Phosphoproteomic Analysis of Plant Membranes. Methods Mol Biol 2021; 2200:441-451. [PMID: 33175392 DOI: 10.1007/978-1-0716-0880-7_22] [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: 06/11/2023]
Abstract
Mass spectrometry (MS) is a powerful tool to investigate plant phosphorylation dynamics on a system-wide scale (phosphoproteomics). Plant membrane phosphoproteomics enables elucidating regulatory patterns in membranes, such as kinase-target relationships in different signaling pathways. Here, we present "ShortPhos," an efficient and simple phosphoproteomics protocol for research on plant membrane proteins, which allows fast and efficient identification and quantification of phosphopeptides from small amounts of starting plant material and/or membrane proteins. This method improves upon the efficiency of plant membrane phosphoproteomics profiling and can be applied to the study of membrane-based signaling networks.
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Affiliation(s)
- Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany.
- School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming, China.
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21
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Lu D, Gao T, Xi L, Krall L, Wu XN. Phosphoproteomics Profiling of Receptor Kinase Mutants. Methods Mol Biol 2021; 2358:73-82. [PMID: 34270046 DOI: 10.1007/978-1-0716-1625-3_4] [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: 06/13/2023]
Abstract
The transmembrane receptor kinase family is the largest protein kinase family in Arabidopsis. Many members of this family play critical roles in plant signaling pathways. However, many of these kinases have yet uncharacterized functions and very little is known about the direct substrates of these kinases. We have developed the "ShortPhos" method, an efficient and simple mass spectrometry (MS)-based phosphoproteomics protocol to perform comparative phosphopeptide profiling of knockout mutants of receptor-like kinases. Through this method, we are able to better understand the functional roles of plant kinases in the context of their signaling networks.
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Affiliation(s)
- Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ting Gao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Leonard Krall
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Na Wu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China.
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22
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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23
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Ren Z, Zhang D, Cao L, Zhang W, Zheng H, Liu Z, Han S, Dong Y, Zhu F, Liu H, Su H, Chen Y, Wu L, Zhu Y, Ku L. Functions and regulatory framework of ZmNST3 in maize under lodging and drought stress. PLANT, CELL & ENVIRONMENT 2020; 43:2272-2286. [PMID: 32562291 DOI: 10.1111/pce.13829] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 05/23/2023]
Abstract
The growth and development of maize are negatively affected by various abiotic stresses including drought, high salinity, extreme temperature, and strong wind. Therefore, it is important to understand the molecular mechanisms underlying abiotic stress resistance in maize. In the present work, we identified that a novel NAC transcriptional factor, ZmNST3, enhances maize lodging resistance and drought stress tolerance. ChIP-Seq and expression of target genes analysis showed that ZmNST3 could directly regulate the expression of genes related to cell wall biosynthesis which could subsequently enhance lodging resistance. Furthermore, we also demonstrated that ZmNST3 affected the expression of genes related to the synthesis of antioxidant enzyme secondary metabolites that could enhance drought resistance. More importantly, we are the first to report that ZmNST3 directly binds to the promoters of CESA5 and Dynamin-Related Proteins2A (DRP2A) and activates the expression of genes related to secondary cell wall cellulose biosynthesis. Additionally, we revealed that ZmNST3 directly binds to the promoters of GST/GlnRS and activates genes which could enhance the production of antioxidant enzymes in vivo. Overall, our work contributes to a comprehensive understanding of the regulatory network of ZmNST3 in regulating maize lodging and drought stress resistance.
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Affiliation(s)
- Zhenzhen Ren
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Dongling Zhang
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Liru Cao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Weiqiang Zhang
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhixue Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shengbo Han
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yahui Dong
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Fangfang Zhu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Huafeng Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Liancheng Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
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24
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Aquino B, da Silva VCH, Massirer KB, Arruda P. Crystal structure of DRIK1, a stress-responsive receptor-like pseudokinase, reveals the molecular basis for the absence of ATP binding. BMC PLANT BIOLOGY 2020; 20:158. [PMID: 32293271 PMCID: PMC7158045 DOI: 10.1186/s12870-020-2328-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/04/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants reprogram metabolism and development to rapidly adapt to biotic and abiotic stress. Protein kinases play a significant role in this process by phosphorylating protein substrates that activate or inactivate signaling cascades that regulate cellular and metabolic adaptations. Despite their importance in plant biology, a notably small fraction of the plant kinomes has been studied to date. RESULTS In this report, we describe ZmDRIK1, a stress-responsive receptor-like pseudokinase whose expression is downregulated under water restriction. We show the structural features and molecular basis of the absence of ATP binding exhibited by ZmDRIK1. The ZmDRIK1 kinase domain lacks conserved amino acids that are essential for phosphorylation activity. The crystal structure of the ZmDRIK1 kinase domain revealed the presence of a spine formed by the side chain of the triad Leu240, Tyr363, and Leu375 that occludes the ATP binding pocket. Although ZmDRIK1 is unable to bind nucleotides, it does bind the small molecule ENMD-2076 which, in a cocrystal structure, revealed the potential to serve as a ZmDRIK1 inhibitor. CONCLUSION ZmDRIK1 is a novel receptor-like pseudokinase responsive to biotic and abiotic stress. The absence of ATP binding and consequently, the absence of phosphorylation activity, was proven by the crystal structure of the apo form of the protein kinase domain. The expression profiling of the gene encoding ZmDRIK1 suggests this kinase may play a role in downregulating the expression of stress responsive genes that are not necessary under normal conditions. Under biotic and abiotic stress, ZmDRIK1 is down-regulated to release the expression of these stress-responsive genes.
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Affiliation(s)
- Bruno Aquino
- Structural Genomics Consortium, Universidade Estadual de Campinas – UNICAMP, Campinas, SP 13083-886 Brazil
| | - Viviane C. H. da Silva
- Structural Genomics Consortium, Universidade Estadual de Campinas – UNICAMP, Campinas, SP 13083-886 Brazil
- Joint Research Center for Genomic Applied to Climate Change (UMIP-GenClima), Campinas, SP 13083-875 Brazil
| | - Katlin B. Massirer
- Structural Genomics Consortium, Universidade Estadual de Campinas – UNICAMP, Campinas, SP 13083-886 Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875 Brazil
| | - Paulo Arruda
- Structural Genomics Consortium, Universidade Estadual de Campinas – UNICAMP, Campinas, SP 13083-886 Brazil
- Joint Research Center for Genomic Applied to Climate Change (UMIP-GenClima), Campinas, SP 13083-875 Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875 Brazil
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970 Brazil
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25
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Cheuk A, Ouellet F, Houde M. The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance. BMC PLANT BIOLOGY 2020; 20:144. [PMID: 32264833 PMCID: PMC7140352 DOI: 10.1186/s12870-020-02355-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/23/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speed up functional gene characterization. RESULTS We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant's life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected. CONCLUSIONS This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.
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Affiliation(s)
- Arnaud Cheuk
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Francois Ouellet
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Mario Houde
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada.
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26
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Bhaskarla V, Zinta G, Ford R, Jain M, Varshney RK, Mantri N. Comparative Root Transcriptomics Provide Insights into Drought Adaptation Strategies in Chickpea ( Cicer arietinum L.). Int J Mol Sci 2020; 21:E1781. [PMID: 32150870 PMCID: PMC7084756 DOI: 10.3390/ijms21051781] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/28/2022] Open
Abstract
Drought adversely affects crop production across the globe. The root system immensely contributes to water management and the adaptability of plants to drought stress. In this study, drought-induced phenotypic and transcriptomic responses of two contrasting chickpea (Cicer arietinum L.) genotypes were compared at the vegetative, reproductive transition, and reproductive stages. At the vegetative stage, drought-tolerant genotype maintained higher root biomass, length, and surface area under drought stress as compared to sensitive genotype. However, at the reproductive stage, root length and surface area of tolerant genotype was lower but displayed higher root diameter than sensitive genotype. The shoot biomass of tolerant genotype was overall higher than the sensitive genotype under drought stress. RNA-seq analysis identified genotype- and developmental-stage specific differentially expressed genes (DEGs) in response to drought stress. At the vegetative stage, a total of 2161 and 1873 DEGs, and at reproductive stage 4109 and 3772 DEGs, were identified in the tolerant and sensitive genotypes, respectively. Gene ontology (GO) analysis revealed enrichment of biological categories related to cellular process, metabolic process, response to stimulus, response to abiotic stress, and response to hormones. Interestingly, the expression of stress-responsive transcription factors, kinases, ROS signaling and scavenging, transporters, root nodulation, and oxylipin biosynthesis genes were robustly upregulated in the tolerant genotype, possibly contributing to drought adaptation. Furthermore, activation/repression of hormone signaling and biosynthesis genes was observed. Overall, this study sheds new insights on drought tolerance mechanisms operating in roots with broader implications for chickpea improvement.
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Affiliation(s)
- Vijay Bhaskarla
- The Pangenomics Group, School of Science, RMIT University, Melbourne 3083, Australia;
| | - Gaurav Zinta
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Rebecca Ford
- School of Natural Sciences, Environmental Futures Research Institute, Griffith University, Brisbane, QLD 4111, Australia;
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, India
| | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne 3083, Australia;
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27
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Schneider HM, Klein SP, Hanlon MT, Kaeppler S, Brown KM, Lynch JP. Genetic control of root anatomical plasticity in maize. THE PLANT GENOME 2020; 13:e20003. [PMID: 33016634 DOI: 10.1002/tpg2.20003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/01/2019] [Indexed: 05/06/2023]
Abstract
Root anatomical phenes have important roles in soil resource capture and plant performance; however, their phenotypic plasticity and genetic architecture is poorly understood. We hypothesized that (a) the responses of root anatomical phenes to water deficit (stress plasticity) and different environmental conditions (environmental plasticity) are genetically controlled and (b) stress and environmental plasticity are associated with different genetic loci than those controlling the expression of phenes under water-stress and well-watered conditions. Root anatomy was phenotyped in a large maize (Zea mays L.) association panel in the field with and without water deficit stress in Arizona and without water deficit stress in South Africa. Anatomical phenes displayed stress and environmental plasticity; many phenotypic responses to water deficit were adaptive, and the magnitude of response varied by genotype. We identified 57 candidate genes associated with stress and environmental plasticity and 64 candidate genes associated with phenes under well-watered and water-stress conditions in Arizona and under well-watered conditions in South Africa. Four candidate genes co-localized between plasticity groups or for phenes expressed under each condition. The genetic architecture of phenotypic plasticity is highly quantitative, and many distinct genes control plasticity in response to water deficit and different environments, which poses a challenge for breeding programs.
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Affiliation(s)
- Hannah M Schneider
- Dep. of Plant Science, Pennsylvania State Univ., University Park, PA, 16802, USA
| | - Stephanie P Klein
- Dep. of Plant Science, Pennsylvania State Univ., University Park, PA, 16802, USA
| | - Meredith T Hanlon
- Dep. of Plant Science, Pennsylvania State Univ., University Park, PA, 16802, USA
| | - Shawn Kaeppler
- Dep. of Agronomy, Univ. of Wisconsin, Madison, WI, 53706, USA
| | - Kathleen M Brown
- Dep. of Plant Science, Pennsylvania State Univ., University Park, PA, 16802, USA
| | - Jonathan P Lynch
- Dep. of Plant Science, Pennsylvania State Univ., University Park, PA, 16802, USA
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28
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Nongpiur RC, Singla-Pareek SL, Pareek A. The quest for osmosensors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:595-607. [PMID: 31145792 DOI: 10.1093/jxb/erz263] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/22/2019] [Indexed: 05/20/2023]
Abstract
Osmotic stress has severe effects on crop productivity. Since climate change is predicted to exacerbate this problem, the development of new crops that are tolerant to osmotic stresses, especially drought and salinity stress, is required. However, only limited success has been achieved to date, primarily because of the lack of a clear understanding of the mechanisms that facilitate osmosensing. Here, we discuss the potential mechanisms of osmosensing in plants. We highlight the roles of proteins such as receptor-like kinases, which sense stress-induced cell wall damage, mechanosensitive calcium channels, which initiate a calcium-induced stress response, and phospholipase C, a membrane-bound enzyme that is integral to osmotic stress perception. We also discuss the roles of aquaporins and membrane-bound histidine kinases, which could potentially detect changes in extracellular osmolarity in plants, as they do in prokaryotes and lower eukaryotes. These putative osmosensors have the potential to serve as master regulators of the osmotic stress response in plants and could prove to be useful targets for the selection of osmotic stress-tolerant crops.
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Affiliation(s)
- Ramsong Chantre Nongpiur
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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29
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Fatima U, Bhorali P, Senthil-Kumar M. Morpho-Pathological and Global Transcriptomic Analysis Reveals the Robust Nonhost Resistance Responses in Chickpea Interaction with Alternaria brassicae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1598-1613. [PMID: 31364484 DOI: 10.1094/mpmi-05-19-0117-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Alternaria blight, caused by Alternaria brassicae, causes considerable yield loss in Brassica crops. While several blight-resistant varieties have been developed using resistance sources from host germplasm, none of them are entirely successful in imparting durable resistance. This has prompted the exploration of novel gene pools of nonhost plant species. Nonhost resistance (NHR) is a durable form of resistance, comprising pre- and postinvasion layers of defense. We aimed to identify the molecular basis of NHR to A. brassicae and identify the layers of NHR operating in a nonhost, chickpea (Cicer arietinum). To elucidate the layers of NHR operating against A. brassicae, we compared the histopathology and infection patterns of A. brassicae in C. arietinum and Brassica juncea. Delayed conidial germination, impeded hyphal growth, suppressed appressorium formation, and limited hyphal penetration occurred in the nonhost plant compared with the host plant, implying the involvement of the preinvasion layer of NHR in C. arietinum. Next, we investigated the molecular basis of robust NHR, in C. arietinum challenged with A. brassicae, by microarray-based global transcriptome profiling. Genes involved in stomatal closure, cuticular wax biosynthesis, cell-wall modification, and secondary metabolite production (contributing to preinvasion NHR) as well as reactive oxygen species (ROS) and cell death (contributing to postinvasion NHR) were found to be upregulated. Consistent with transcriptomic analysis, the morpho-pathological analysis revealed stomatal closure, ROS accumulation, and localized cell death in C. arietinum as the defense strategies against A. brassicae. Thus, we identified NHR-contributing genes with potential applications in blight resistance gene transfer to B. juncea.
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Affiliation(s)
- Urooj Fatima
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi 110 067, India
| | - Priyadarshini Bhorali
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-785013, Assam, India
| | - Muthappa Senthil-Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi 110 067, India
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30
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Liu J, Sun X, Liao W, Zhang J, Liang J, Xu W. Involvement of OsGF14b Adaptation in the Drought Resistance of Rice Plants. RICE (NEW YORK, N.Y.) 2019; 12:82. [PMID: 31728660 PMCID: PMC6856252 DOI: 10.1186/s12284-019-0346-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/04/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Drought stress is one of the major abiotic stresses that restrict plant growth and development. 14-3-3 proteins have been validated to regulate many biological processes in plants. Previous research demonstrated that OsGF14b plays different roles in panicle and leaf blast resistance. In this study, we researched the function of OsGF14b in drought resistance in rice. FINDINGS Here, we report that OsGF14b was strongly induced by soil drought stress. In comparison with wild type (WT), the osgf14b mutant exhibited improved resistance to drought and osmotic stress by changing the content of stress-relevant parameters, complementation of the osgf14b mutant restored the drought sensitivity to WT levels, whereas the OsGF14b-overexpression lines exhibited enhanced sensitivity to drought and osmotic stress. The osgf14b mutant plants were hypersensitive to abscisic acid (ABA), while the OsGF14b-overexpression plants showed reduced sensitivity to ABA. Furthermore, mutation and overexpression of OsGF14b affected the expression of stress-related genes under normal growth conditions and/or drought stress conditions. CONCLUSIONS We have demonstrated that OsGF14b is involved in the drought resistance of rice plants, partially in an ABA-dependent manner.
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Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Xinjiao Sun
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Wencheng Liao
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jiansheng Liang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
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31
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Gu W, Zhang A, Sun H, Gu Y, Chao J, Tian R, Duan JA. Identifying resurrection genes through the differentially expressed genes between Selaginella tamariscina (Beauv.) spring and Selaginella moellendorffii Hieron under drought stress. PLoS One 2019; 14:e0224765. [PMID: 31721818 PMCID: PMC6853609 DOI: 10.1371/journal.pone.0224765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
Selaginella tamariscina (Beauv.) spring, a primitive vascular resurrection plant, can survive extreme drought and recover when water becomes available. To identify drought-inducible genes and to clarify the molecular mechanism of drought tolerance, a comparative transcriptional pattern analysis was conducted between S. tamariscina and Selaginella moellendorffii Hieron (drought sensitive). 133 drought related genes were identified, including 72 functional genes and 61 regulatory genes. And several drought responsive reactions, such as antioxidant activity, osmotic balance, cuticle defense and signal transduction were highlighted in S. tamariscina under drought. Notably, besides peroxidase, catalase and L-ascorbate oxidase genes, DEGs associated with phenylalanine metabolism and polyamine catabolism could be alternative ways to enhance antioxidant ability in S. tamariscina. DEGs related to soluble carbohydrate metabolism, late embryogenesis abundant protein (LEA) and aquaporin protein (AQP) confirmed that osmotic adjustment could resist drought during desiccation. DEGs involved in xyloglucan metabolic process, pectin metabolic process and cutin biosynthesis may also contribute to drought tolerance of S. tamariscina by cuticle defense. Drought-responsive genes encoding protein kinases, calcium sensors, transcription factors (TFs) and plant hormones also help to drought resistance of S. tamariscina. The preliminary validation experiments were performed and the results were consistent with our hypothetical integrated regulatory network. The results of this study provide candidate resurrection genes and an integrated regulatory network for further studies on the molecular mechanisms of stress tolerance in S. tamariscina.
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Affiliation(s)
- Wei Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Aqin Zhang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongmei Sun
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuchen Gu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianguo Chao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Rong Tian
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, China
- * E-mail:
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Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics. G3-GENES GENOMES GENETICS 2019; 9:3181-3199. [PMID: 31395652 PMCID: PMC6778798 DOI: 10.1534/g3.119.400456] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The impact of climate change that comes with a dramatic increase of long periods of extreme summer drought associated with heat is a fundamental challenge for European forests. As a result, forests are expected to shift their distribution patterns toward north-east, which may lead to a dramatic loss in value of European forest land. Consequently, unraveling key processes that underlie drought stress tolerance is not only of great scientific but also of utmost economic importance for forests to withstand future heat and drought wave scenarios. To reveal drought stress-related molecular patterns we applied cross-species comparative transcriptomics of three major European oak species: the less tolerant deciduous pedunculate oak (Quercus robur), the deciduous but quite tolerant pubescent oak (Q. pubescens), and the very tolerant evergreen holm oak (Q. ilex). We found 415, 79, and 222 differentially expressed genes during drought stress in Q. robur, Q. pubescens, and Q. ilex, respectively, indicating species-specific response mechanisms. Further, by comparative orthologous gene family analysis, 517 orthologous genes could be characterized that may play an important role in drought stress adaptation on the genus level. New regulatory candidate pathways and genes in the context of drought stress response were identified, highlighting the importance of the antioxidant capacity, the mitochondrial respiration machinery, the lignification of the water transport system, and the suppression of drought-induced senescence - providing a valuable knowledge base that could be integrated in breeding programs in the face of climate change.
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Iquebal MA, Sharma P, Jasrotia RS, Jaiswal S, Kaur A, Saroha M, Angadi UB, Sheoran S, Singh R, Singh GP, Rai A, Tiwari R, Kumar D. RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat. Sci Rep 2019; 9:13917. [PMID: 31558740 PMCID: PMC6763491 DOI: 10.1038/s41598-019-49915-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 08/12/2019] [Indexed: 01/08/2023] Open
Abstract
Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Amandeep Kaur
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Monika Saroha
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - U B Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - G P Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi, 110012, India.
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Meng HL, Zhang W, Zhang GH, Wang JJ, Meng ZG, Long GQ, Yang SC. Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima. PLoS One 2018; 13:e0202848. [PMID: 30500823 PMCID: PMC6268015 DOI: 10.1371/journal.pone.0202848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022] Open
Abstract
Marsdenia tenacissima is a well-known anti-cancer medicinal plant used in traditional Chinese medicine, which often grows on the karst landform and the water conservation capacity of land is very poorly and drought occurrences frequently. We found M. tenacissima has strong drought resistance because of continuousdrought16 d, the leaves of M. tenacissima were fully curly and dying. But the leaves were fully almost recovering after re-watering 24h. The activity of SOD and POD were almost doubled under drought stress. The content of osmotic regulating substance proline and soluble sugar were three times than control group. But after re-watering, these indexes were declined rapidly. Three cDNA libraries of control, drought stress, and re-watering treatments were constructed. There were 43,129,228, 47,116,844, and 42,815,454 clean reads with Q20 values of 98.06, 98.04, and 97.88respectively.SRA accession number of raw data was PRJNA498187 on NCBI. A total of 8672, 6043, and 6537 differentially expressed genes (DEGs) were identified in control vs drought stress, control vs re-watering, and drought stress vs re-watering, respectively. In addition, 1039, 1016, and 980 transcription factors (TFs) were identified, respectively. Among them, 363, 267, and 299 TFs were identified as DEGs in drought stress, re-watering, and drought stress and re-watering, respectively. These differentially expressed TFs mainly belonged to the bHLH, bZIP, C2H2, ERF, MYB, MYB-related, and NAC families. A comparative analysis found that 1174 genes were up-regulated and 2344 were down-regulated under drought stress and this pattern was the opposite to that found after re-watering. Among the up-regulated genes, 64 genes were homologous to known functional genes that directly protect plants against drought stress. Furthermore, 44 protein kinases and 38 TFs with opposite expression patterns under drought stress and re-watering were identified, which are possibly candidate regulators for drought stress resistance in M. tenacissima. Our study is the first to characterize the M. tenacissima transcriptome in response to drought stress, and will serve as a useful resource for future studies on the functions of candidate protein kinases and TFs involved in M. tenacissima drought stress resistance.
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Affiliation(s)
- Heng-Ling Meng
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Wei Zhang
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, People’s Republic of China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Jian-Jun Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Zhen-Gui Meng
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
| | - Guang-Qiang Long
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming,Yunnan, People’s Republic of China
- * E-mail: (GQL); (SCY)
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G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants. Biochem J 2018; 475:3331-3357. [PMID: 30413679 DOI: 10.1042/bcj20160819] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Heterotrimeric G proteins composed of Gα, Gβ, and Gγ subunits are vital eukaryotic signaling elements that convey information from ligand-regulated G protein-coupled receptors (GPCRs) to cellular effectors. Heterotrimeric G protein-based signaling pathways are fundamental to human health [Biochimica et Biophysica Acta (2007) 1768, 994-1005] and are the target of >30% of pharmaceuticals in clinical use [Biotechnology Advances (2013) 31, 1676-1694; Nature Reviews Drug Discovery (2017) 16, 829-842]. This review focuses on phosphorylation of G protein subunits as a regulatory mechanism in mammals, budding yeast, and plants. This is a re-emerging field, as evidence for phosphoregulation of mammalian G protein subunits from biochemical studies in the early 1990s can now be complemented with contemporary phosphoproteomics and genetic approaches applied to a diversity of model systems. In addition, new evidence implicates a family of plant kinases, the receptor-like kinases, which are monophyletic with the interleukin-1 receptor-associated kinase/Pelle kinases of metazoans, as possible GPCRs that signal via subunit phosphorylation. We describe early and modern observations on G protein subunit phosphorylation and its functional consequences in these three classes of organisms, and suggest future research directions.
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Fàbregas N, Lozano-Elena F, Blasco-Escámez D, Tohge T, Martínez-Andújar C, Albacete A, Osorio S, Bustamante M, Riechmann JL, Nomura T, Yokota T, Conesa A, Alfocea FP, Fernie AR, Caño-Delgado AI. Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth. Nat Commun 2018; 9:4680. [PMID: 30409967 PMCID: PMC6224425 DOI: 10.1038/s41467-018-06861-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/26/2018] [Indexed: 01/04/2023] Open
Abstract
Drought represents a major threat to food security. Mechanistic data describing plant responses to drought have been studied extensively and genes conferring drought resistance have been introduced into crop plants. However, plants with enhanced drought resistance usually display lower growth, highlighting the need for strategies to uncouple drought resistance from growth. Here, we show that overexpression of BRL3, a vascular-enriched member of the brassinosteroid receptor family, can confer drought stress tolerance in Arabidopsis. Whereas loss-of-function mutations in the ubiquitously expressed BRI1 receptor leads to drought resistance at the expense of growth, overexpression of BRL3 receptor confers drought tolerance without penalizing overall growth. Systematic analyses reveal that upon drought stress, increased BRL3 triggers the accumulation of osmoprotectant metabolites including proline and sugars. Transcriptomic analysis suggests that this results from differential expression of genes in the vascular tissues. Altogether, this data suggests that manipulating BRL3 expression could be used to engineer drought tolerant crops. Drought resistant plants typically have reduced growth. Here the authors show that overexpression of the BRL3 brassinosteroid receptor confers drought tolerance and accumulation of osmoprotectant metabolites without penalizing growth, demonstrating that drought response and growth can be uncoupled.
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Affiliation(s)
- Norma Fàbregas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.,Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Fidel Lozano-Elena
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain
| | - David Blasco-Escámez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany.,NAIST Graduate school of Biological Sciences, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | | | | | - Sonia Osorio
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", University of Málaga-Consejo Superior de Investigaciones Científicas. Department of Molecular Biology and Biochemistry, 29071, Málaga, Spain
| | - Mariana Bustamante
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Minemachi, Utsunomiya, 321-8505, Japan
| | - Takao Yokota
- Department of Biosciences, Teikyo University, Toyosatodai, Utsunomiya, 320-8551, Japan
| | - Ana Conesa
- Microbiology and Cell Science Department, IFAS, Genetics Institute, University of Florida, Gainesville, 32603, USA
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, D-14476, Potsdam-Golm, Germany
| | - Ana I Caño-Delgado
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain.
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Zhu GR, Yan X, Zhu D, Deng X, Wu JS, Xia J, Yan YM. Lysine acetylproteome profiling under water deficit reveals key acetylated proteins involved in wheat grain development and starch biosynthesis. J Proteomics 2018; 185:8-24. [DOI: 10.1016/j.jprot.2018.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023]
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Liang X, Zhou JM. Receptor-Like Cytoplasmic Kinases: Central Players in Plant Receptor Kinase-Mediated Signaling. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:267-299. [PMID: 29719165 DOI: 10.1146/annurev-arplant-042817-040540] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Receptor kinases (RKs) are of paramount importance in transmembrane signaling that governs plant reproduction, growth, development, and adaptation to diverse environmental conditions. Receptor-like cytoplasmic kinases (RLCKs), which lack extracellular ligand-binding domains, have emerged as a major class of signaling proteins that regulate plant cellular activities in response to biotic/abiotic stresses and endogenous extracellular signaling molecules. By associating with immune RKs, RLCKs regulate multiple downstream signaling nodes to orchestrate a complex array of defense responses against microbial pathogens. RLCKs also associate with RKs that perceive brassinosteroids and signaling peptides to coordinate growth, pollen tube guidance, embryonic and stomatal patterning, floral organ abscission, and abiotic stress responses. The activity and stability of RLCKs are dynamically regulated not only by RKs but also by other RLCK-associated proteins. Analyses of RLCK-associated components and substrates have suggested phosphorylation relays as a major mechanism underlying RK-mediated signaling.
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Affiliation(s)
- Xiangxiu Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, 100101 Beijing, China;
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, 100101 Beijing, China;
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Meng LS. Compound Synthesis or Growth and Development of Roots/Stomata Regulate Plant Drought Tolerance or Water Use Efficiency/Water Uptake Efficiency. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3595-3604. [PMID: 29589939 DOI: 10.1021/acs.jafc.7b05990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Water is crucial to plant growth and development because it serves as a medium for all cellular functions. Thus, the improvement of plant drought tolerance or water use efficiency/water uptake efficiency is important in modern agriculture. In this review, we mainly focus on new genetic factors for ameliorating drought tolerance or water use efficiency/water uptake efficiency of plants and explore the involvement of these genetic factors in the regulation of improving plant drought tolerance or water use efficiency/water uptake efficiency, which is a result of altered stomata density and improving root systems (primary root length, hair root growth, and lateral root number) and enhanced production of osmotic protectants, which is caused by transcription factors, proteinases, and phosphatases and protein kinases. These results will help guide the synthesis of a model for predicting how the signals of genetic and environmental stress are integrated at a few genetic determinants to control the establishment of either water use efficiency or water uptake efficiency. Collectively, these insights into the molecular mechanism underpinning the control of plant drought tolerance or water use efficiency/water uptake efficiency may aid future breeding or design strategies to increase crop yield.
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Affiliation(s)
- Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , People's Republic of China
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Abstract
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
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Sun M, Qian X, Chen C, Cheng S, Jia B, Zhu Y, Sun X. Ectopic Expression of GsSRK in Medicago sativa Reveals Its Involvement in Plant Architecture and Salt Stress Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:226. [PMID: 29520291 PMCID: PMC5827113 DOI: 10.3389/fpls.2018.00226] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/07/2018] [Indexed: 05/23/2023]
Abstract
Receptor-like kinases (RLK) play fundamental roles in plant growth and stress responses. Compared with other RLKs, little information is provided concerning the S-locus LecRLK subfamily, which is characterized by an extracellular G-type lectin domain and an S-locus-glycop domain. Until now, the function of the G-type lectin domain is still unknown. In a previous research, we identified a Glycine soja S-locus LecRLK gene GsSRK, which conferred increased salt stress tolerance in transgenic Arabidopsis. In this study, to investigate the role of the G-type lectin domain and to breed transgenic alfalfa with superior salt stress tolerance, we transformed the full-length GsSRK (GsSRK-f) and a truncated version of GsSRK (GsSRK-t) deleting the G-type lectin domain into alfalfa. Our results showed that overexpression of GsSRK-t, but not GsSRK-f, resulted in changes of plant architecture, as evidenced by more branches but shorter shoots of GsSRK-t transgenic alfalfa, indicating a potential role of the extracellular G-type lectin domain in regulating plant architecture. Furthermore, we also found that transgenic alfalfa overexpressing either GsSRK-f or GsSRK-t showed increased salt stress tolerance, and GsSRK-t transgenic alfalfa displayed better growth (more branches and higher fresh weight) than GsSRK-f lines under salt stress. In addition, our results suggested that both GsSRK-f and GsSRK-t were involved in ion homeostasis, ROS scavenging, and osmotic regulation. Under salt stress, the Na+ content in the transgenic lines was significantly lower, while the K+ content was slightly higher than that in WT. Moreover, the transgenic lines displayed reduced ion leakage and MDA content, but increased SOD activity and proline content than WT. Notably, no obvious difference in these physiological indices was observed between GsSRK-f and GsSRK-t transgenic lines, implying that deletion of the GsSRK G-type lectin domain does not affect its physiological function in salt stress responses. In conclusion, results in this research reveal the dual role of GsSRK in regulating both plant architecture and salt stress responses.
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Affiliation(s)
- Mingzhe Sun
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
- Crop Stress Molecular Biology Laboratory, Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xue Qian
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Chao Chen
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Shufei Cheng
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Bowei Jia
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
- Crop Stress Molecular Biology Laboratory, Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanming Zhu
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
- Crop Stress Molecular Biology Laboratory, Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoli Sun
- Plant Bioengineering Laboratory, College of Life Science, Northeast Agricultural University, Harbin, China
- Crop Stress Molecular Biology Laboratory, Agronomy College, Heilongjiang Bayi Agricultural University, Daqing, China
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Jagodzik P, Tajdel-Zielinska M, Ciesla A, Marczak M, Ludwikow A. Mitogen-Activated Protein Kinase Cascades in Plant Hormone Signaling. FRONTIERS IN PLANT SCIENCE 2018; 9:1387. [PMID: 30349547 PMCID: PMC6187979 DOI: 10.3389/fpls.2018.01387] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/31/2018] [Indexed: 05/02/2023]
Abstract
Mitogen-activated protein kinase (MAPK) modules play key roles in the transduction of environmental and developmental signals through phosphorylation of downstream signaling targets, including other kinases, enzymes, cytoskeletal proteins or transcription factors, in all eukaryotic cells. A typical MAPK cascade consists of at least three sequentially acting serine/threonine kinases, a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK) and finally, the MAP kinase (MAPK) itself, with each phosphorylating, and hence activating, the next kinase in the cascade. Recent advances in our understanding of hormone signaling pathways have led to the discovery of new regulatory systems. In particular, this research has revealed the emerging role of crosstalk between the protein components of various signaling pathways and the involvement of this crosstalk in multiple cellular processes. Here we provide an overview of current models and mechanisms of hormone signaling with a special emphasis on the role of MAPKs in cell signaling networks. One-sentence summary: In this review we highlight the mechanisms of crosstalk between MAPK cascades and plant hormone signaling pathways and summarize recent findings on MAPK regulation and function in various cellular processes.
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Affiliation(s)
- Przemysław Jagodzik
- Department of Plant Physiology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Małgorzata Tajdel-Zielinska
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Agata Ciesla
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Małgorzata Marczak
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Agnieszka Ludwikow
- Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
- *Correspondence: Agnieszka Ludwikow,
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Natural variation identifies genes affecting drought-induced abscisic acid accumulation in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:11536-11541. [PMID: 29073083 DOI: 10.1073/pnas.1705884114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accumulation of the stress hormone abscisic acid (ABA) in response to drought and low water-potential controls many downstream acclimation mechanisms. However, mechanisms controlling ABA accumulation itself are less known. There was a 10-fold range of variation in ABA levels among nearly 300 Arabidopsis thaliana accessions exposed to the same low water-potential severity. Genome-wide association analysis (GWAS) identified genomic regions containing clusters of ABA-associated SNPs. Candidate genes within these regions included few genes with known stress or ABA-related function. The GWAS data were used to guide reverse genetic analysis, which found effectors of ABA accumulation. These included plasma-membrane-localized signaling proteins such as receptor-like kinases, aspartic protease, a putative lipid-binding START domain protein, and other membrane proteins of unknown function as well as a RING U-box protein and possible effect of tonoplast transport on ABA accumulation. Putative loss-of-function polymorphisms within the START domain protein were associated with climate factors at accession sites of origin, indicating its potential involvement in drought adaptation. Overall, using ABA accumulation as a basis for a combined GWAS-reverse genetic strategy revealed the broad natural variation in low-water-potential-induced ABA accumulation and was successful in identifying genes that affect ABA levels and may act in upstream drought-related sensing and signaling mechanisms. ABA effector loci were identified even when each one was of incremental effect, consistent with control of ABA accumulation being distributed among the many branches of ABA metabolism or mediated by genes with partially redundant function.
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Wu XN, Xi L, Pertl-Obermeyer H, Li Z, Chu LC, Schulze WX. Highly Efficient Single-Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations. FRONTIERS IN PLANT SCIENCE 2017; 8:1673. [PMID: 29042862 PMCID: PMC5632542 DOI: 10.3389/fpls.2017.01673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 05/30/2023]
Abstract
Mass spectrometry (MS)-based large scale phosphoproteomics has facilitated the investigation of plant phosphorylation dynamics on a system-wide scale. However, generating large scale data sets for membrane phosphoproteins usually requires fractionation of samples and extended hands-on laboratory time. To overcome these limitations, we developed "ShortPhos," an efficient and simple phosphoproteomics protocol optimized for research on plant membrane proteins. The optimized workflow allows fast and efficient identification and quantification of phosphopeptides, even from small amounts of starting plant materials. "ShortPhos" can produce label-free datasets with a high quantitative reproducibility. In addition, the "ShortPhos" protocol recovered more phosphorylation sites from membrane proteins, especially plasma membrane and vacuolar proteins, when compared to our previous workflow and other membrane-based data in the PhosPhAt 4.0 database. We applied "ShortPhos" to study kinase-substrate relationships within a nitrate-induction experiment on Arabidopsis roots. The "ShortPhos" identified significantly more known kinase-substrate relationships compared to previous phosphoproteomics workflows, producing new insights into nitrate-induced signaling pathways.
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Hosseini SA, Maillard A, Hajirezaei MR, Ali N, Schwarzenberg A, Jamois F, Yvin JC. Induction of Barley Silicon Transporter HvLsi1 and HvLsi2, increased silicon concentration in the shoot and regulated Starch and ABA Homeostasis under Osmotic stress and Concomitant Potassium Deficiency. FRONTIERS IN PLANT SCIENCE 2017; 8:1359. [PMID: 28824688 PMCID: PMC5541011 DOI: 10.3389/fpls.2017.01359] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/20/2017] [Indexed: 05/18/2023]
Abstract
Drought is one of the major stress factors reducing cereal production worldwide. There is ample evidence that the mineral nutrient status of plants plays a critical role in increasing plant tolerance to different biotic and abiotic stresses. In this regard, the important role of various nutrients e.g., potassium (K) or silicon (Si) in the mitigation of different stress factors, such as drought, heat or frost has been well documented. Si application has been reported to ameliorate plant nutrient deficiency. Here, we used K and Si either solely or in combination to investigate whether an additive positive effect on barley growth can be achieved under osmotic stress and which mechanisms contribute to a better tolerance to osmotic stress. To achieve this goal, barley plants were subjected to polyethylene glycol (PEG)-induced osmotic stress under low or high K supply and two Si regimes. The results showed that barley silicon transporters HvLsi1 and HvLsi2 regulate the accumulation of Si in the shoot only when plant suffered from K deficiency. Si, in turn, increased the starch level under both osmotic stress and K deficiency and modulated the glycolytic and TCA pathways. Hormone profiling revealed that the beneficial effect of Si is most likely mediated also by ABA homeostasis and active cytokinin isopentenyl adenine (iP). We conclude that Si may effectively improve stress tolerance under K deficient condition in particular when additional stress like osmotic stress interferes.
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Affiliation(s)
- Seyed A Hosseini
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
| | - Anne Maillard
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
| | - Mohammad R Hajirezaei
- Molecular Plant Nutrition Group, Physiology and Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant ResearchGatersleben, Germany
| | - Nusrat Ali
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
| | - Adrian Schwarzenberg
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
| | - Frank Jamois
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
| | - Jean-Claude Yvin
- Plant Nutrition Department, Centre Mondial de I'lnnovation RoullierSaint Malo, France
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Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM. Progress towards a public chemogenomic set for protein kinases and a call for contributions. PLoS One 2017; 12:e0181585. [PMID: 28767711 PMCID: PMC5540273 DOI: 10.1371/journal.pone.0181585] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/03/2017] [Indexed: 01/01/2023] Open
Abstract
Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.
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Affiliation(s)
- David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David M. Andrews
- AstraZeneca, Darwin Building, Cambridge Science Park, Cambridge, United Kingdom
| | - Richard Angell
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephen J. Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jonathan M. Elkins
- Structural Genomics Consortium, Universidade Estadual de Campinas—UNICAMP, Campinas, Sao Paulo, Brazil
| | | | - Mathias Frederiksen
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Opher Gileadi
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Nathanael Gray
- Harvard Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Alice Hooper
- Drug Discovery Group, Translational Research Office, University College London School of Pharmacy, 29–39 Brunswick Square, London, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Stefan Laufer
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, Tübingen, Germany
| | - Ulrich Luecking
- Bayer Pharma AG, Drug Discovery, Müllerstrasse 178, Berlin, Germany
| | - Michael Michaelides
- Oncology Chemistry, AbbVie, 1 North Waukegan Road, North Chicago, Illinois, United States of America
| | - Susanne Müller
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, and Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 15, Frankfurt am Main, Germany
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - R. Aldrin Denny
- Worldwide Medicinal Chemistry, Pfizer Inc., Cambridge, Massachusetts, United States of America
| | - Kumar S. Saikatendu
- Global Research Externalization, Takeda California, Inc., 10410 Science Center Drive, San Diego, California, United States of America
| | | | - William J. Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. Topological features of a gene co-expression network predict patterns of natural diversity in environmental response. Proc Biol Sci 2017; 284:20170914. [PMID: 28615505 PMCID: PMC5474086 DOI: 10.1098/rspb.2017.0914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/17/2017] [Indexed: 01/26/2023] Open
Abstract
Molecular interactions affect the evolution of complex traits. For instance, adaptation may be constrained by pleiotropic or epistatic effects, both of which can be reflected in the structure of molecular interaction networks. To date, empirical studies investigating the role of molecular interactions in phenotypic evolution have been idiosyncratic, offering no clear patterns. Here, we investigated the network topology of genes putatively involved in local adaptation to two abiotic stressors-drought and cold-in Arabidopsis thaliana Our findings suggest that the gene-interaction topologies for both cold and drought stress response are non-random, with genes that show genetic variation in drought expression response (eGxE) being significantly more peripheral and cold response genes being significantly more central than genes which do not show GxE. We suggest that the observed topologies reflect different constraints on the genetic pathways involved in environmental response. The approach presented here may inform predictive models linking genetic variation in molecular signalling networks with phenotypic variation, specifically traits involved in environmental response.
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Affiliation(s)
- David L Des Marais
- Arnold Arboretum and Department of Organismic and Evolutionary Biology, Harvard University, 1300 Centre Street, Boston, MA 20131, USA
| | - Rafael F Guerrero
- Department of Biology, Indiana University, Jordan Hall 142, Bloomington, IN 47405, USA
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, 408 Life Sciences Building, University Park, PA 16802, USA
| | - Samuel V Scarpino
- Department of Mathematics and Statistics and Vermont Complex Systems Center, University of Vermont, 210 Colchester Avenue, Burlington, VT 05405, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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Khan F, Chai HH, Ajmera I, Hodgman C, Mayes S, Lu C. A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress. Genes (Basel) 2017; 8:E121. [PMID: 28420201 PMCID: PMC5406868 DOI: 10.3390/genes8040121] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 11/18/2022] Open
Abstract
The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome.
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Affiliation(s)
- Faraz Khan
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham LE12 5RD, UK.
| | - Hui Hui Chai
- Crops for the Future, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Ishan Ajmera
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Nottingham LE12 5RD, UK.
| | - Charlie Hodgman
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Nottingham LE12 5RD, UK.
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham LE12 5RD, UK.
- Crops for the Future, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
| | - Chungui Lu
- School of Animal Rural and Environmental Sciences, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK.
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Kimura S, Waszczak C, Hunter K, Wrzaczek M. Bound by Fate: The Role of Reactive Oxygen Species in Receptor-Like Kinase Signaling. THE PLANT CELL 2017; 29:638-654. [PMID: 28373519 PMCID: PMC5435433 DOI: 10.1105/tpc.16.00947] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/08/2017] [Accepted: 03/29/2017] [Indexed: 05/19/2023]
Abstract
In plants, receptor-like kinases (RLKs) and extracellular reactive oxygen species (ROS) contribute to the communication between the environment and the interior of the cell. Apoplastic ROS production is a frequent result of RLK signaling in a multitude of cellular processes; thus, by their nature, these two signaling components are inherently linked. However, it is as yet unclear how ROS signaling downstream of receptor activation is executed. In this review, we provide a broad view of the intricate connections between RLKs and ROS signaling and describe the regulatory events that control and coordinate extracellular ROS production. We propose that concurrent initiation of ROS-dependent and -independent signaling linked to RLKs might be a critical element in establishing cellular responses. Furthermore, we discuss the possible ROS sensing mechanisms in the context of the biochemical environment in the apoplast. We suggest that RLK-dependent modulation of apoplastic and intracellular conditions facilitates ROS perception and signaling. Based on data from plant and animal models, we argue that specific RLKs could be components of the ROS sensing machinery or ROS sensors. The importance of the crosstalk between RLK and ROS signaling is discussed in the context of stomatal immunity. Finally, we highlight challenges in the understanding of these signaling processes and provide perspectives for future research.
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Affiliation(s)
- Sachie Kimura
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, FI-00014 Helsinki, Finland
| | - Cezary Waszczak
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, FI-00014 Helsinki, Finland
| | - Kerri Hunter
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, FI-00014 Helsinki, Finland
| | - Michael Wrzaczek
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, FI-00014 Helsinki, Finland
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50
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Bhattacharjee A, Sharma R, Jain M. Over-Expression of OsHOX24 Confers Enhanced Susceptibility to Abiotic Stresses in Transgenic Rice via Modulating Stress-Responsive Gene Expression. FRONTIERS IN PLANT SCIENCE 2017; 8:628. [PMID: 28484484 PMCID: PMC5399076 DOI: 10.3389/fpls.2017.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Homeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT). OsHOX24 over-expression rice seedlings showed reduced root and shoot growth under salinity and desiccation stress (DS) conditions. Various physiological and phenotypic assays confirmed higher susceptibility of rice transgenics toward abiotic stresses as compared to WT at mature and reproductive stages of rice development too. Global gene expression profiling revealed differential regulation of several genes in the transgenic plants under control and DS conditions. Many of these differentially expressed genes were found to be involved in transcriptional regulatory activities, besides carbohydrate, nucleic acid and lipid metabolic processes and response to abiotic stress and hormones. Taken together, our findings highlighted the role of OsHOX24 in regulation of abiotic stress responses via modulating the expression of stress-responsive genes in rice.
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Affiliation(s)
| | | | - Mukesh Jain
- National Institute of Plant Genome ResearchNew Delhi, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru UniversityNew Delhi, India
- *Correspondence: Mukesh Jain, ;
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