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Jorge GL, Kim D, Xu C, Cho SH, Su L, Xu D, Bartley LE, Stacey G, Thelen JJ. Unveiling orphan receptor-like kinases in plants: novel client discovery using high-confidence library predictions in the Kinase-Client (KiC) assay. FRONTIERS IN PLANT SCIENCE 2024; 15:1372361. [PMID: 38633461 PMCID: PMC11021772 DOI: 10.3389/fpls.2024.1372361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Plants are remarkable in their ability to adapt to changing environments, with receptor-like kinases (RLKs) playing a pivotal role in perceiving and transmitting environmental cues into cellular responses. Despite extensive research on RLKs from the plant kingdom, the function and activity of many kinases, i.e., their substrates or "clients", remain uncharted. To validate a novel client prediction workflow and learn more about an important RLK, this study focuses on P2K1 (DORN1), which acts as a receptor for extracellular ATP (eATP), playing a crucial role in plant stress resistance and immunity. We designed a Kinase-Client (KiC) assay library of 225 synthetic peptides, incorporating previously identified P2K phosphorylated peptides and novel predictions from a deep-learning phosphorylation site prediction model (MUsite) and a trained hidden Markov model (HMM) based tool, HMMER. Screening the library against purified P2K1 cytosolic domain (CD), we identified 46 putative substrates, including 34 novel clients, 27 of which may be novel peptides, not previously identified experimentally. Gene Ontology (GO) analysis among phosphopeptide candidates revealed proteins associated with important biological processes in metabolism, structure development, and response to stress, as well as molecular functions of kinase activity, catalytic activity, and transferase activity. We offer selection criteria for efficient further in vivo experiments to confirm these discoveries. This approach not only expands our knowledge of P2K1's substrates and functions but also highlights effective prediction algorithms for identifying additional potential substrates. Overall, the results support use of the KiC assay as a valuable tool in unraveling the complexities of plant phosphorylation and provide a foundation for predicting the phosphorylation landscape of plant species based on peptide library results.
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Affiliation(s)
- Gabriel Lemes Jorge
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Daewon Kim
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Chunhui Xu
- Institute for Data Science and Informatics, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sung-Hwan Cho
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Lingtao Su
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Shandong University of Science and Technology, Qingdao, Shandong, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Gary Stacey
- Division of Plant Science & Technology, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jay J. Thelen
- Division of Biochemistry, C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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Pahuja S, Bheri M, Bisht D, Pandey GK. Calcium signalling components underlying NPK homeostasis: potential avenues for exploration. Biochem J 2023; 480:1015-1034. [PMID: 37418287 DOI: 10.1042/bcj20230156] [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: 04/23/2023] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Plants require the major macronutrients, nitrogen (N), phosphorus (P) and potassium (K) for normal growth and development. Their deficiency in soil directly affects vital cellular processes, particularly root growth and architecture. Their perception, uptake and assimilation are regulated by complex signalling pathways. To overcome nutrient deficiencies, plants have developed certain response mechanisms that determine developmental and physiological adaptations. The signal transduction pathways underlying these responses involve a complex interplay of components such as nutrient transporters, transcription factors and others. In addition to their involvement in cross-talk with intracellular calcium signalling pathways, these components are also engaged in NPK sensing and homeostasis. The NPK sensing and homeostatic mechanisms hold the key to identify and understand the crucial players in nutrient regulatory networks in plants under both abiotic and biotic stresses. In this review, we discuss calcium signalling components/pathways underlying plant responses to NPK sensing, with a focus on the sensors, transporters and transcription factors involved in their respective signalling and homeostasis.
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Affiliation(s)
- Sonam Pahuja
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Diksha Bisht
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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Kim D, Chen D, Ahsan N, Jorge GL, Thelen JJ, Stacey G. The Raf-like MAPKKK INTEGRIN-LINKED KINASE 5 regulates purinergic receptor-mediated innate immunity in Arabidopsis. THE PLANT CELL 2023; 35:1572-1592. [PMID: 36762404 PMCID: PMC10118279 DOI: 10.1093/plcell/koad029] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/31/2023] [Indexed: 06/17/2023]
Abstract
Mitogen-activated protein (MAP) kinase signaling cascades play important roles in eukaryotic defense against various pathogens. Activation of the extracellular ATP (eATP) receptor P2K1 triggers MAP kinase 3 and 6 (MPK3/6) phosphorylation, which leads to an elevated plant defense response. However, the mechanism by which P2K1 activates the MAPK cascade is unclear. In this study, we show that in Arabidopsis thaliana, P2K1 phosphorylates the Raf-like MAP kinase kinase kinase (MAPKKK) INTEGRIN-LINKED KINASE 5 (ILK5) on serine 192 in the presence of eATP. The interaction between P2K1 and ILK5 was confirmed both in vitro and in planta and their interaction was enhanced by ATP treatment. Similar to P2K1 expression, ILK5 expression levels were highly induced by treatment with ATP, flg22, Pseudomonas syringae pv. tomato DC3000, and various abiotic stresses. ILK5 interacts with and phosphorylates the MAP kinase MKK5. Moreover, phosphorylation of MPK3/6 was significantly reduced upon ATP treatment in ilk5 mutant plants, relative to wild-type (WT). The ilk5 mutant plants showed higher susceptibility to P. syringae pathogen infection relative to WT plants. Plants expressing only the mutant ILK5S192A protein, with decreased kinase activity, did not activate the MAPK cascade upon ATP addition. These results suggest that eATP activation of P2K1 results in transphosphorylation of the Raf-like MAPKKK ILK5, which subsequently triggers the MAPK cascade, culminating in activation of MPK3/6 associated with an elevated innate immune response.
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Affiliation(s)
- Daewon Kim
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
| | - Dongqin Chen
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
| | - Nagib Ahsan
- Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
| | - Gabriel Lemes Jorge
- Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
| | - Jay J Thelen
- Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
| | - Gary Stacey
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
- Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA
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Uemoto K, Mori F, Yamauchi S, Kubota A, Takahashi N, Egashira H, Kunimoto Y, Araki T, Takemiya A, Ito H, Endo M. Root PRR7 Improves the Accuracy of the Shoot Circadian Clock through Nutrient Transport. PLANT & CELL PHYSIOLOGY 2023; 64:352-362. [PMID: 36631969 PMCID: PMC10016326 DOI: 10.1093/pcp/pcad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The circadian clock allows plants to anticipate and adapt to periodic environmental changes. Organ- and tissue-specific properties of the circadian clock and shoot-to-root circadian signaling have been reported. While this long-distance signaling is thought to coordinate physiological functions across tissues, little is known about the feedback regulation of the root clock on the shoot clock in the hierarchical circadian network. Here, we show that the plant circadian clock conveys circadian information between shoots and roots through sucrose and K+. We also demonstrate that K+ transport from roots suppresses the variance of period length in shoots and then improves the accuracy of the shoot circadian clock. Sucrose measurements and qPCR showed that root sucrose accumulation was regulated by the circadian clock. Furthermore, root circadian clock genes, including PSEUDO-RESPONSE REGULATOR7 (PRR7), were regulated by sucrose, suggesting the involvement of sucrose from the shoot in the regulation of root clock gene expression. Therefore, we performed time-series measurements of xylem sap and micrografting experiments using prr7 mutants and showed that root PRR7 regulates K+ transport and suppresses variance of period length in the shoot. Our modeling analysis supports the idea that root-to-shoot signaling contributes to the precision of the shoot circadian clock. We performed micrografting experiments that illustrated how root PRR7 plays key roles in maintaining the accuracy of shoot circadian rhythms. We thus present a novel directional signaling pathway for circadian information from roots to shoots and propose that plants modulate physiological events in a timely manner through various timekeeping mechanisms.
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Affiliation(s)
- Kyohei Uemoto
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto, 606-8501 Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192 Japan
| | - Fumito Mori
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540 Japan
| | - Shota Yamauchi
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512 Japan
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192 Japan
| | - Nozomu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192 Japan
| | - Haruki Egashira
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192 Japan
| | - Yumi Kunimoto
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-Cho, Ikoma, Nara, 630-0192 Japan
| | - Takashi Araki
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Yoshida-Konoecho, Sakyo-ku, Kyoto, 606-8501 Japan
| | - Atsushi Takemiya
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512 Japan
| | - Hiroshi Ito
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru, Minami-ku, Fukuoka, 815-8540 Japan
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Zhao Y, Wang L, Zhao P, Liu Z, Guo S, Li Y, Liu H. Genome-wide identification, characterization and expression analysis of HAK genes and decoding their role in responding to potassium deficiency and abiotic stress in Medicago truncatula. PeerJ 2022; 10:e14034. [PMID: 36168431 PMCID: PMC9509677 DOI: 10.7717/peerj.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/18/2022] [Indexed: 01/19/2023] Open
Abstract
Background The HAK family is the largest potassium (K+) transporter family, vital in K+ uptake, plant growth, and both plant biotic and abiotic stress responses. Although HAK family members have been characterized and functionally investigated in many species, these genes are still not studied in detail in Medicago truncatula, a good model system for studying legume genetics. Methods In this study, we screened the M. truncatula HAK family members (MtHAKs). Furthermore, we also conducted the identification, phylogenetic analysis, and prediction of conserved motifs of MtHAKs. Moreover, we studied the expression levels of MtHAKs under K+ deficiency, drought, and salt stresses using quantitative real-time PCR (qRT-PCR). Results We identified 20 MtHAK family members and classified them into three clusters based on phylogenetic relationships. Conserved motif analyses showed that all MtHAK proteins besides MtHAK10 contained the highly conserved K+ transport domain (GVVYGDLGTSPLY). qRT-PCR analysis showed that several MtHAK genes in roots were induced by abiotic stress. In particular, MtHAK15, MtHAK17, and MtHAK18 were strongly up-regulated in the M. truncatula roots under K+ deficiency, drought, and salt stress conditions, thereby implying that these genes are good candidates for high-affinity K+ uptake and therefore have essential roles in drought and salt tolerance. Discussions Our results not only provided the first genetic description and evolutionary relationships of the K+ transporter family in M. truncatula, but also the potential information responding to K+ deficiency and abiotic stresses, thereby laying the foundation for molecular breeding of stress-resistant legume crops in the future.
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Affiliation(s)
- Yanxue Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Pengcheng Zhao
- College of Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhongjie Liu
- Key Laboratory of Genetics and Fruit Development, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yang Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hao Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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6
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Su J, Lu YJ, Staal J, Ludwików A. Editorial: Protein phosphorylation and dephosphorylation in plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2022; 13:1020772. [PMID: 36160988 PMCID: PMC9504057 DOI: 10.3389/fpls.2022.1020772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Jianbin Su
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Yi-Ju Lu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Jens Staal
- VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Wan C, Liu Y, Tian S, Guo J, Bai X, Zhu H, Kang Z, Guo J. A serine-rich effector from the stripe rust pathogen targets a Raf-like kinase to suppress host immunity. PLANT PHYSIOLOGY 2022; 190:762-778. [PMID: 35567492 PMCID: PMC9434189 DOI: 10.1093/plphys/kiac218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 05/16/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst) is an important obligate pathogen in wheat (Triticum aestivum L.) and secretes effectors into plant cells to promote infection. Identifying host targets of effector proteins and clarifying their roles in pathogen infection is essential for understanding pathogen virulence. In this study, we identified a serine-rich effector, Pst27791, from Pst that suppresses cell death in Nicotiana benthamiana. Stable overexpression of Pst27791 in wheat suppressed reactive oxygen species accumulation and the salicylic acid-dependent defense response. Transgenic wheat expressing the RNA interference construct of Pst27791 exhibited high resistance to Pst virulent isolate CYR31, indicating its importance in pathogenesis. Pst27791 interacting with wheat rapidly accelerated fibrosarcoma (Raf)-like kinase TaRaf46 in yeast and in planta. Knocking down TaRaf46 expression in wheat attenuated Pst infection and increased wheat immunity. The overexpression of TaRaf46 decreased wheat resistance to Pst and repressed MAPK activation in wheat. Pst27791 may stabilize TaRaf46 through the inhibition of proteasome-mediated degradation in N. benthamiana. The ability of Pst27791 to enhance Pst colonization was compromised when TaRaf46 was silenced, suggesting that the virulence of Pst27791 is mediated by TaRaf46. Overall, these results indicate that Raf-like kinase TaRaf46 is exploited by the Pst effector as a negative regulator of plant immunity to promote infection in wheat.
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Affiliation(s)
- Cuiping Wan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Yan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuxin Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jia Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingxuan Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Haochuan Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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8
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Brauer EK, Ahsan N, Popescu GV, Thelen JJ, Popescu SC. Back From the Dead: The Atypical Kinase Activity of a Pseudokinase Regulator of Cation Fluxes During Inducible Immunity. FRONTIERS IN PLANT SCIENCE 2022; 13:931324. [PMID: 36035673 PMCID: PMC9403797 DOI: 10.3389/fpls.2022.931324] [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: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Pseudokinases are thought to lack phosphotransfer activity due to altered canonical catalytic residues within their kinase domain. However, a subset of pseudokinases maintain activity through atypical phosphotransfer mechanisms. The Arabidopsis ILK1 is a pseudokinase from the Raf-like MAP3K family and is the only known plant pseudokinase with confirmed protein kinase activity. ILK1 activity promotes disease resistance and molecular pattern-induced root growth inhibition through its stabilization of the HAK5 potassium transporter with the calmodulin-like protein CML9. ILK1 also has a kinase-independent function in salt stress suggesting that it interacts with additional proteins. We determined that members of the ILK subfamily are the sole pseudokinases within the Raf-like MAP3K family and identified 179 novel putative ILK1 protein interactors. We also identified 70 novel peptide targets for ILK1, the majority of which were phosphorylated in the presence of Mn2+ instead of Mg2+ in line with modifications in ILK1's DFG cofactor binding domain. Overall, the ILK1-targeted or interacting proteins included diverse protein types including transporters (HAK5, STP1), protein kinases (MEKK1, MEKK3), and a cytokinin receptor (AHK2). The expression of 31 genes encoding putative ILK1-interacting or phosphorylated proteins, including AHK2, were altered in the root and shoot in response to molecular patterns suggesting a role for these genes in immunity. We describe a potential role for ILK1 interactors in the context of cation-dependent immune signaling, highlighting the importance of K+ in MAMP responses. This work further supports the notion that ILK1 is an atypical kinase with an unusual cofactor dependence that may interact with multiple proteins in the cell.
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Affiliation(s)
- Elizabeth K. Brauer
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States
| | - Nagib Ahsan
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - George V. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Jay J. Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sorina C. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
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Jadhav KP, Saykhedkar GR, Tamilarasi PM, Devasree S, Ranjani RV, Sarankumar C, Bharathi P, Karthikeyan A, Arulselvi S, Vijayagowri E, Ganesan KN, Paranidharan V, Nair SK, Babu R, Ramalingam J, Raveendran M, Senthil N. GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.). Front Genet 2022; 13:890133. [PMID: 35937985 PMCID: PMC9348272 DOI: 10.3389/fgene.2022.890133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022] Open
Abstract
Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi, threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%–18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.
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Affiliation(s)
- Kashmiri Prakash Jadhav
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Gajanan R. Saykhedkar
- Asian Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, India
| | | | - Subramani Devasree
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rajagopalan Veera Ranjani
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Chandran Sarankumar
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Pukalenthy Bharathi
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Soosai Arulselvi
- Agricultural College and Research Institute, Thanjavur, Tamil Nadu Agricultural University, Thanjavur, India
| | - Esvaran Vijayagowri
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kalipatty Nalliappan Ganesan
- Department of Forage Crops, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India
| | - Vaikuntavasan Paranidharan
- Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
| | - Sudha K. Nair
- Asian Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, India
| | - Raman Babu
- Corteva Agrisciences, Multi Crop Research Centre, Hyderabad, India
| | - Jegadeesan Ramalingam
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Muthurajan Raveendran
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Natesan Senthil
- Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
- *Correspondence: Natesan Senthil,
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Sathee L, Jagadhesan B, Pandesha PH, Barman D, Adavi B S, Nagar S, Krishna GK, Tripathi S, Jha SK, Chinnusamy V. Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation. Front Genet 2022; 13:900897. [PMID: 35774509 PMCID: PMC9237392 DOI: 10.3389/fgene.2022.900897] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.
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Affiliation(s)
- Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
| | - B. Jagadhesan
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pratheek H. Pandesha
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Roy and Diana Vagelos Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Dipankar Barman
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sandeep Adavi B
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shivani Nagar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. K. Krishna
- Department of Plant Physiology, College of Agriculture, KAU, Thrissur, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Lekshmy Sathee, ; Viswanathan Chinnusamy,
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Meng X, Yu Y, Song T, Yu Y, Cui N, Ma Z, Chen L, Fan H. Transcriptome Sequence Analysis of the Defense Responses of Resistant and Susceptible Cucumber Strains to Podosphaera xanthii. FRONTIERS IN PLANT SCIENCE 2022; 13:872218. [PMID: 35645993 PMCID: PMC9134894 DOI: 10.3389/fpls.2022.872218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew (PM) caused by Podosphaera xanthii poses a continuous threat to the performance and yield of the cucumber (Cucumis sativus L.). Control in the initial stages of infection is particularly important. Here, we studied the differential physiological and transcriptomic changes between PM-resistant strain B21-a-2-1-2 and PM-susceptible strain B21-a-2-2-2 at the early stage of P. xanthii attack. When challenged with P. xanthii, the tolerant line can postpone the formation of the pathogen primary germ. Comparative transcriptomic analysis suggested that DEGs related to the cell wall and to pathogen and hormone responses were similar enriched in both cucumber lines under P. xanthii infection. Notably, the number of DEGs triggered by P. xanthii in B21-a-2-1-2 was quintuple that in B21-a-2-2-2, revealing that the success of defense of resistant cucumber is due to rapidly mobilizing multiple responses. The unique responses detected were genes related to SA signaling, MAPK signaling, and Dof and WRKY transcription factors. Furthermore, 5 P. xanthii -inducible hub genes were identified, including GLPK, ILK1, EIN2, BCDHβ1, and RGGA, which are considered to be key candidate genes for disease control. This study combined multiple analytical approaches to capture potential molecular players and will provide key resources for developing cucumber cultivars resistant to pathogen stress.
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Affiliation(s)
- Xiangnan Meng
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yongbo Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Tiefeng Song
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yang Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Na Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Zhangtong Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Lijie Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang, China
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12
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Qiao Z, Yates TB, Shrestha HK, Engle NL, Flanagan A, Morrell‐Falvey JL, Sun Y, Tschaplinski TJ, Abraham PE, Labbé J, Wang Z, Hettich RL, Tuskan GA, Muchero W, Chen J. Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2454-2468. [PMID: 34272801 PMCID: PMC8633507 DOI: 10.1111/pbi.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 05/22/2023]
Abstract
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor-root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated-transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down-regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
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Affiliation(s)
- Zhenzhen Qiao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Timothy B. Yates
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTNUSA
| | - Him K. Shrestha
- Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Yali Sun
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jessy Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
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Chen P, Li Z, Zhang D, Shen W, Xie Y, Zhang J, Jiang L, Li X, Shen X, Geng D, Wang L, Niu C, Bao C, Yan M, Li H, Li C, Yan Y, Zou Y, Micheletti D, Koot E, Ma F, Guan Q. Insights into the effect of human civilization on Malus evolution and domestication. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2206-2220. [PMID: 34161653 PMCID: PMC8541786 DOI: 10.1111/pbi.13648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 05/09/2023]
Abstract
The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.
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Affiliation(s)
- Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Mingjia Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Haiyan Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yangjun Zou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | | | - Emily Koot
- The New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
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Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening. PLoS One 2021; 16:e0256319. [PMID: 34428253 PMCID: PMC8384167 DOI: 10.1371/journal.pone.0256319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.
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Nayyeripasand L, Garoosi GA, Ahmadikhah A. Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage. RICE (NEW YORK, N.Y.) 2021; 14:9. [PMID: 33420909 PMCID: PMC7797017 DOI: 10.1186/s12284-020-00433-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/07/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. RESULTS Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79-42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. CONCLUSION Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.
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Affiliation(s)
- Leila Nayyeripasand
- Agricultural Biotechnology Department, Faculty of Agriculture, Imam Khomeini International University, Qazvin, Iran
| | - Ghasem Ali Garoosi
- Agricultural Biotechnology Department, Faculty of Agriculture, Imam Khomeini International University, Qazvin, Iran.
| | - Asadollah Ahmadikhah
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshi University, G.C. Velenjak, Tehran, Iran.
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Luo L, Wan Q, Zhang K, Zhang X, Guo R, Wang C, Zheng C, Liu F, Ding Z, Wan Y. AhABI4s Negatively Regulate Salt-Stress Response in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:741641. [PMID: 34721468 PMCID: PMC8551806 DOI: 10.3389/fpls.2021.741641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 05/04/2023]
Abstract
Soil salinity is one of the major factors that limit the area of cultivable land and yield potential of crops. The ability of salt tolerance varies with plant species. Peanut (Arachis hypogaea L.) is a moderately salt-sensitive and economically important crop, however, their biological processes involved in salt-stress response remain unclear. In this study, we investigated the role of A. hypogaea L. ABSCISIC ACID INSENSITIVE 4s (AhABI4s) in salt tolerance and elucidated its mode of action in peanuts. The results showed that the downregulation of AhABI4s via whole plant virus-induced gene silencing has enhanced the survival rate, biomass accumulation, and root/shoot ratio of peanut seedlings in response to salt-stress. Transcriptomics, quantitative proteomics, and phosphoproteomic analyses were performed using AhABI4s-silenced and Mock plants. The expression pattern of 15,247 genes, 1,900 proteins, and 2,620 phosphorylation sites were affected by silencing of AhABI4s in peanut leaf and root after sodium chloride (NaCl) treatment. Among them, 63 potential downstream target genes of ABI4 changed consistently at both transcription and translation levels, and the protein/phosphorylation levels of 31 ion transporters/channels were also affected. Electrophoretic mobility shift assays (EMSA) showed that ABI4 was able to bind to the promoters of HSP70, fructokinase (FRK), and pyruvate kinase (PK) coding genes in vitro. In addition, we also detected a binding preference of AhABI4 for CACT(G/T)GCA motif in the promoters of down-regulated genes in peanut leaf. Collectively, the potential downstream targets which were regulated at the levels of transcription and translation, binding preference, and in vivo phosphorylation sites that had been revealed in this study will provide new insight into the AhABI4s-mediated salt tolerance regulation mechanism in peanuts.
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Affiliation(s)
- Lu Luo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, China
| | - Qian Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Kun Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Xiurong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Ruijie Guo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Cai Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- *Correspondence: Fengzhen Liu
| | - Zhaojun Ding
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, China
- Zhaojun Ding
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
- Yongshan Wan
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17
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Genome-wide characterization and expression analysis of HAK K + transport family in Ipomoea. 3 Biotech 2021; 11:3. [PMID: 33269187 DOI: 10.1007/s13205-020-02552-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022] Open
Abstract
The potassium transporter high-affinity K+ transporter/K+ uptake permease/K+ transporter (HAK/KUP/KT) family plays a vital role in potassium uptake, and potassium ion (K+)-mediated environmental stress. In the present study, we identified 22 IbHAK/KUP/KT (HAK) genes in sweet potato [Ipomoea batata (L.) Lam] and the same number of HAK genes from sweet potato wild relative Ipomoea trifida. Phylogeny analysis indicated that the HAKs can be divided into five clades. Chromosomal distribution and genome synteny analyses revealed two tandem-duplicated gene pairs IbHAK16/17 and IbHAK17/18 on chromosomes 13 and eight segmental-duplicated gene pairs on chromosomes 1, 3, 5, 8, 10, 12, 14 among the IbHAK gene family. Eleven orthologous HAK gene pairs between I. batata and I. trifida were involved in the duplication of genomic blocks based on comparative genomic analysis. The Ka/Ks ratios of these IbHAK genes ranged from 0.02 to 0.55(< 1), further indicated that purifying selection was the primary force driving the evolution of HAKs in Ipomoea. A heat map based on RNA-seq data showed that 13 HAKs in Xushu32 (a K+-tolerant sweet potato genotype) and 10 HAKs in Ningzi1 (a K+-sensitive sweet potato genotype) in response to K+ deficiency stress. Quantitative real-time PCR (qRT-PCR) analysis revealed IbHAK2, -3, -8, -10, -11, -18, -19, and -21 were induced in both Xushu32 and Ningzi1 under low K+ stress. Compared with other IbHAK genes, IbHAK8 showed more strongly upregulation after exposure to drought and salt stress. Furthermore, co-expression analysis showed that only IbHAK8 of 22 IbHAK genes involved in network interactions with 30 genes related to abiotic and biotic stresses. Taken together, these results are helpful for further functional studies on IbHAK and molecular breeding of sweet potato. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02552-3.
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Raddatz N, Morales de los Ríos L, Lindahl M, Quintero FJ, Pardo JM. Coordinated Transport of Nitrate, Potassium, and Sodium. FRONTIERS IN PLANT SCIENCE 2020; 11:247. [PMID: 32211003 PMCID: PMC7067972 DOI: 10.3389/fpls.2020.00247] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/18/2020] [Indexed: 05/19/2023]
Abstract
Potassium (K+) and nitrogen (N) are essential nutrients, and their absorption and distribution within the plant must be coordinated for optimal growth and development. Potassium is involved in charge balance of inorganic and organic anions and macromolecules, control of membrane electrical potential, pH homeostasis and the regulation of cell osmotic pressure, whereas nitrogen is an essential component of amino acids, proteins, and nucleic acids. Nitrate (NO3 -) is often the primary nitrogen source, but it also serves as a signaling molecule to the plant. Nitrate regulates root architecture, stimulates shoot growth, delays flowering, regulates abscisic acid-independent stomata opening, and relieves seed dormancy. Plants can sense K+/NO3 - levels in soils and adjust accordingly the uptake and root-to-shoot transport to balance the distribution of these ions between organs. On the other hand, in small amounts sodium (Na+) is categorized as a "beneficial element" for plants, mainly as a "cheap" osmolyte. However, at high concentrations in the soil, Na+ can inhibit various physiological processes impairing plant growth. Hence, plants have developed specific mechanisms to transport, sense, and respond to a variety of Na+ conditions. Sodium is taken up by many K+ transporters, and a large proportion of Na+ ions accumulated in shoots appear to be loaded into the xylem by systems that show nitrate dependence. Thus, an adequate supply of mineral nutrients is paramount to reduce the noxious effects of salts and to sustain crop productivity under salt stress. In this review, we will focus on recent research unraveling the mechanisms that coordinate the K+-NO3 -; Na+-NO3 -, and K+-Na+ transports, and the regulators controlling their uptake and allocation.
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Affiliation(s)
| | | | | | | | - José M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Seville, Spain
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19
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Zhu G, Gao W, Song X, Sun F, Hou S, Liu N, Huang Y, Zhang D, Ni Z, Chen Q, Guo W. Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2020; 20:23. [PMID: 31937242 PMCID: PMC6961271 DOI: 10.1186/s12870-019-2187-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/05/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. RESULTS Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. CONCLUSIONS This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.
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Affiliation(s)
- Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenwei Gao
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Xiaohui Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Fenglei Sun
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Sen Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Na Liu
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Yajie Huang
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Dayong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhiyong Ni
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Quanjia Chen
- Engineering Research Center for Cotton (the Ministry of Education), Xinjiang Agricultural University, Urumqi, 830052 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Engineering Research Center of Hybrid Cotton Development (the Ministry of Education), Nanjing Agricultural University, Nanjing, 210095 China
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20
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Cai K, Gao H, Wu X, Zhang S, Han Z, Chen X, Zhang G, Zeng F. The Ability to Regulate Transmembrane Potassium Transport in Root Is Critical for Drought Tolerance in Barley. Int J Mol Sci 2019; 20:E4111. [PMID: 31443572 PMCID: PMC6747136 DOI: 10.3390/ijms20174111] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/11/2019] [Accepted: 08/20/2019] [Indexed: 01/26/2023] Open
Abstract
In this work, the effect of drought on K+ uptake in root and its translocation from root to shoot was investigated using six barley genotypes contrasting in drought tolerance. Results showed that drought conditions caused significant changes in K+ uptake and translocation in a time- and genotype-specific manner, which consequently resulted in a significant difference in tissue K+ contents and drought tolerance levels between the contrasting barley genotypes. The role of K+ transporters and channels and plasma membrane (PM) H+-ATPase in barley's adaptive response to drought stress was further investigated at the transcript level. The expression of genes conferring K+ uptake (HvHAK1, HvHAK5, HvKUP1, HvKUP2 and HvAKT1) and xylem loading (HvSKOR) in roots were all affected by drought stress in a time- and genotype-specific manner, indicating that the regulation of these K+ transporters and channels is critical for root K+ uptake and root to shoot K+ translocation in barley under drought stress. Furthermore, the barley genotypes showed a strong correlation between H+ efflux and K+ influx under drought stress, which was further confirmed by the significant up-regulation of HvHA1 and HvHA2. These results suggested an important role of plasma membrane H+-ATPase activity and/or expression in regulating the activity of K+ transporters and channels under drought stress. Taken together, it may be concluded that the genotypic difference in drought stress tolerance in barley is conferred by the difference in the ability to regulate K+ transporters and channels in root epidermis and stele.
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Affiliation(s)
- Kangfeng Cai
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Huaizhou Gao
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaojian Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shuo Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhigang Han
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaohui Chen
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Fanrong Zeng
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China.
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21
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Ragel P, Raddatz N, Leidi EO, Quintero FJ, Pardo JM. Regulation of K + Nutrition in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:281. [PMID: 30949187 PMCID: PMC6435592 DOI: 10.3389/fpls.2019.00281] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/20/2019] [Indexed: 05/17/2023]
Abstract
Modern agriculture relies on mineral fertilization. Unlike other major macronutrients, potassium (K+) is not incorporated into organic matter but remains as soluble ion in the cell sap contributing up to 10% of the dry organic matter. Consequently, K+ constitutes a chief osmoticum to drive cellular expansion and organ movements, such as stomata aperture. Moreover, K+ transport is critical for the control of cytoplasmic and luminal pH in endosomes, regulation of membrane potential, and enzyme activity. Not surprisingly, plants have evolved a large ensemble of K+ transporters with defined functions in nutrient uptake by roots, storage in vacuoles, and ion translocation between tissues and organs. This review describes critical transport proteins governing K+ nutrition, their regulation, and coordinated activity, and summarizes our current understanding of signaling pathways activated by K+ starvation.
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Affiliation(s)
- Paula Ragel
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
- Centre for Organismal Studies, Universität Heidelberg, Heidelberg, Germany
| | - Natalia Raddatz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Eduardo O. Leidi
- Instituto de Recursos Naturales y Agrobiologia de Sevilla, Consejo Superior de Investigaciones Cientificas, Seville, Spain
| | - Francisco J. Quintero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - José M. Pardo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
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22
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Bokros N, Popescu SC, Popescu GV. Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions. BMC Bioinformatics 2019; 20:99. [PMID: 30871456 PMCID: PMC6419318 DOI: 10.1186/s12859-019-2624-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses of entire gene families are widely employed in the fields of evolutionary and functional genomics of both well established and newly sequenced plant genomes. Currently, plant gene families are typically identified using one of two major ways: 1) HMM-profile based searches using models built on Arabidopsis thaliana genes or 2) coding sequence homology searches using curated databases. Integrated databases containing functionally annotated genes and gene families have been developed for model organisms and several important crops; however, a comprehensive methodology for gene family annotation is currently lacking, preventing automated annotation of newly sequenced genomes. Results This paper proposes a combined measure of homology identification, motif conservation, phylogenomic and integrated gene expression analyses to define gene family structures in multiple plant species. The MAP3K gene families in seven plant species, including two currently unexamined species Gossypium hirsutum, and Zostera marina, were characterized to reveal new insights into their collective function and evolution and demonstrate the effectiveness of our novel methodology. Conclusion Compared with recent reports, this methodology performs significantly better for the identification and analysis of gene family members in several monocots/dicots, diploid as well as polyploid plant species. Electronic supplementary material The online version of this article (10.1186/s12859-019-2624-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Norbert Bokros
- Department of Biochemistry, Molecular Biology, Plant Pathology and Entomology, Mississippi State University, Mississippi State, MS, 39762, USA.,Institute for Genomics, Biocomputing and Bioengineering, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Plant Pathology and Entomology, Mississippi State University, Mississippi State, MS, 39762, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing and Bioengineering, Mississippi State University, Mississippi State, MS, 39762, USA. .,The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
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23
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Ragel P, Raddatz N, Leidi EO, Quintero FJ, Pardo JM. Regulation of K + Nutrition in Plants. FRONTIERS IN PLANT SCIENCE 2019. [PMID: 30949187 DOI: 10.3389/fpls.2019.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Modern agriculture relies on mineral fertilization. Unlike other major macronutrients, potassium (K+) is not incorporated into organic matter but remains as soluble ion in the cell sap contributing up to 10% of the dry organic matter. Consequently, K+ constitutes a chief osmoticum to drive cellular expansion and organ movements, such as stomata aperture. Moreover, K+ transport is critical for the control of cytoplasmic and luminal pH in endosomes, regulation of membrane potential, and enzyme activity. Not surprisingly, plants have evolved a large ensemble of K+ transporters with defined functions in nutrient uptake by roots, storage in vacuoles, and ion translocation between tissues and organs. This review describes critical transport proteins governing K+ nutrition, their regulation, and coordinated activity, and summarizes our current understanding of signaling pathways activated by K+ starvation.
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Affiliation(s)
- Paula Ragel
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
- Centre for Organismal Studies, Universität Heidelberg, Heidelberg, Germany
| | - Natalia Raddatz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Eduardo O Leidi
- Instituto de Recursos Naturales y Agrobiologia de Sevilla, Consejo Superior de Investigaciones Cientificas, Seville, Spain
| | - Francisco J Quintero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - José M Pardo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
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24
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Brauer EK, Popescu GV, Singh DK, Calviño M, Gupta K, Gupta B, Chakravarthy S, Popescu SC. Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae. PLoS Biol 2018; 16:e2005956. [PMID: 30540739 PMCID: PMC6322785 DOI: 10.1371/journal.pbio.2005956] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 01/07/2019] [Accepted: 11/16/2018] [Indexed: 11/18/2022] Open
Abstract
Plant protein kinases form redundant signaling pathways to perceive microbial pathogens and activate immunity. Bacterial pathogens repress cellular immune responses by secreting effectors, some of which bind and inhibit multiple host kinases. To understand how broadly bacterial effectors may bind protein kinases and the function of these kinase interactors, we first tested kinase–effector (K-E) interactions using the Pseudomonas syringae pv. tomato–tomato pathosystem. We tested interactions between five individual effectors (HopAI1, AvrPto, HopA1, HopM1, and HopAF1) and 279 tomato kinases in tomato cells. Over half of the tested kinases interacted with at least one effector, and 48% of these kinases interacted with more than three effectors, suggesting a role in the defense. Next, we characterized the role of select multi-effector–interacting kinases and revealed their roles in basal resistance, effector-triggered immunity (ETI), or programmed cell death (PCD). The immune function of several of these kinases was only detectable in the presence of effectors, suggesting that these kinases are critical when particular cell functions are perturbed or that their role is typically masked. To visualize the kinase networks underlying the cellular responses, we derived signal-specific networks. A comparison of the networks revealed a limited overlap between ETI and basal immunity networks. In addition, the basal immune network complexity increased when exposed to some of the effectors. The networks were used to successfully predict the role of a new set of kinases in basal immunity. Our work indicates the complexity of the larger kinase-based defense network and demonstrates how virulence- and avirulence-associated bacterial effectors alter sectors of the defense network. Some bacterial pathogens secrete virulence factors called effectors, which influence host tissues during infection. The impact of such bacterial effectors on the transmission of immune signals in plants remains poorly understood. In this study, we developed an integrative network approach to discover interactions between bacterial effectors and a class of host signal-mediating enzymes called protein kinases. We also characterized the functions of the targets of these kinases in order to understand how bacterial effectors might disrupt the flow of information in signaling pathways within plant cells. We show that plants activate larger signaling networks when inoculated with pathogens that produce effectors. We also find that plant signaling networks are specific to individual effectors and that the networks include kinases with both positive and negative effects on plant resistance to pathogens. We propose that the topology of immune signaling networks is determined by the plant’s ability to activate compensatory pathways in response to the effectors’ network-disruptive actions. Conversely, pathogens may increase their virulence both by disrupting host signaling at the membrane-located end of the signaling network and by recruiting cytosolic kinases. This work provides a framework for the study of plant–pathogen communication and could be used to prioritize targets for improving resistance in crops.
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Affiliation(s)
- Elizabeth K. Brauer
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
- The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania
| | - Dharmendra K. Singh
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Mauricio Calviño
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Kamala Gupta
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Bhaskar Gupta
- The Boyce Thompson Institute for Plant Research, Ithaca, New York, United States of America
| | - Suma Chakravarthy
- Department of Plant Pathology, Cornell University, Ithaca, New York, United States of America
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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25
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Wang X, Hao L, Zhu B, Jiang Z. Plant Calcium Signaling in Response to Potassium Deficiency. Int J Mol Sci 2018; 19:E3456. [PMID: 30400321 PMCID: PMC6275041 DOI: 10.3390/ijms19113456] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/19/2018] [Accepted: 11/01/2018] [Indexed: 01/23/2023] Open
Abstract
Potassium (K⁺) is an essential macronutrient of living cells and is the most abundant cation in the cytosol. K⁺ plays a role in several physiological processes that support plant growth and development. However, soil K⁺ availability is very low and variable, which leads to severe reductions in plant growth and yield. Various K⁺ shortage-activated signaling cascades exist. Among these, calcium signaling is the most important signaling system within plant cells. This review is focused on the possible roles of calcium signaling in plant responses to low-K⁺ stress. In plants, intracellular calcium levels are first altered in response to K⁺ deficiency, resulting in calcium signatures that exhibit temporal and spatial features. In addition, calcium channels located within the root epidermis and root hair zone can then be activated by hyperpolarization of plasma membrane (PM) in response to low-K⁺ stress. Afterward, calcium sensors, including calmodulin (CaM), CaM-like protein (CML), calcium-dependent protein kinase (CDPK), and calcineurin B-like protein (CBL), can act in the sensing of K⁺ deprivation. In particular, the important components regarding CBL/CBL-interacting protein kinase (CBL/CIPK) complexes-involved in plant responses to K⁺ deficiency are also discussed.
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Affiliation(s)
- Xiaoping Wang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Ling Hao
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Biping Zhu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| | - Zhonghao Jiang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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26
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Murphy F, He Q, Armstrong M, Giuliani LM, Boevink PC, Zhang W, Tian Z, Birch PRJ, Gilroy EM. The Potato MAP3K StVIK Is Required for the Phytophthora infestans RXLR Effector Pi17316 to Promote Disease. PLANT PHYSIOLOGY 2018; 177:398-410. [PMID: 29588335 PMCID: PMC5933144 DOI: 10.1104/pp.18.00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/04/2018] [Indexed: 05/19/2023]
Abstract
Plant pathogens deliver effectors to manipulate processes in their hosts, creating a suitable environment for invasion and proliferation. Yet, little is known about the host proteins that are targeted by effectors from filamentous pathogens. Here, we show that stable transgenic expression in potato (Solanum tuberosum) and transient expression in Nicotiana benthamiana of the arginine-any amino acid-leucine-arginine effector Pi17316 enhances leaf colonization by the late blight pathogen Phytophthora infestans Expression of Pi17316 also attenuates cell death triggered by the pathogen-associated molecular pattern Infestin1 (INF1), indicating that the effector suppresses pattern-triggered immunity. However, this effector does not attenuate cell death triggered by a range of resistance proteins, showing that it specifically suppresses INF1-triggered cell death (ICD). In yeast two-hybrid assays, Pi17316 interacts directly with the potato ortholog of VASCULAR HIGHWAY1-interacting kinase (StVIK), encoding a predicted MEK kinase (MAP3K). Interaction in planta was confirmed by coimmunoprecipitation and occurs at the plant plasma membrane. Virus-induced gene silencing of VIK in N. benthamiana attenuated P. infestans colonization, whereas transient overexpression of StVIK enhanced colonization, indicating that this host protein acts as a susceptibility factor. Moreover, VIK overexpression specifically attenuated ICD, indicating that it is a negative regulator of immunity. The abilities of Pi17316 to enhance P. infestans colonization or suppress ICD were compromised significantly in NbVIK-silenced plants, demonstrating that the effector activity of Pi17316 is mediated by this MAP3K. Thus, StVIK is exploited by P. infestans as a susceptibility factor to promote late blight disease.
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Affiliation(s)
- Fraser Murphy
- Division of Plant Science, University of Dundee (at James Hutton Institute), Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Qin He
- Division of Plant Science, University of Dundee (at James Hutton Institute), Invergowrie, Dundee DD2 5DA, United Kingdom
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Miles Armstrong
- Division of Plant Science, University of Dundee (at James Hutton Institute), Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Licida M Giuliani
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Wei Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhendong Tian
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Paul R J Birch
- Division of Plant Science, University of Dundee (at James Hutton Institute), Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Eleanor M Gilroy
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
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27
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La Verde V, Dominici P, Astegno A. Towards Understanding Plant Calcium Signaling through Calmodulin-Like Proteins: A Biochemical and Structural Perspective. Int J Mol Sci 2018; 19:E1331. [PMID: 29710867 PMCID: PMC5983762 DOI: 10.3390/ijms19051331] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022] Open
Abstract
Ca2+ ions play a key role in a wide variety of environmental responses and developmental processes in plants, and several protein families with Ca2+-binding domains have evolved to meet these needs, including calmodulin (CaM) and calmodulin-like proteins (CMLs). These proteins have no catalytic activity, but rather act as sensor relays that regulate downstream targets. While CaM is well-studied, CMLs remain poorly characterized at both the structural and functional levels, even if they are the largest class of Ca2+ sensors in plants. The major structural theme in CMLs consists of EF-hands, and variations in these domains are predicted to significantly contribute to the functional versatility of CMLs. Herein, we focus on recent advances in understanding the features of CMLs from biochemical and structural points of view. The analysis of the metal binding and structural properties of CMLs can provide valuable insight into how such a vast array of CML proteins can coexist, with no apparent functional redundancy, and how these proteins contribute to cellular signaling while maintaining properties that are distinct from CaM and other Ca2+ sensors. An overview of the principal techniques used to study the biochemical properties of these interesting Ca2+ sensors is also presented.
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Affiliation(s)
- Valentina La Verde
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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28
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Shi X, Long Y, He F, Zhang C, Wang R, Zhang T, Wu W, Hao Z, Wang Y, Wang GL, Ning Y. The fungal pathogen Magnaporthe oryzae suppresses innate immunity by modulating a host potassium channel. PLoS Pathog 2018; 14:e1006878. [PMID: 29385213 PMCID: PMC5809103 DOI: 10.1371/journal.ppat.1006878] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/12/2018] [Accepted: 01/12/2018] [Indexed: 11/19/2022] Open
Abstract
Potassium (K+) is required by plants for growth and development, and also contributes to immunity against pathogens. However, it has not been established whether pathogens modulate host K+ signaling pathways to enhance virulence and subvert host immunity. Here, we show that the effector protein AvrPiz-t from the rice blast pathogen Magnaporthe oryzae targets a K+ channel to subvert plant immunity. AvrPiz-t interacts with the rice plasma-membrane-localized K+ channel protein OsAKT1 and specifically suppresses the OsAKT1-mediated K+ currents. Genetic and phenotypic analyses show that loss of OsAKT1 leads to decreased K+ content and reduced resistance against M. oryzae. Strikingly, AvrPiz-t interferes with the association of OsAKT1 with its upstream regulator, the cytoplasmic kinase OsCIPK23, which also plays a positive role in K+ absorption and resistance to M. oryzae. Furthermore, we show a direct correlation between blast disease resistance and external K+ status in rice plants. Together, our data present a novel mechanism by which a pathogen suppresses plant host immunity by modulating a host K+ channel. Plant nutritional status can greatly influence plant immunity in response to pathogen invasion. Rice blast, a devastating rice disease caused by the hemibiotrophic fungus Magnaporthe oryzae, causes a significant reduction in yield and affects food security. In this study, we demonstrate that the M. oryzae secreted protein AvrPiz-t interacts with rice OsAKT1, a potassium (K+) channel protein, and suppresses OsAKT1-mediated inward K+ currents, possibly by competing with the OsAKT1 upstream regulator, OsCIPK23. We also show that both OsAKT1 and OsCIPK23 are required for K+ uptake and resistance against M. oryzae infection in rice. This study provides new insights into the molecular basis of pathogen-mediated perturbation of a plant nutrition pathway.
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Affiliation(s)
- Xuetao Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Long
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chongyang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
- * E-mail: (YW); (GLW); (YN)
| | - Guo-Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (YW); (GLW); (YN)
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (YW); (GLW); (YN)
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Ou W, Mao X, Huang C, Tie W, Yan Y, Ding Z, Wu C, Xia Z, Wang W, Zhou S, Li K, Hu W. Genome-Wide Identification and Expression Analysis of the KUP Family under Abiotic Stress in Cassava ( Manihot esculenta Crantz). Front Physiol 2018; 9:17. [PMID: 29416511 PMCID: PMC5787556 DOI: 10.3389/fphys.2018.00017] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022] Open
Abstract
KT/HAK/KUP (KUP) family is responsible for potassium ion (K+) transport, which plays a vital role in the response of plants to abiotic stress by maintaining osmotic balance. However, our understanding of the functions of the KUP family in the drought-resistant crop cassava (Manihot esculenta Crantz) is limited. In the present study, 21 cassava KUP genes (MeKUPs) were identified and classified into four clusters based on phylogenetic relationships, conserved motifs, and gene structure analyses. Transcriptome analysis revealed the expression diversity of cassava KUPs in various tissues of three genotypes. Comparative transcriptome analysis showed that the activation of MeKUP genes by drought was more in roots than that in leaves of Arg7 and W14 genotypes, whereas less in roots than that in leaves of SC124 variety. These findings indicate that different cassava genotypes utilize various drought resistance mechanism mediated by KUP genes. Specific KUP genes showed broad upregulation after exposure to salt, osmotic, cold, H2O2, and abscisic acid (ABA) treatments. Taken together, this study provides insights into the KUP-mediated drought response of cassava at transcription levels and identifies candidate genes that may be utilized in improving crop tolerance to abiotic stress.
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Affiliation(s)
- Wenjun Ou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Xiang Mao
- Wuhan Centre for Disease Prevention and Control, Wuhan, China
| | - Chao Huang
- College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhiqiang Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenquan Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shiyi Zhou
- Hubei Key Laboratory of Purification and Application of Plant Anticancer Active Ingredients, Chemistry and Biology Science College, Hubei University of Education, Wuhan, China
| | - Kaimian Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China.,Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Chen G, Liu C, Gao Z, Zhang Y, Jiang H, Zhu L, Ren D, Yu L, Xu G, Qian Q. OsHAK1, a High-Affinity Potassium Transporter, Positively Regulates Responses to Drought Stress in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1885. [PMID: 29163608 PMCID: PMC5671996 DOI: 10.3389/fpls.2017.01885] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/17/2017] [Indexed: 05/04/2023]
Abstract
Drought is one of the environmental factors that severely restrict plant distribution and crop production. Recently, we reported that the high-affinity potassium transporter OsHAK1 plays important roles in K acquisition and translocation in rice over low and high K concentration ranges, however, knowledge on the regulatory roles of OsHAK1 in osmotic/drought stress is limited. Here, transcript levels of OsHAK1 were found transiently elevated by water deficit in roots and shoots, consistent with the enhanced GUS activity in transgenic plants under stress. Under drought conditions, OsHAK1 knockout mutants (KO) presented lower tolerance to the stress and displayed stunted growth at both the vegetative and reproductive stages. Phenotypic analysis of OsHAK1 overexpression seedlings (Ox) demonstrated that they present better tolerance to drought stress than wild-type (WT). Compared to WT seedlings, OsHAK1 overexpressors had lower level of lipid peroxidation, higher activities of antioxidant enzymes (POX and CAT) and higher proline accumulation. Furthermore, qPCR analysis revealed that OsHAK1 act as a positive regulator of the expression of stress-responsive genes as well as of two well-known rice channel genes (OsTPKb and OsAKT1) involved in K homeostasis and stress responses in transgenic plants under dehydration. Most important, OsHAK1-Ox plants displayed enhanced drought tolerance at the reproductive stage, resulting in 35% more grain yield than WT under drought conditions, and without exhibiting significant differences under normal growth conditions. Consequently, OsHAK1 can be considered to be used in molecular breeding for improvement of drought tolerance in rice.
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Affiliation(s)
- Guang Chen
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Chaolei Liu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hongzhen Jiang
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ling Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, China
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Yu X, Feng B, He P, Shan L. From Chaos to Harmony: Responses and Signaling upon Microbial Pattern Recognition. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:109-137. [PMID: 28525309 PMCID: PMC6240913 DOI: 10.1146/annurev-phyto-080516-035649] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs) are detected as nonself by host pattern recognition receptors (PRRs) and activate pattern-triggered immunity (PTI). Microbial invasions often trigger the production of host-derived endogenous signals referred to as danger- or damage-associated molecular patterns (DAMPs), which are also perceived by PRRs to modulate PTI responses. Collectively, PTI contributes to host defense against infections by a broad range of pathogens. Remarkable progress has been made toward demonstrating the cellular and physiological responses upon pattern recognition, elucidating the molecular, biochemical, and genetic mechanisms of PRR activation, and dissecting the complex signaling networks that orchestrate PTI responses. In this review, we present an update on the current understanding of how plants recognize and respond to nonself patterns, a process from which the seemingly chaotic responses form into a harmonic defense.
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Affiliation(s)
- Xiao Yu
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843;
| | - Baomin Feng
- Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843
| | - Ping He
- Department of Biochemistry and Biophysics and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843
| | - Libo Shan
- Department of Plant Pathology and Microbiology and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas 77843;
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Popescu SC, Brauer EK, Dimlioglu G, Popescu GV. Insights into the Structure, Function, and Ion-Mediated Signaling Pathways Transduced by Plant Integrin-Linked Kinases. FRONTIERS IN PLANT SCIENCE 2017; 8:376. [PMID: 28421082 PMCID: PMC5376563 DOI: 10.3389/fpls.2017.00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/06/2017] [Indexed: 05/04/2023]
Abstract
Kinases facilitate detection of extracellular signals and set in motion cellular responses for plant adaptation and survival. Some of the energy utilized for kinase signal processing is produced through the activity of ion transporters. Additionally, the synergy between cellular ions and signal transduction influences plant response to pathogens, and their growth and development. In plants, the signaling elements that connect cell wall and membrane sensors with ion homeostasis and transport-mediated processes are largely unknown. Current research indicates that plant Integrin-Linked Kinases (ILKs), a subfamily Raf-like MAP2K Kinases, may have evolved to fulfill this role. In this review, we explore new findings on plant ILKs placing a particular focus on the connection between ILKs proteins unique structural features and ILKs functions. The ankyrin repeat motifs and the kinase domains of ILKs in Arabidopsis and land plants lineage, respectively, are analyzed and discussed as potential determinants of ILKs' metal ion cofactor specificity and their enzymatic and interaction activities. Further, ILKs regulation through gene expression, subcellular localization, and ions and ion transporters is reviewed in the context of recent studies. Finally, using evidence from literature and interactomics databanks, we infer ILKs-dependent cellular pathways and highlight their potential in transmitting multiple types of signals originating at the interface between the cell wall and plasma membrane.
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Affiliation(s)
- Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Plant Pathology, and Entomology, Mississippi State University, StarkvilleMS, USA
| | - Elizabeth K. Brauer
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, OttawaON, Canada
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Plant Pathology, and Entomology, Mississippi State University, StarkvilleMS, USA
| | - George V. Popescu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, StarkvilleMS, USA
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