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Bano N, Aalam S, Bag SK. Tubby-like proteins (TLPs) transcription factor in different regulatory mechanism in plants: a review. PLANT MOLECULAR BIOLOGY 2022; 110:455-468. [PMID: 36255595 DOI: 10.1007/s11103-022-01301-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023]
Abstract
Tubby-like proteins (TLPs) transcription factors are found in single-celled to multi-cellular eukaryotes in the form of large multigene families. TLPs are identified through a specific signature of carboxyl terminal tubby domain, required for plasma membrane tethering and amino terminal F-box domain communicate as functional SCF-type E3 ligases. The comprehensive distribution of TLP gene family members in diverse species indicates some conserved functions of TLPs in multicellular organisms. Plant TLPs have higher gene members than animals and these members reported important role in multiple physiological and developmental processes and various environmental stress responses. Although the TLPs are suggested to be a putative transcription factors but their functional mechanism is not much clear. This review provides significant recent updates on TLP-mediated regulation with an insight into its functional roles, origin and evolution and also phytohormones related regulation to combat with various stresses and its involvement in adaptive stress response in crop plants.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahre Aalam
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Rahman FU, Khan IA, Aslam A, Liu R, Sun L, Wu Y, Aslam MM, Khan AU, Li P, Jiang J, Fan X, Liu C, Zhang Y. Transcriptome analysis reveals pathogenesis-related gene 1 pathway against salicylic acid treatment in grapevine ( Vitis vinifera L). Front Genet 2022; 13:1033288. [PMID: 36338979 PMCID: PMC9631220 DOI: 10.3389/fgene.2022.1033288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 08/27/2023] Open
Abstract
Salicylic acid (SA) is a well-studied phenolic plant hormone that plays an important role in plant defense against the hemi-biothrophic and biothrophic pathogens and depends on the living cells of host for the successful infection. In this study, a pathogenesis test was performed between Vitis davidii and V. vinifera cultivars against grape white rot disease (Coniella diplodiella). V. davidii was found to be resistant against this disease. SA contents were found to be higher in the resistant grape cultivar after different time points. RNA-seq analysis was conducted on susceptible grapevine cultivars after 12, 24, and 48 h of SA application with the hypothesis that SA may induce defense genes in susceptible cultivars. A total of 511 differentially expressed genes (DEGs) were identified from the RNA-seq data, including some important genes, VvWRKY1/2, VvNPR1, VvTGA2, and VvPR1, for the SA defense pathway. DEGs related to phytohormone signal transduction and flavonoid biosynthetic pathways were also upregulated. The quantitative real-time PCR (qRT-PCR) results of the significantly expressed transcripts were found to be consistent with the transcriptome data, with a high correlation between the two analyses. The pathogenesis-related gene 1 (VvPR1), which is an important marker gene for plant defense, was selected for further promoter analysis. The promoter sequence showed that it contains some important cis-elements (W-box, LS7, as-1, and TCA-element) to recruit the transcription factors VvWRKY, VvNPR1, and VvTGA2 to express the VvPR1 gene in response to SA treatment. Furthermore, the VvPR1 promoter was serially deleted into different fragments (-1,837, -1,443, -1,119, -864, -558, -436, and -192 ) bp and constructed vectors with the GUS reporter gene. Deletion analysis revealed that the VvPR1 promoter between -1837 bp to -558 bp induced significant GUS expression with respect to the control. On the basis of these results, the -558 bp region was assumed to be an important part of the VvPR1 promoter, and this region contained the important cis-elements related to SA, such as TCA-element (-1,472 bp), LS7 (-1,428 bp), and as-1 (-520 bp), that recruit the TFs and induce the expression of the VvPR1 gene. This study expanded the available information regarding SA-induced defense in susceptible grapes and recognized the molecular mechanisms through which this defense might be mediated.
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Affiliation(s)
- Faiz Ur Rahman
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Institute of Horticultural Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Irshad Ahmad Khan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ali Aslam
- Faculty of Agriculture and Veterinary Sciences, Superior University, Lahore, Pakistan
| | - Ruitao Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yandi Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Muhammad Muzammal Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Asad Ullah Khan
- The Key Laboratory for Crop Germplasm Resource of Zhejiang Province, Hangzhou, China
| | - Peng Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Shi Z, Zhao B, Song W, Liu Y, Zhou M, Wang J, Zhao J, Ren W. Genome-wide identification and characterization of the MAPKKK, MKK, and MPK families in Chinese elite maize inbred line Huangzaosi. THE PLANT GENOME 2022; 15:e20216. [PMID: 35535627 DOI: 10.1002/tpg2.20216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Mitogen-activated protein kinase (MAPK or MPK) cascades consist of three protein kinase components, MAPK kinase kinases (MAPKKKs), MAPK kinases (MKKs and MPKs), which are indispensable for various plant physiological processes. The functions of MAPK families have been extensively studied in maize (Zea mays L.) and other plant species, but little is known about MAPK families in the elite Chinese maize line Huangzaosi (hzs). In this study, we observed that overall performance of Huangzaosi was substantially better than that of B73 under drought conditions at the seedling and V16 stages with a favorable root/canopy ratio. In silico analyses identified 72, 10, and 24 MAPKKKs, MKKs, and MPKs, respectively, in Huangzaosi. Examinations of phylogenetic relationships among Arabidopsis thaliana (L.) Heynh., rice (Oryza sativa L.), and maize (lines B73 and hzs), gene structures, conserved protein motifs, and chromosomal locations revealed their evolutionary relationships. The basal gene expression levels and tissue specificities of all three MAPK families in hzs reflected the diversity in the MAPK functions related to growth and development. The quantitative real-time polymerase chain reaction (qPCR) assay indicated that certain MAPK genes with high basal expression levels in the primary and crown roots responded differentially to drought between B73 and hzs, suggesting that these genes may contribute to their distinct drought tolerance at different developmental stages. The important information regarding the evolution and expression of hzs MAPK family members generated in this study provides a new avenue for the better understanding on the regulatory mechanism of MAPK cascade in the core inbred line hzs, which may be useful to guide the development of new maize cultivars with desirable traits (e.g., drought resistance).
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Affiliation(s)
- Zi Shi
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Bingbing Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Ya Liu
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Miaoyi Zhou
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Jiarong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
| | - Wen Ren
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture & Forestry Sciences, No. 9 Shuguang Garden Middle Road, Beijing, 100097, China
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Peng Z, Jiang X, Wang Z, Wang X, Li H, He S, Pan Z, Qayyum A, Rehman A, Du X. Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton. Int J Mol Sci 2021; 22:12649. [PMID: 34884455 PMCID: PMC8657469 DOI: 10.3390/ijms222312649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.
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Affiliation(s)
- Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xuran Jiang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
| | - Zhenzhen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Zhaoe Pan
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan;
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; (Z.P.); (X.J.); (H.L.); (S.H.); (Z.P.)
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, China; (Z.W.); (X.W.)
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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Paul A, Srivastava AP, Subrahmanya S, Shen G, Mishra N. In-silico genome wide analysis of Mitogen activated protein kinase kinase kinase gene family in C. sinensis. PLoS One 2021; 16:e0258657. [PMID: 34735479 PMCID: PMC8568164 DOI: 10.1371/journal.pone.0258657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/01/2021] [Indexed: 11/19/2022] Open
Abstract
Mitogen activated protein kinase kinase kinase (MAPKKK) form the upstream component of MAPK cascade. It is well characterized in several plants such as Arabidopsis and rice however the knowledge about MAPKKKs in tea plant is largely unknown. In the present study, MAPKKK genes of tea were obtained through a genome wide search using Arabidopsis thaliana as the reference genome. Among 59 candidate MAPKKK genes in tea, 17 genes were MEKK-like, 31 genes were Raf-like and 11 genes were ZIK- like. Additionally, phylogenetic relationships were established along with structural analysis, which includes gene structure, its location as well as conserved motifs, cis-acting regulatory elements and functional domain signatures that were systematically examined. Also, on the basis of one orthologous gene found between tea and Arabidopsis, functional interaction was carried out in C. sinensis based on an Arabidopsis association model. The expressional profiles indicated major involvement of MAPKKK genes from tea in response to various abiotic stress factors. Taken together, this study provides the targets for additional inclusive identification, functional study, and provides comprehensive knowledge for a better understanding of the MAPKKK cascade regulatory network in C. sinensis.
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Affiliation(s)
- Abhirup Paul
- Department of Biochemistry, REVA University, Bangalore, Karnataka, India
| | - Anurag P. Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India
| | - Shreya Subrahmanya
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
| | - Guoxin Shen
- Sericultural Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Neelam Mishra
- Department of Botany, St. Joseph’s College Autonomous, Bangalore, Karnataka, India
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Yuan Y, Qin L, Su H, Yang S, Wei X, Wang Z, Zhao Y, Li L, Liu H, Tian B, Zhang X. Transcriptome and Coexpression Network Analyses Reveal Hub Genes in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis) During Different Stages of Plasmodiophora brassicae Infection. FRONTIERS IN PLANT SCIENCE 2021; 12:650252. [PMID: 34447397 PMCID: PMC8383047 DOI: 10.3389/fpls.2021.650252] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 07/20/2021] [Indexed: 05/15/2023]
Abstract
Clubroot, caused by the soil-borne protist Plasmodiophora brassicae, is one of the most destructive diseases of Chinese cabbage worldwide. However, the clubroot resistance mechanisms remain unclear. In this study, in both clubroot-resistant (DH40R) and clubroot-susceptible (DH199S) Chinese cabbage lines, the primary (root hair infection) and secondary (cortical infection) infection stages started 2 and 5 days after inoculation (dai), respectively. With the extension of the infection time, cortical infection was blocked and complete P. brassica resistance was observed in DH40R, while disease scales of 1, 2, and 3 were observed at 8, 13, and 22 dai in DH199S. Transcriptome analysis at 0, 2, 5, 8, 13, and 22 dai identified 5,750 relative DEGs (rDEGs) between DH40R and DH199S. The results indicated that genes associated with auxin, PR, disease resistance proteins, oxidative stress, and WRKY and MYB transcription factors were involved in clubroot resistance regulation. In addition, weighted gene coexpression network analysis (WGCNA) identified three of the modules whose functions were highly associated with clubroot-resistant, including ten hub genes related to clubroot resistance (ARF2, EDR1, LOX4, NHL3, NHL13, NAC29, two AOP1, EARLI 1, and POD56). These results provide valuable information for better understanding the molecular regulatory mechanism of Chinese cabbage clubroot resistance.
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Affiliation(s)
- Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Liuyue Qin
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Henan Su
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Lin Li
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
| | - Honglei Liu
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Baoming Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Rice Lesion Mimic Mutants (LMM): The Current Understanding of Genetic Mutations in the Failure of ROS Scavenging during Lesion Formation. PLANTS 2021; 10:plants10081598. [PMID: 34451643 PMCID: PMC8400881 DOI: 10.3390/plants10081598] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 01/02/2023]
Abstract
Rice lesion mimic mutants (LMMs) form spontaneous lesions on the leaves during vegetative growth without pathogenic infections. The rice LMM group includes various mutants, including spotted leaf mutants, brown leaf mutants, white-stripe leaf mutants, and other lesion-phenotypic mutants. These LMM mutants exhibit a common phenotype of lesions on the leaves linked to chloroplast destruction caused by the eruption of reactive oxygen species (ROS) in the photosynthesis process. This process instigates the hypersensitive response (HR) and programmed cell death (PCD), resulting in lesion formation. The reasons for lesion formation have been studied extensively in terms of genetics and molecular biology to understand the pathogen and stress responses. In rice, the lesion phenotypes of most rice LMMs are inherited according to the Mendelian principles of inheritance, which remain in the subsequent generations. These rice LMM genetic traits have highly developed innate self-defense mechanisms. Thus, although rice LMM plants have undesirable agronomic traits, the genetic principles of LMM phenotypes can be used to obtain high grain yields by deciphering the efficiency of photosynthesis, disease resistance, and environmental stress responses. From these ailing rice LMM plants, rice geneticists have discovered novel proteins and physiological causes of ROS in photosynthesis and defense mechanisms. This review discusses recent studies on rice LMMs for the Mendelian inheritances, molecular genetic mapping, and the genetic definition of each mutant gene.
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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Irieda H, Takano Y. Epidermal chloroplasts are defense-related motile organelles equipped with plant immune components. Nat Commun 2021; 12:2739. [PMID: 34016974 PMCID: PMC8137707 DOI: 10.1038/s41467-021-22977-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
In addition to conspicuous large mesophyll chloroplasts, where most photosynthesis occurs, small epidermal chloroplasts have also been observed in plant leaves. However, the functional significance of this small organelle remains unclear. Here, we present evidence that Arabidopsis epidermal chloroplasts control the entry of fungal pathogens. In entry trials, specialized fungal cells called appressoria triggered dynamic movement of epidermal chloroplasts. This movement is controlled by common regulators of mesophyll chloroplast photorelocation movement, designated as the epidermal chloroplast response (ECR). The ECR occurs when the PEN2 myrosinase-related higher-layer antifungal system becomes ineffective, and blockage of the distinct steps of the ECR commonly decreases preinvasive nonhost resistance against fungi. Furthermore, immune components were preferentially localized to epidermal chloroplasts, contributing to antifungal nonhost resistance in the pen2 background. Our findings reveal that atypical small chloroplasts act as defense-related motile organelles by specifically positioning immune components in the plant epidermis, which is the first site of contact between the plant and pathogens. Thus, this work deepens our understanding of the functions of epidermal chloroplasts. Leaf epidermal cells contain small chloroplasts which likely contribute little to photosynthesis and whose function is unclear. Here the authors show that these chloroplasts move toward the leaf surface in response to invasion trials by non-adapted fungal pathogens and contribute to non-host resistance.
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Affiliation(s)
- Hiroki Irieda
- Academic Assembly, Institute of Agriculture, Shinshu University, Nagano, Japan.
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10
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Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops. Int J Mol Sci 2021; 22:ijms22031292. [PMID: 33525517 PMCID: PMC7866018 DOI: 10.3390/ijms22031292] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.
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Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [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: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
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Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
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12
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Fàbregas N, Yoshida T, Fernie AR. Role of Raf-like kinases in SnRK2 activation and osmotic stress response in plants. Nat Commun 2020; 11:6184. [PMID: 33273465 PMCID: PMC7712759 DOI: 10.1038/s41467-020-19977-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
Environmental drought and high salinity impose osmotic stress, which inhibits plant growth and yield. Thus, understanding how plants respond to osmotic stress is critical to improve crop productivity. Plants have multiple signalling pathways in response to osmotic stress in which the phytohormone abscisic acid (ABA) plays important roles. However, since little is known concerning key early components, the global osmotic stress-signalling network remains to be elucidated. Here, we review recent advances in the identification of osmotic-stress activated Raf-like protein kinases as regulators of ABA-dependent and -independent signalling pathways and discuss the plant stress-responsive kinase network from an evolutionary perspective. A better understanding of how plants respond to osmotic stress could potentially help improve crop yields. Here Fàbregas et al. review the recent characterization of Raf-like kinases that act in both in ABA-dependent and -independent responses to osmotic stress.
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Affiliation(s)
- Norma Fàbregas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Takuya Yoshida
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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13
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Kosaka A, Suemoto H, Singkaravanit-Ogawa S, Takano Y. Plant defensin expression triggered by fungal pathogen invasion depends on EDR1 protein kinase and ORA59 transcription factor in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2020; 15:1823120. [PMID: 32985920 PMCID: PMC7671030 DOI: 10.1080/15592324.2020.1823120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Arabidopsis thaliana exhibits durable 'non-host' resistance against the hemibiotrophic fungal pathogen Colletotrichum tropicale that infects mulberry plants. Arabidopsis non-host resistance comprises two layers of defense: preinvasive and postinvasive resistance. The EDR1 protein kinase contributes to Arabidopsis preinvasive resistance against C. tropicale by inducing the expression of plant defensin (PDF) genes. Here we report that the expressions of multiple PDF genes were strongly induced in Arabidopsis upon invasion by C. tropicale. Invasion by a necrotrophic pathogen, Alternaria brassicicola, also induced PDF expression. Importantly, PDF expression triggered upon invasion by both pathogens was inhibited in edr1 mutants, indicating the requirement of EDR1 for PDF expression in postinvasive resistance by Arabidopsis. Analysis of ora59 mutants also revealed that this gene is critical for induced PDF expression following pathogen invasion. Furthermore, inoculation assays of A. brassicicola indicated that ORA59 is involved in postinvasive resistance against the pathogen, suggesting invasion-triggered PDF expression contributes to postinvasive resistance in Arabidopsis.
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Affiliation(s)
- Ayumi Kosaka
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Haruka Suemoto
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Yoshitaka Takano
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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14
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Wang W, Shao A, Amombo E, Fan S, Xu X, Fu J. Transcriptome-wide identification of MAPKKK genes in bermudagrass ( Cynodon dactylon L.) and their potential roles in low temperature stress responses. PeerJ 2020; 8:e10159. [PMID: 33194398 PMCID: PMC7602684 DOI: 10.7717/peerj.10159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
As upstream components of MAPK cascades, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascades. MAPK cascades are universal modules of signal transduction in eukaryotic organisms and play crucial roles in plant development processes and in responses to biotic and abiotic stress and signal transduction. Members of the MAPKKK gene family have been identified in several plants,however, MAPKKKs have not been systematically studied in bermudagrass (Cynodon dactylon L.). In this study, 55 potential CdMAPKKKs were produced from bermudagrass transcriptome data, of which 13 belonged to the MEKK, 38 to the Raf, and 4 to the ZIK subfamily. Multiple alignment and conserved motif analysis of CdMAPKKKs supported the evolutionary relationships inferred from phylogenetic analyses. Moreover, the distribution pattern in Poaceae species indicated that members of the MAPKKK family were conserved among almost all diploid species, and species-specific polyploidy or higher duplication ratios resulted in an expansion of the MAPKKK family. In addition, 714 co-functional links which were significantly enriched in signal transduction, responses to temperature stimuli, and other important biological processes of 55 CdMAPKKKs were identified using co-functional gene networks analysis; 30 and 19 co-functional genes involved in response to cold or heat stress, respectively, were also identified. Results of promoter analyses, and interaction network investigation of all CdMAPKKKs based on the rice homologs suggested that CdMAPKKKs are commonly associated with regulation of numerous biological processes. Furthermore, 12 and 13 CdMAPKKKs were significantly up- and downregulated, respectively, in response to low temperature stress; among them, six CdMAPKKKs were significantly induced by low temperature stress, at least at one point in time. This is the first study to conduct identification and functional analysis of the MAPKKK gene family in bermudagrass, and our results provide a foundation for further research on the functions of CdMAPKKKs in response to low temperature stress.
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Affiliation(s)
- Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Erick Amombo
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
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15
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Nasim Z, Fahim M, Gawarecka K, Susila H, Jin S, Youn G, Ahn JH. Role of AT1G72910, AT1G72940, and ADR1-LIKE 2 in Plant Immunity under Nonsense-Mediated mRNA Decay-Compromised Conditions at Low Temperatures. Int J Mol Sci 2020; 21:E7986. [PMID: 33121126 PMCID: PMC7663611 DOI: 10.3390/ijms21217986] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 01/26/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) removes aberrant transcripts to avoid the accumulation of truncated proteins. NMD regulates nucleotide-binding, leucine-rich repeat (NLR) genes to prevent autoimmunity; however, the function of a large number of NLRs still remains poorly understood. Here, we show that three NLR genes (AT1G72910, AT1G72940, and ADR1-LIKE 2) are important for NMD-mediated regulation of defense signaling at lower temperatures. At 16 °C, the NMD-compromised up-frameshift protein1 (upf1) upf3 mutants showed growth arrest that can be rescued by the artificial miRNA-mediated knockdown of the three NLR genes. mRNA levels of these NLRs are induced by Pseudomonas syringae inoculation and exogenous SA treatment. Mutations in AT1G72910, AT1G72940, and ADR1-LIKE 2 genes resulted in increased susceptibility to Pseudomonas syringae, whereas their overexpression resulted in severely stunted growth, which was dependent on basal disease resistance genes. The NMD-deficient upf1 upf3 mutants accumulated higher levels of NMD signature-containing transcripts from these NLR genes at 16 °C. Furthermore, mRNA degradation kinetics showed that these NMD signature-containing transcripts were more stable in upf1 upf3 mutants. Based on these findings, we propose that AT1G72910, AT1G72940, and ADR1-LIKE 2 are directly regulated by NMD in a temperature-dependent manner and play an important role in modulating plant immunity at lower temperatures.
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Affiliation(s)
- Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Muhammad Fahim
- Centre for Omic Sciences, Islamia College University, Peshawar 25120, Pakistan;
| | - Katarzyna Gawarecka
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea; (Z.N.); (K.G.); (H.S.); (S.J.); (G.Y.)
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16
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Expanding the Toolkit of Fluorescent Biosensors for Studying Mitogen Activated Protein Kinases in Plants. Int J Mol Sci 2020; 21:ijms21155350. [PMID: 32731410 PMCID: PMC7432370 DOI: 10.3390/ijms21155350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/25/2020] [Accepted: 07/26/2020] [Indexed: 12/11/2022] Open
Abstract
Mitogen-activated protein kinases (MAPKs) are key regulators of numerous biological processes in plants. To better understand the mechanisms by which these kinases function, high resolution measurement of MAPK activation kinetics in different biological contexts would be beneficial. One method to measure MAPK activation in plants is via fluorescence-based genetically-encoded biosensors, which can provide real-time readouts of the temporal and spatial dynamics of kinase activation in living tissue. Although fluorescent biosensors have been widely used to study MAPK dynamics in animal cells, there is currently only one MAPK biosensor that has been described for use in plants. To facilitate creation of additional plant-specific MAPK fluorescent biosensors, we report the development of two new tools: an in vitro assay for efficiently characterizing MAPK docking domains and a translocation-based kinase biosensor for use in plants. The implementation of these two methods has allowed us to expand the available pool of plant MAPK biosensors, while also providing a means to generate more specific and selective MAPK biosensors in the future. Biosensors developed using these methods have the potential to enhance our understanding of the roles MAPKs play in diverse plant signaling networks affecting growth, development, and stress response.
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Hayashi M, Sugimoto H, Takahashi H, Seki M, Shinozaki K, Sawasaki T, Kinoshita T, Inoue SI. Raf-like kinases CBC1 and CBC2 negatively regulate stomatal opening by negatively regulating plasma membrane H +-ATPase phosphorylation in Arabidopsis. Photochem Photobiol Sci 2020; 19:88-98. [PMID: 31904040 DOI: 10.1039/c9pp00329k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Stomatal pores, which are surrounded by pairs of guard cells in the plant epidermis, regulate gas exchange between plants and the atmosphere, thereby controlling photosynthesis and transpiration. Blue light works as a signal to guard cells, to induce intracellular signaling and open stomata. Blue light receptor phototropins (phots) are activated by blue light; phot-mediated signals promote plasma membrane (PM) H+-ATPase activity via C-terminal Thr phosphorylation, serving as the driving force for stomatal opening in guard cells. However, the details of this signaling process are not fully understood. In this study, through an in vitro screening of phot-interacting protein kinases, we obtained the CBC1 and CBC2 that had been reported as signal transducers in stomatal opening. Promoter activities of CBC1 and CBC2 indicated that both genes were expressed in guard cells. Single and double knockout mutants of CBC1 and CBC2 showed no lesions in the context of phot-mediated phototropism, chloroplast movement, or leaf flattening. In contrast, the cbc1cbc2 double mutant showed larger stomatal opening under both dark and blue light conditions. Interestingly, the level of phosphorylation of C-terminal Thr of PM H+-ATPase was higher in double mutant guard cells. The larger stomatal openings of the double mutant were effectively suppressed by the phytohormone abscisic acid (ABA). CBC1 and CBC2 interacted with BLUS1 and PM H+-ATPase in vitro. From these results, we conclude that CBC1 and CBC2 act as negative regulators of stomatal opening, probably via inhibition of PM H+-ATPase activity.
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Affiliation(s)
- Maki Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Hodaka Sugimoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Hirotaka Takahashi
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Motoaki Seki
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Tatsuya Sawasaki
- Proteo-Science Center (PROS), Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shin-Ichiro Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan.
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18
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Chen L, Wu Q, He T, Lan J, Ding L, Liu T, Wu Q, Pan Y, Chen T. Transcriptomic and Metabolomic Changes Triggered by Fusarium solani in Common Bean ( Phaseolus vulgaris L.). Genes (Basel) 2020; 11:E177. [PMID: 32046085 PMCID: PMC7073522 DOI: 10.3390/genes11020177] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/25/2020] [Accepted: 02/03/2020] [Indexed: 12/29/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) is a major legume and is frequently attacked by fungal pathogens, including Fusarium solani f. sp. phaseoli (FSP), which cause Fusarium root rot. FSP substantially reduces common bean yields across the world, including China, but little is known about how common bean plants defend themselves against this fungal pathogen. In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and metabolomic processes in common bean infected with FSP. There were 29,722 differentially regulated genes and 300 differentially regulated metabolites between control and infected plants. The combined omics approach revealed that FSP is perceived by PAMP-triggered immunity and effector-triggered immunity. Infected seedlings showed that common bean responded by cell wall modification, ROS generation, and a synergistic hormone-driven defense response. Further analysis showed that FSP induced energy metabolism, nitrogen mobilization, accumulation of sugars, and arginine and proline metabolism. Importantly, metabolic pathways were most significantly enriched, which resulted in increased levels of metabolites that were involved in the plant defense response. A correspondence between the transcript pattern and metabolite profile was observed in the discussed pathways. The combined omics approach enhances our understanding of the less explored pathosystem and will provide clues for the development of common bean cultivars' resistant to FSP.
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Affiliation(s)
- Limin Chen
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China; (L.C.); (T.H.); (T.L.); (Y.P.)
| | - Quancong Wu
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China; (L.C.); (T.H.); (T.L.); (Y.P.)
| | - Tianjun He
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China; (L.C.); (T.H.); (T.L.); (Y.P.)
| | - Jianjun Lan
- Plant Protection Station of Songyang County, Lishui 323400, China;
| | - Li Ding
- Weihai Academy of Agricultural Sciences, No. 411, Tongyi Road, Weihai 311300, China;
| | - Tingfu Liu
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China; (L.C.); (T.H.); (T.L.); (Y.P.)
| | - Qianqian Wu
- School of Agricultural and Food Science, Zhejiang A&F University, Hangzhou 311300, China;
| | - Yiming Pan
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China; (L.C.); (T.H.); (T.L.); (Y.P.)
| | - Tingting Chen
- College of Ecology, Lishui University, Lishui, Zhejiang 323000, China;
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19
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Sari E, Cabral AL, Polley B, Tan Y, Hsueh E, Konkin DJ, Knox RE, Ruan Y, Fobert PR. Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat. BMC Genomics 2019; 20:925. [PMID: 31795948 PMCID: PMC6891979 DOI: 10.1186/s12864-019-6161-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Fusarium head blight (FHB) resistance in the durum wheat breeding gene pool is rarely reported. Triticum turgidum ssp. carthlicum line Blackbird is a tetraploid relative of durum wheat that offers partial FHB resistance. Resistance QTL were identified for the durum wheat cv. Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B in a previous study. The objective of this study was to identify the defense mechanisms underlying the resistance of Blackbird and report candidate regulator defense genes and single nucleotide polymorphism (SNP) markers within these genes for high-resolution mapping of resistance QTL reported for the durum wheat cv. Strongfield/Blackbird population. RESULTS Gene network analysis identified five networks significantly (P < 0.05) associated with the resistance to FHB spread (Type II FHB resistance) one of which showed significant correlation with both plant height and relative maturity traits. Two gene networks showed subtle differences between Fusarium graminearum-inoculated and mock-inoculated plants, supporting their involvement in constitutive defense. The candidate regulator genes have been implicated in various layers of plant defense including pathogen recognition (mainly Nucleotide-binding Leucine-rich Repeat proteins), signaling pathways including the abscisic acid and mitogen activated protein (MAP) kinase, and downstream defense genes activation including transcription factors (mostly with dual roles in defense and development), and cell death regulator and cell wall reinforcement genes. The expression of five candidate genes measured by quantitative real-time PCR was correlated with that of RNA-seq, corroborating the technical and analytical accuracy of RNA-sequencing. CONCLUSIONS Gene network analysis allowed identification of candidate regulator genes and genes associated with constitutive resistance, those that will not be detected using traditional differential expression analysis. This study also shed light on the association of developmental traits with FHB resistance and partially explained the co-localization of FHB resistance with plant height and maturity QTL reported in several previous studies. It also allowed the identification of candidate hub genes within the interval of three previously reported FHB resistance QTL for the Strongfield/Blackbird population and associated SNPs for future high resolution mapping studies.
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Affiliation(s)
- Ehsan Sari
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada.
| | - Adrian L Cabral
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Brittany Polley
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Yifang Tan
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Emma Hsueh
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre R Fobert
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
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20
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Ahmad S, Guo Y. Signal Transduction in Leaf Senescence: Progress and Perspective. PLANTS 2019; 8:plants8100405. [PMID: 31658600 PMCID: PMC6843215 DOI: 10.3390/plants8100405] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023]
Abstract
Leaf senescence is a degenerative process that is genetically controlled and involves nutrient remobilization prior to the death of leaf tissues. Age is a key developmental determinant of the process along with other senescence inducing factors. At the cellular level, different hormones, signaling molecules, and transcription factors contribute to the regulation of senescence. This review summarizes the recent progress in understanding the complexity of the senescence process with primary focuses on perception and transduction of senescence signals as well as downstream regulatory events. Future directions in this field and potential applications of related techniques in crop improvement will be discussed.
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Affiliation(s)
- Salman Ahmad
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
- Plant Breeding & Genetics Division, Nuclear Institute for Food & Agriculture, Tarnab, Peshawar P.O. Box 446, Pakistan.
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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21
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Yin K, Qiu JL. Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180322. [PMID: 30967029 PMCID: PMC6367152 DOI: 10.1098/rstb.2018.0322] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant disease resistance is essential for sustainable agriculture. Genome editing has been revolutionizing plant biology and biotechnology by enabling precise, targeted genome modifications. Editing provides new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. Here, we first summarize the challenges for breeding resistant crops. Next, we focus on applications of genome editing technology in generating plants with resistance to bacterial, fungal and viral diseases. Finally, we discuss the potential of genome editing for breeding crops that present novel disease resistance in the future. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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22
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Different Pathogen Defense Strategies in Arabidopsis: More than Pathogen Recognition. Cells 2018; 7:cells7120252. [PMID: 30544557 PMCID: PMC6315839 DOI: 10.3390/cells7120252] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/26/2018] [Accepted: 12/03/2018] [Indexed: 01/03/2023] Open
Abstract
Plants constantly suffer from simultaneous infection by multiple pathogens, which can be divided into biotrophic, hemibiotrophic, and necrotrophic pathogens, according to their lifestyles. Many studies have contributed to improving our knowledge of how plants can defend against pathogens, involving different layers of defense mechanisms. In this sense, the review discusses: (1) the functions of PAMP (pathogen-associated molecular pattern)-triggered immunity (PTI) and effector-triggered immunity (ETI), (2) evidence highlighting the functions of salicylic acid (SA) and jasmonic acid (JA)/ethylene (ET)-mediated signaling pathways downstream of PTI and ETI, and (3) other defense aspects, including many novel small molecules that are involved in defense and phenomena, including systemic acquired resistance (SAR) and priming. In particular, we mainly focus on SA and (JA)/ET-mediated signaling pathways. Interactions among them, including synergistic effects and antagonistic effects, are intensively explored. This might be critical to understanding dynamic disease regulation.
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23
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Genome-wide Identification of Jatropha curcas MAPK, MAPKK, and MAPKKK Gene Families and Their Expression Profile Under Cold Stress. Sci Rep 2018; 8:16163. [PMID: 30385801 PMCID: PMC6212503 DOI: 10.1038/s41598-018-34614-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in all eukaryotic organisms, controlling cell division, growth, development, and hormone signaling. Additionally, they can be activated in response to a variety of biotic and abiotic stressors. Although the evolution and expression patterns of MAPK cascade families have been systematically investigated in several model plants (e.g., Arabidopsis, rice, and poplar), we still know very little about MAPK, MAPKK, and MAPKKK families in Jatropha curcas, an economically important species. Therefore, this study performed genome-wide identification and transcriptional expression analysis of these three families in J. curcas. We identified 12 J. curcas MAPK (JcMAPKs), 5 JcMAPKKs, and 65 JcMAPKKKs. Phylogenetic analysis classified all JcMAPKs and JcMAPKKs into four subgroups, whereas JcMAPKKKs were grouped into three subfamilies (MEKK, RAF, and ZIK). Similarities in exon/intron structures supported the evolutionary relationships within subgroups and subfamilies. Conserved motif analysis indicated that all J. curcas MAPK cascades possessed typical, 200–300 amino-acid protein kinase domains. MAPK cascade genes were presented throughout all 11 chromosomes. Gene duplication analysis suggested that after JcMAPK and JcMAPKKK diverged, 3 and 19 tandem duplicates occurred under strong purifying selection. Furthermore, RNA-seq and qRT-PCR analyses revealed that some MAPK cascade genes are predominantly expressed in specific tissues. Moreover, their expression levels significantly increased under cold treatment. Our results should provide insight into the roles of MAPK cascade genes in regulating J. curcas stress responses and in hormonal signal transduction. Furthermore, these data have important applications in the genetic improvement of J. curcas.
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Wang A, Shu X, Niu X, Zhao W, Ai P, Li P, Zheng A. Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection. PLoS One 2018; 13:e0202309. [PMID: 30372430 PMCID: PMC6205584 DOI: 10.1371/journal.pone.0202309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/09/2018] [Indexed: 01/29/2023] Open
Abstract
The biotrophic soil-borne fungus Tilletia horrida causes rice kernel smut, an important disease affecting the production of rice male sterile lines in most hybrid rice growing regions of the world. There are no successful ways of controlling this disease and there has been little study of mechanisms of resistance to T. horrida. Based on transcriptional data of different infection time points, we found 23, 782 and 23, 718 differentially expressed genes (fragments per kilobase of transcript sequence per million, FPKM >1) in Jiangcheng 3A (resistant to T. horrida) and 9311A (susceptible to T. horrida), respectively. In order to illuminate the differential responses of the two rice male sterile lines to T. horrida, we identified gene co-expression modules using the method of weighted gene co-expression network analysis (WGCNA) and compared the different biological functions of gene co-expression networks in key modules at different infection time points. The results indicated that gene co-expression networks in the two rice genotypes were different and that genes contained in some modules of the two groups may play important roles in resistance to T. horrida, such as DTH8 and OsHop/Sti1a. Furthermore, these results provide a global view of the responses of two different phenotypes to T. horrida, and assist our understanding of the regulation of expression changes after T. horrida infection.
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Affiliation(s)
- Aijun Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xinyue Shu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xianyu Niu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Wenjuan Zhao
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Peng Ai
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
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Michelotti V, Lamontanara A, Buriani G, Orrù L, Cellini A, Donati I, Vanneste JL, Cattivelli L, Tacconi G, Spinelli F. Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl. BMC Genomics 2018; 19:585. [PMID: 30081820 PMCID: PMC6090863 DOI: 10.1186/s12864-018-4967-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options for controlling this disease are very limited and rely primarily on the use of bactericidal compounds, such as copper, and resistance inducers. Among the latter, the most widely studied is acibenzolar-S-methyl. To elucidate the early molecular reaction of kiwifruit plants (Actinidia chinensis var. chinensis) to Psa infection and acibenzolar-S-methyl treatment, a RNA seq analysis was performed at different phases of the infection process, from the epiphytic phase to the endophytic invasion on acibenzolar-S-methyl treated and on non-treated plants. The infection process was monitored in vivo by confocal laser scanning microscopy. RESULTS De novo assembly of kiwifruit transcriptome revealed a total of 39,607 transcripts, of which 3360 were differentially expressed during the infection process, primarily 3 h post inoculation. The study revealed the coordinated changes of important gene functional categories such as signaling, hormonal balance and transcriptional regulation. Among the transcription factor families, AP2/ERF, MYB, Myc, bHLH, GATA, NAC, WRKY and GRAS were found differentially expressed in response to Psa infection and acibenzolar-S-methyl treatment. Finally, in plants treated with acibenzolar-S-methyl, a number of gene functions related to plant resistance, such as PR proteins, were modulated, suggesting the set-up of a more effective defense response against the pathogen. Weighted-gene coexpression network analysis confirmed these results. CONCLUSIONS Our work provides an in-depth description of the plant molecular reactions to Psa, it highlights the metabolic pathway related to acibenzolar-S-methyl-induced resistance and it contributes to the development of effective control strategies in open field.
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Affiliation(s)
- Vania Michelotti
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Antonella Lamontanara
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Giampaolo Buriani
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Luigi Orrù
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Antonio Cellini
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Irene Donati
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
| | - Joel L. Vanneste
- The New Zealand Institute for Plant & Food Research Ltd, Ruakura Research Centre, Bisley Road, Ruakura, Private Bag 3123, Hamilton, 3240 New Zealand
| | - Luigi Cattivelli
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Gianni Tacconi
- Council for agriculture research and economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, CAP, 29017 Fiorenzuola d’Arda, Piacenza Italy
| | - Francesco Spinelli
- Department of Agricultural Sciences Alma Mater Studiorum, University of Bologna, viale Fanin 46, 40127 Bologna, Italy
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Wu L, Zhang X, Xu B, Li Y, Jia L, Wang R, Ren X, Wang G, Xia Q. Identification and expression analysis of EDR1-like genes in tobacco ( Nicotiana tabacum) in response to Golovinomyces orontii. PeerJ 2018; 6:e5244. [PMID: 30018863 PMCID: PMC6044316 DOI: 10.7717/peerj.5244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/26/2018] [Indexed: 01/15/2023] Open
Abstract
ENHANCED DISEASE RESISTANCE1 (EDR1) encodes a Raf-like mitogen-activated protein kinase, and it acts as a negative regulator of disease resistance and ethylene-induced senescence. Mutations in the EDR1 gene can enhance resistance to powdery mildew both in monocotyledonous and dicotyledonous plants. However, little is known about EDR1-like gene members from a genome-wide perspective in plants. In this study, the tobacco (Nicotiana tabacum)EDR1-like gene family was first systematically analyzed. We identified 19 EDR1-like genes in tobacco, and compared them to those from Arabidopsis, tomato and rice. Phylogenetic analyses divided the EDR1-like gene family into six clades, among them monocot and dicot plants were respectively divided into two sub-clades. NtEDR1-1A and NtEDR1-1B were classified into clade I in which the other members have been reported to negatively regulate plant resistance to powdery mildew. The expression patterns of tobacco EDR1-like genes were analyzed after plants were challenged by Golovinomyces orontii, and showed that several other EDR1-like genes were induced after infection, as well as NtEDR1-1A and NtEDR1-1B. Expression analysis showed that NtEDR1-13 and NtEDR1-16 had exclusively abundant expression patterns in roots and leaves, respectively, and the remaining NtEDR1-like members were actively expressed in most of the tissue/organ samples investigated. Our findings will contribute to further study of the physiological functions of EDR1-like genes in tobacco.
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Affiliation(s)
- Lei Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xiaoying Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Bingxin Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yueyue Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ling Jia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Rengang Wang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Xueliang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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Andersen EJ, Ali S, Byamukama E, Yen Y, Nepal MP. Disease Resistance Mechanisms in Plants. Genes (Basel) 2018; 9:E339. [PMID: 29973557 PMCID: PMC6071103 DOI: 10.3390/genes9070339] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 06/29/2018] [Indexed: 12/24/2022] Open
Abstract
Plants have developed a complex defense system against diverse pests and pathogens. Once pathogens overcome mechanical barriers to infection, plant receptors initiate signaling pathways driving the expression of defense response genes. Plant immune systems rely on their ability to recognize enemy molecules, carry out signal transduction, and respond defensively through pathways involving many genes and their products. Pathogens actively attempt to evade and interfere with response pathways, selecting for a decentralized, multicomponent immune system. Recent advances in molecular techniques have greatly expanded our understanding of plant immunity, largely driven by potential application to agricultural systems. Here, we review the major plant immune system components, state of the art knowledge, and future direction of research on plant⁻pathogen interactions. In our review, we will discuss how the decentralization of plant immune systems have provided both increased evolutionary opportunity for pathogen resistance, as well as additional mechanisms for pathogen inhibition of such defense responses. We conclude that the rapid advances in bioinformatics and molecular biology are driving an explosion of information that will advance agricultural production and illustrate how complex molecular interactions evolve.
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Affiliation(s)
- Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, 57007 SD, USA.
| | - Shaukat Ali
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, 57007 SD, USA.
| | - Emmanuel Byamukama
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, 57007 SD, USA.
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, 57007 SD, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, 57007 SD, USA.
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Abstract
In the protozoan parasite Toxoplasma gondii, protein kinases have been shown to play key roles in regulating parasite motility, invasion, replication, egress, and survival within the host. The tyrosine kinase-like (TKL) family of proteins are an unexplored set of kinases in Toxoplasma. Of the eight annotated TKLs in the Toxoplasma genome, a recent genome-wide loss-of-function screen showed that six are important for tachyzoite fitness. By utilizing an endogenous tagging approach, we showed that these six T. gondii TKLs (TgTKLs) localize to various subcellular compartments, including the nucleus, the cytosol, the inner membrane complex, and the Golgi apparatus. To gain insight into the function of TKLs in Toxoplasma, we first characterized TgTKL1, which contains the plant-like enhanced disease resistance 1 (EDR1) domain and localizes to the nucleus. TgTKL1 knockout parasites displayed significant defects in progression through the lytic cycle; we show that the defects were due to specific impairment of host cell attachment. Transcriptomics analysis identified over 200 genes of diverse functions that were differentially expressed in TgTKL1 knockout parasites. Importantly, numerous genes implicated in host cell attachment and invasion were among those most significantly downregulated, resulting in defects in microneme secretion and processing. Significantly, all of the mice inoculated intraperitoneally with TgTKL1 knockout parasites survived the infection, suggesting that TgTKL1 plays an essential role in acute toxoplasmosis. Together, these findings suggest that TgTKL1 mediates a signaling pathway that regulates the expression of multiple factors required for parasite virulence, underscoring the potential of this kinase as a novel therapeutic target. Toxoplasma gondii is a protozoan parasite that can cause chronic and life-threatening disease in mammals; new drugs are greatly needed for treatment. One attractive group of drug targets consists of parasite kinases containing unique features that distinguish them from host proteins. In this report, we identify and characterize a previously unstudied kinase, TgTKL1, that localizes to the nucleus and contains a domain architecture unique to plants and protozoa. By disrupting TgTKL1, we showed that this kinase is required for the proper expression of hundreds of genes, including many that are required for the parasite to gain entry into the host cell. Specifically, parasites lacking TgTKL1 have defects in host cell attachment, resulting in impaired growth in vitro and a complete loss of virulence in mice. This report provides insight into the importance of the parasite tyrosine kinase-like kinases and establishes TgTKL1 as a novel and essential virulence factor in Toxoplasma.
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Jing T, Wang L, Liu H, Wuyun TN, Du H. Genome-Wide Identification of Mitogen-activated Protein Kinase Cascade Genes and Transcriptional Profiling Analysis during Organ Development in Eucommia ulmoides. Sci Rep 2017; 7:17732. [PMID: 29255270 PMCID: PMC5735150 DOI: 10.1038/s41598-017-17615-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/28/2017] [Indexed: 11/08/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) cascades, which play crucial roles in plant development processes, are universal modules of signal transduction in eukaryotes and consist of a core module of three sequentially phosphorylated kinases: MAPK, MAPK kinase (MAPKK), and MAPKK kinase (MAPKKK). This is the first report on the identification and analysis of MAPK cascades in Eucommia ulmoides. We conducted a genome-wide screening and identified 13 EuMAPKs, five EuMAPKKs, and 57 EuMAPKKKs. The construction of phylogenetic trees revealed that EuMAPKs and EuMAPKKs were divided into four groups (A, B, C, and D), and EuMAPKKKs were divided into three subfamilies (MEKK, RAF, and ZIK). These subfamilies were further confirmed by conserved domain/motif analysis and gene structure analysis. Based on the expression profiles of all identified EuMAPK cascades in various organs at different developmental stages, three genes (EuRAF22-2, EuRAF34-1, and EuRAF33-2) with stable expression patterns at all stages of fruit or leaf development, three genes (EuRAF2-3, EuMPK11, and EuMEKK21) with differential expression patterns, and two highly expressed genes (EuZIK1 and EuMKK2) were screened and validated by qRT-PCR. Overall, our results could be used for further research on the precise role of MAPK cascades during organ development in E. ulmoides.
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Affiliation(s)
- Teng Jing
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, 450003, China
- The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou, Henan, 450003, China
| | - Lin Wang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, 450003, China
- The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou, Henan, 450003, China
| | - Huimin Liu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, 450003, China
- The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou, Henan, 450003, China
| | - Ta-Na Wuyun
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, 450003, China.
- The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou, Henan, 450003, China.
| | - Hongyan Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, 450003, China.
- The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou, Henan, 450003, China.
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Zhou H, Ren S, Han Y, Zhang Q, Qin L, Xing Y. Identification and Analysis of Mitogen-Activated Protein Kinase (MAPK) Cascades in Fragaria vesca. Int J Mol Sci 2017; 18:ijms18081766. [PMID: 28805715 PMCID: PMC5578155 DOI: 10.3390/ijms18081766] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules in eukaryotes, including yeasts, plants and animals. MAPK cascades are responsible for protein phosphorylation during signal transduction events, and typically consist of three protein kinases: MAPK, MAPK kinase, and MAPK kinase kinase. In this current study, we identified a total of 12 FvMAPK, 7 FvMAPKK, 73 FvMAPKKK, and one FvMAPKKKK genes in the recently published Fragaria vesca genome sequence. This work reported the classification, annotation and phylogenetic evaluation of these genes and an assessment of conserved motifs and the expression profiling of members of the gene family were also analyzed here. The expression profiles of the MAPK and MAPKK genes in different organs and fruit developmental stages were further investigated using quantitative real-time reverse transcription PCR (qRT-PCR). Finally, the MAPK and MAPKK expression patterns in response to hormone and abiotic stresses (salt, drought, and high and low temperature) were investigated in fruit and leaves of F. vesca. The results provide a platform for further characterization of the physiological and biochemical functions of MAPK cascades in strawberry.
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Affiliation(s)
- Heying Zhou
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
| | - Suyue Ren
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
| | - Yuanfang Han
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
| | - Qing Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China.
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β-carbonic anhydrases play a role in salicylic acid perception in Arabidopsis. PLoS One 2017; 12:e0181820. [PMID: 28753666 PMCID: PMC5533460 DOI: 10.1371/journal.pone.0181820] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/07/2017] [Indexed: 11/19/2022] Open
Abstract
The plant hormone salicylic acid (SA) is required for defense responses. NON EXPRESSER OFPATHOGENESISRELATED1 (NPR1) and NONRECOGNITION OFBTH-4 (NRB4) are required for the response to SA in Arabidopsis (Arabidopsis thaliana). Here, we isolated several interactors of NRB4 using yeast two-hybrid assays. Two of these interactors, βCA1 and βCA2, are β-carbonic anhydrase family proteins. Since double mutant βca1 βca2 plants did not show any obvious phenotype, we investigated other βCAs and found that NRB4 also interacts with βCA3 and βCA4. Moreover, several βCAs interacted with NPR1 in yeast, including one that interacted in a SA-dependent manner. This interaction was abolished in loss-of-function alleles of NPR1. Interactions between βCAs and both NRB4 and NPR1 were also detected in planta, with evidence for a triple interaction, NRB4-βCA1-NPR1. The quintuple mutant βca1 βca2 βca3 βca4 βca6 showed partial insensitivity to SA. These findings suggest that one of the functions of carbonic anhydrases is to modulate the perception of SA in plants.
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Arabidopsis glycosylphosphatidylinositol-anchored protein LLG1 associates with and modulates FLS2 to regulate innate immunity. Proc Natl Acad Sci U S A 2017; 114:5749-5754. [PMID: 28507137 DOI: 10.1073/pnas.1614468114] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Plants detect and respond to pathogen invasion with membrane-localized pattern recognition receptors (PRRs), which recognize pathogen-associated molecular patterns (PAMPs) and activate downstream immune responses. Here we report that Arabidopsis thaliana LORELEI-LIKE GPI-ANCHORED PROTEIN 1 (LLG1), a coreceptor of the receptor-like kinase FERONIA, regulates PRR signaling. In a forward genetic screen for suppressors of enhanced disease resistance 1 (edr1), we identified the point mutation llg1-3, which suppresses edr1 disease resistance but does not affect plant growth and development. The llg1 mutants show enhanced susceptibility to various virulent pathogens, indicating that LLG1 has an important role in plant immunity. LLG1 constitutively associates with the PAMP receptor FLAGELLIN SENSING 2 (FLS2) and the elongation factor-Tu receptor, and forms a complex with BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1 in a ligand-dependent manner, indicating that LLG1 functions as a key component of PAMP-recognition immune complexes. Moreover, LLG1 contributes to accumulation and ligand-induced degradation of FLS2, and is required for downstream innate immunity responses, including ligand-induced phosphorylation of BOTRYTIS-INDUCED KINASE 1 and production of reactive oxygen species. Taken together, our findings reveal that LLG1 associates with PAMP receptors and modulates their function to regulate disease responses. As LLG1 functions as a coreceptor of FERONIA and plays central roles in plant growth and development, our findings indicate that LLG1 participates in separate pathways, and may suggest a potential connection between development and innate immunity in plants.
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Wang M, Yue H, Feng K, Deng P, Song W, Nie X. Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC Genomics 2016; 17:668. [PMID: 27549916 PMCID: PMC4994377 DOI: 10.1186/s12864-016-2993-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/03/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Mitogen-activated protein kinase kinase kinases (MAPKKKs) are the important components of MAPK cascades, which play the crucial role in plant growth and development as well as in response to diverse stresses. Although this family has been systematically studied in many plant species, little is known about MAPKKK genes in wheat (Triticum aestivum L.), especially those involved in the regulatory network of stress processes. RESULTS In this study, we identified 155 wheat MAPKKK genes through a genome-wide search method based on the latest available wheat genome information, of which 29 belonged to MEKK, 11 to ZIK and 115 to Raf subfamily, respectively. Then, chromosome localization, gene structure and conserved protein motifs and phylogenetic relationship as well as regulatory network of these TaMAPKKKs were systematically investigated and results supported the prediction. Furthermore, a total of 11 homologous groups between A, B and D sub-genome and 24 duplication pairs among them were detected, which contributed to the expansion of wheat MAPKKK gene family. Finally, the expression profiles of these MAPKKKs during development and under different abiotic stresses were investigated using the RNA-seq data. Additionally, 10 tissue-specific and 4 salt-responsive TaMAPKKK genes were selected to validate their expression level through qRT-PCR analysis. CONCLUSIONS This study for the first time reported the genome organization, evolutionary features and expression profiles of the wheat MAPKKK gene family, which laid the foundation for further functional analysis of wheat MAPKKK genes, and contributed to better understanding the roles and regulatory mechanism of MAPKKKs in wheat.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling, 712100 Shaanxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, 3 Taicheng Road, Yangling, 712100 Shaanxi China
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Royaert S, Jansen J, da Silva DV, de Jesus Branco SM, Livingstone DS, Mustiga G, Marelli JP, Araújo IS, Corrêa RX, Motamayor JC. Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil. BMC Genomics 2016; 17:107. [PMID: 26865216 PMCID: PMC4750280 DOI: 10.1186/s12864-016-2415-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. Results We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’. Conclusions We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Royaert
- Mars Center for Cocoa Science, CP 55, Itajuípe, BA, CEP 45.630-000, Brazil.
| | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands.
| | - Daniela Viana da Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | - Samuel Martins de Jesus Branco
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | | | - Guiliana Mustiga
- Mars, Incorporated, 13601 Old Cutler Road, Miami, FL, 33158, USA.
| | | | - Ioná Santos Araújo
- Departamento de Ciências Vegetais, Universidade Federal Rural do Semi-Arido, BR 110 - Km 47, Bairro Pres. Costa e Silva, Mossoró, RN, CEP 59.625-900, Brazil.
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
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Zhang X, Dong J, Liu H, Wang J, Qi Y, Liang Z. Transcriptome Sequencing in Response to Salicylic Acid in Salvia miltiorrhiza. PLoS One 2016; 11:e0147849. [PMID: 26808150 PMCID: PMC4726470 DOI: 10.1371/journal.pone.0147849] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/08/2016] [Indexed: 12/30/2022] Open
Abstract
Salvia miltiorrhiza is a traditional Chinese herbal medicine, whose quality and yield are often affected by diseases and environmental stresses during its growing season. Salicylic acid (SA) plays a significant role in plants responding to biotic and abiotic stresses, but the involved regulatory factors and their signaling mechanisms are largely unknown. In order to identify the genes involved in SA signaling, the RNA sequencing (RNA-seq) strategy was employed to evaluate the transcriptional profiles in S. miltiorrhiza cell cultures. A total of 50,778 unigenes were assembled, in which 5,316 unigenes were differentially expressed among 0-, 2-, and 8-h SA induction. The up-regulated genes were mainly involved in stimulus response and multi-organism process. A core set of candidate novel genes coding SA signaling component proteins was identified. Many transcription factors (e.g., WRKY, bHLH and GRAS) and genes involved in hormone signal transduction were differentially expressed in response to SA induction. Detailed analysis revealed that genes associated with defense signaling, such as antioxidant system genes, cytochrome P450s and ATP-binding cassette transporters, were significantly overexpressed, which can be used as genetic tools to investigate disease resistance. Our transcriptome analysis will help understand SA signaling and its mechanism of defense systems in S. miltiorrhiza.
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Affiliation(s)
- Xiaoru Zhang
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Juane Dong
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, People's Republic of China
- * E-mail: (JD); (ZL)
| | - Hailong Liu
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Jiao Wang
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Yuexin Qi
- College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Zongsuo Liang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, People's Republic of China
- * E-mail: (JD); (ZL)
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Mithoe SC, Ludwig C, Pel MJC, Cucinotta M, Casartelli A, Mbengue M, Sklenar J, Derbyshire P, Robatzek S, Pieterse CMJ, Aebersold R, Menke FLH. Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase. EMBO Rep 2016; 17:441-54. [PMID: 26769563 DOI: 10.15252/embr.201540806] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/02/2015] [Indexed: 01/19/2023] Open
Abstract
Pattern recognition receptors (PRRs) play a key role in plant and animal innate immunity. PRR binding of their cognate ligand triggers a signaling network and activates an immune response. Activation of PRR signaling must be controlled prior to ligand binding to prevent spurious signaling and immune activation. Flagellin perception in Arabidopsis through FLAGELLIN-SENSITIVE 2 (FLS2) induces the activation of mitogen-activated protein kinases (MAPKs) and immunity. However, the precise molecular mechanism that connects activated FLS2 to downstream MAPK cascades remains unknown. Here, we report the identification of a differentially phosphorylated MAP kinase kinase kinase that also interacts with FLS2. Using targeted proteomics and functional analysis, we show that MKKK7 negatively regulates flagellin-triggered signaling and basal immunity and this requires phosphorylation of MKKK7 on specific serine residues. MKKK7 attenuates MPK6 activity and defense gene expression. Moreover, MKKK7 suppresses the reactive oxygen species burst downstream of FLS2, suggesting that MKKK7-mediated attenuation of FLS2 signaling occurs through direct modulation of the FLS2 complex.
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Affiliation(s)
- Sharon C Mithoe
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Christina Ludwig
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Michiel J C Pel
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mara Cucinotta
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Alberto Casartelli
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Malick Mbengue
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Jan Sklenar
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Paul Derbyshire
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Corné M J Pieterse
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Frank L H Menke
- Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
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Liu S, Bartnikas LM, Volko SM, Ausubel FM, Tang D. Mutation of the Glucosinolate Biosynthesis Enzyme Cytochrome P450 83A1 Monooxygenase Increases Camalexin Accumulation and Powdery Mildew Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:227. [PMID: 26973671 PMCID: PMC4774424 DOI: 10.3389/fpls.2016.00227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 02/10/2016] [Indexed: 05/06/2023]
Abstract
Small secondary metabolites, including glucosinolates and the major phytoalexin camalexin, play important roles in immunity in Arabidopsis thaliana. We isolated an Arabidopsis mutant with increased resistance to the powdery mildew fungus Golovinomyces cichoracearum and identified a mutation in the gene encoding cytochrome P450 83A1 monooxygenase (CYP83A1), which functions in glucosinolate biosynthesis. The cyp83a1-3 mutant exhibited enhanced defense responses to G. cichoracearum and double mutant analysis showed that this enhanced resistance requires NPR1, EDS1, and PAD4, but not SID2 or EDS5. In cyp83a1-3 mutants, the expression of genes related to camalexin synthesis increased upon G. cichoracearum infection. Significantly, the cyp83a1-3 mutant also accumulated higher levels of camalexin. Decreasing camalexin levels by mutation of the camalexin synthetase gene PAD3 or the camalexin synthesis regulator AtWRKY33 compromised the powdery mildew resistance in these mutants. Consistent with these observations, overexpression of PAD3 increased camalexin levels and enhanced resistance to G. cichoracearum. Taken together, our data indicate that accumulation of higher levels of camalexin contributes to increased resistance to powdery mildew.
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Affiliation(s)
- Simu Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology – Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Lisa M. Bartnikas
- Department of Molecular Biology, Massachusetts General Hospital, BostonMA, USA
| | - Sigrid M. Volko
- Department of Molecular Biology, Massachusetts General Hospital, BostonMA, USA
- Department of Genetics, Harvard Medical School, BostonMA, USA
| | - Frederick M. Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, BostonMA, USA
- Department of Genetics, Harvard Medical School, BostonMA, USA
| | - Dingzhong Tang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology – Chinese Academy of SciencesBeijing, China
- *Correspondence: Dingzhong Tang,
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Liu Y, Zhou M, Gao Z, Ren W, Yang F, He H, Zhao J. RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize. PLoS One 2015; 10:e0143128. [PMID: 26599013 PMCID: PMC4658043 DOI: 10.1371/journal.pone.0143128] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/30/2015] [Indexed: 02/06/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.
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Affiliation(s)
- Ya Liu
- Maize Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, P.R.China
| | - Miaoyi Zhou
- Maize Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, P.R.China
| | - Zhaoxu Gao
- School of Life Sciences and School of Advanced Agriculture Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P.R.China
| | - Wen Ren
- Maize Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, P.R.China
| | - Fengling Yang
- Maize Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, P.R.China
| | - Hang He
- School of Life Sciences and School of Advanced Agriculture Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, P.R.China
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agricultural and Forestry Science, Beijing 100097, P.R.China
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Virk N, Li D, Tian L, Huang L, Hong Y, Li X, Zhang Y, Liu B, Zhang H, Song F. Arabidopsis Raf-Like Mitogen-Activated Protein Kinase Kinase Kinase Gene Raf43 Is Required for Tolerance to Multiple Abiotic Stresses. PLoS One 2015. [PMID: 26222830 PMCID: PMC4519275 DOI: 10.1371/journal.pone.0133975] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are critical signaling modules that mediate the transduction of extracellular stimuli into intracellular response. A relatively large number of MAPKKKs have been identified in a variety of plant genomes but only a few of them have been studied for their biological function. In the present study, we identified an Arabidopsis Raf-like MAPKKK gene Raf43 and studied its function in biotic and abiotic stress response using a T-DNA insertion mutant raf43-1 and two Raf43-overexpressing lines Raf43-OE#1 and Raf43-OE#13. Expression of Raf43 was induced by multiple abiotic and biotic stresses including treatments with drought, mannitol and oxidative stress or defense signaling molecule salicylic acid and infection with necrotrophic fungal pathogen Botrytis cinerea. Seed germination and seedling root growth of raf43-1 were significantly inhibited on MS medium containing mannitol, NaCl, H2O2 or methyl viologen (MV) while seed germination and seedling root growth of the Raf43-OE#1 and Raf43-OE#13 lines was similar to wild type Col-0 under the above stress conditions. Soil-grown raf43-1 plants exhibited reduced tolerance to MV, drought and salt stress. Abscisic acid inhibited significantly seed germination and seedling root growth of the raf43-1 line but had no effect on the two Raf43-overexpressing lines. Expression of stress-responsive RD17 and DREB2A genes was significantly down-regulated in raf43-1 plants. However, the raf43-1 and Raf43-overexpressing plants showed similar disease phenotype to the wild type plants after infection with B. cinerea or Pseudomonas syringae pv. tomato DC3000. Our results demonstrate that Raf43, encoding for a Raf-like MAPKKK, is required for tolerance to multiple abiotic stresses in Arabidopsis.
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Affiliation(s)
- Nasar Virk
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dayong Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Limei Tian
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Lei Huang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yongbo Hong
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohui Li
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yafen Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bo Liu
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huijuan Zhang
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- * E-mail:
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Jiang M, Wen F, Cao J, Li P, She J, Chu Z. Genome-wide exploration of the molecular evolution and regulatory network of mitogen-activated protein kinase cascades upon multiple stresses in Brachypodium distachyon. BMC Genomics 2015; 16:228. [PMID: 25886731 PMCID: PMC4404688 DOI: 10.1186/s12864-015-1452-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/09/2015] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Brachypodium distachyon is emerging as a widely recognized model plant that has very close relations with several economically important Poaceae species. MAPK cascade is known to be an evolutionarily conserved signaling module involved in multiple stresses. Although the gene sequences of MAPK and MAPKK family have been fully identified in B. distachyon, the information related to the upstream MAPKKK gene family especially the regulatory network among MAPKs, MAPKKs and MAPKKKs upon multiple stresses remains to be understood. RESULTS In this study, we have identified MAPKKKs which belong to the biggest gene family of MAPK cascade kinases. We have systematically investigated the evolution of whole MAPK cascade kinase gene family in terms of gene structures, protein structural organization, chromosomal localization, orthologs construction and gene duplication analysis. Our results showed that most BdMAPK cascade kinases were located at the low-CpG-density region, and the clustered members in each group shared similar structures of the genes and proteins. Synteny analysis showed that 62 or 21 pairs of duplicated orthologs were present between B. distachyon and Oryza sativa, or between B. distachyon and Arabidopsis thaliana respectively. Gene expression data revealed that BdMAPK cascade kinases were rapidly regulated by stresses and phytohormones. Importantly, we have constructed a regulation network based on co-expression patterns of the expression profiles upon multiple stresses performed in this study. CONCLUSIONS BdMAPK cascade kinases were involved in the signaling pathways of multiple stresses in B. distachyon. The network of co-expression regulation showed the most of duplicated BdMAPK cascade kinase gene orthologs demonstrated their convergent function, whereas few of them developed divergent function in the evolutionary process. The molecular evolution analysis of identified MAPK family genes and the constructed MAPK cascade regulation network under multiple stresses provide valuable information for further investigation of the functions of BdMAPK cascade kinase genes.
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Affiliation(s)
- Min Jiang
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China.
| | - Feng Wen
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China. .,Current address: College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China.
| | - Jianmei Cao
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China.
| | - Peng Li
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China.
| | - Jessica She
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China. .,Program of Biochemistry and Immunology, University of Toronto, 100 St. George Street, Toronto, M5G 3G3, Ontario, Canada.
| | - Zhaoqing Chu
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China.
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Zhao T, Rui L, Li J, Nishimura MT, Vogel JP, Liu N, Liu S, Zhao Y, Dangl JL, Tang D. A truncated NLR protein, TIR-NBS2, is required for activated defense responses in the exo70B1 mutant. PLoS Genet 2015; 11:e1004945. [PMID: 25617755 PMCID: PMC4305288 DOI: 10.1371/journal.pgen.1004945] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022] Open
Abstract
During exocytosis, the evolutionarily conserved exocyst complex tethers Golgi-derived vesicles to the target plasma membrane, a critical function for secretory pathways. Here we show that exo70B1 loss-of-function mutants express activated defense responses upon infection and express enhanced resistance to fungal, oomycete and bacterial pathogens. In a screen for mutants that suppress exo70B1 resistance, we identified nine alleles of TIR-NBS2 (TN2), suggesting that loss-of-function of EXO70B1 leads to activation of this nucleotide binding domain and leucine-rich repeat-containing (NLR)-like disease resistance protein. This NLR-like protein is atypical because it lacks the LRR domain common in typical NLR receptors. In addition, we show that TN2 interacts with EXO70B1 in yeast and in planta. Our study thus provides a link between the exocyst complex and the function of a 'TIR-NBS only' immune receptor like protein. Our data are consistent with a speculative model wherein pathogen effectors could evolve to target EXO70B1 to manipulate plant secretion machinery. TN2 could monitor EXO70B1 integrity as part of an immune receptor complex.
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Affiliation(s)
- Ting Zhao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lu Rui
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Juan Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Marc T. Nishimura
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - John P. Vogel
- Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, California, United States of America
| | - Na Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Simu Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Yaofei Zhao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School of Chinese Academy of Sciences, Beijing, China
| | - Jeffery L. Dangl
- Howard Hughes Medical Institute and Department of Biology, University of North Carolina at Chapel Hill, North Carolina, United States of America
| | - Dingzhong Tang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Bruggeman Q, Raynaud C, Benhamed M, Delarue M. To die or not to die? Lessons from lesion mimic mutants. FRONTIERS IN PLANT SCIENCE 2015; 6:24. [PMID: 25688254 PMCID: PMC4311611 DOI: 10.3389/fpls.2015.00024] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/12/2015] [Indexed: 05/19/2023]
Abstract
Programmed cell death (PCD) is a ubiquitous genetically regulated process consisting in an activation of finely controlled signaling pathways that lead to cellular suicide. Although some aspects of PCD control appear evolutionary conserved between plants, animals and fungi, the extent of conservation remains controversial. Over the last decades, identification and characterization of several lesion mimic mutants (LMM) has been a powerful tool in the quest to unravel PCD pathways in plants. Thanks to progress in molecular genetics, mutations causing the phenotype of a large number of LMM and their related suppressors were mapped, and the identification of the mutated genes shed light on major pathways in the onset of plant PCD such as (i) the involvements of chloroplasts and light energy, (ii) the roles of sphingolipids and fatty acids, (iii) a signal perception at the plasma membrane that requires efficient membrane trafficking, (iv) secondary messengers such as ion fluxes and ROS and (v) the control of gene expression as the last integrator of the signaling pathways.
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Affiliation(s)
- Quentin Bruggeman
- Institut de Biologie des Plantes, UMR CNRS 8618, Université Paris-Sud, Saclay Plant SciencesOrsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR CNRS 8618, Université Paris-Sud, Saclay Plant SciencesOrsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR CNRS 8618, Université Paris-Sud, Saclay Plant SciencesOrsay, France
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR CNRS 8618, Université Paris-Sud, Saclay Plant SciencesOrsay, France
- *Correspondence: Marianne Delarue, Institut de Biologie des Plantes, UMR CNRS 8618, Université Paris-Sud, Saclay Plant Sciences, Bâtiment 630, Route de Noetzlin, 91405 Orsay Cedex, France e-mail:
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Soil drench treatment with ß-aminobutyric acid increases drought tolerance of potato. PLoS One 2014; 9:e114297. [PMID: 25489951 PMCID: PMC4260862 DOI: 10.1371/journal.pone.0114297] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/07/2014] [Indexed: 01/01/2023] Open
Abstract
The non-protein amino acid β-aminobutyric acid (BABA) is known to be a priming agent for a more efficient activation of cellular defence responses and a potent inducer of resistance against biotic and abiotic stresses in plants. Nevertheless, most of the studies on priming have been carried out in Arabidopsis. In potato, the effect of BABA was demonstrated only on biotic stress tolerance. We investigated the effect of BABA on the drought tolerance of potato and found that soil drenched with BABA at a final concentration of 0.3 mM improves the drought tolerance of potato. Water loss from the leaves of the primed plants is attenuated and the yield is increased compared to the unprimed drought-stressed plants. The metabolite composition of the tubers of the BABA-treated plants is less affected by drought than the tuber composition of the non-treated plants. Nitric oxide and ROS (reactive oxygen species) production is increased in the BABA-treated roots but not in the leaves. In the leaves of the BABA-treated plants, the expression of the drought-inducible gene StDS2 is delayed, but the expression of ETR1, encoding an ethylene receptor, is maintained for a longer period under the drought conditions than in the leaves of the non-treated, drought-stressed control plants. This result suggests that the ethylene-inducible gene expression remains suppressed in primed plants leading to a longer leaf life and increased tuber yield compared to the non-treated, drought-stressed plants. The priming effect of BABA in potato, however, is transient and reverts to an unprimed state within a few weeks.
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Kaljunen H, Panneerselvam S, Mueller-Dieckmann J. Cloning, overexpression, purification and preliminary X-ray analysis of the protein kinase domain of enhanced disease resistance 1 (EDR1) from Arabidopsis thaliana. Acta Crystallogr F Struct Biol Commun 2014; 70:959-62. [PMID: 25005098 PMCID: PMC4089541 DOI: 10.1107/s2053230x14011844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/21/2014] [Indexed: 11/10/2022] Open
Abstract
Enhanced disease resistance 1 is a member of the Raf-like mitogen-activated protein kinase kinase kinase (MAPKKK) family that negatively regulates disease resistance, ethylene-induced senescence and programmed cell death in response to both abiotic and biotic stresses. A catalytically inactive form of the EDR1 kinase domain was successfully cloned, expressed, purified and crystallized. Crystallization was conducted in the presence of the ATP analogue AMP-PNP. The crystals belonged to space group P3221 and contained two molecules in the asymmetric unit. The crystals diffracted X-rays to 2.55 Å resolution.
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Luna E, van Hulten M, Zhang Y, Berkowitz O, López A, Pétriacq P, Sellwood MA, Chen B, Burrell M, van de Meene A, Pieterse CM, Flors V, Ton J. Plant perception of β-aminobutyric acid is mediated by an aspartyl-tRNA synthetase. Nat Chem Biol 2014; 10:450-6. [PMID: 24776930 PMCID: PMC4028204 DOI: 10.1038/nchembio.1520] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 03/27/2014] [Indexed: 12/26/2022]
Abstract
Specific chemicals can prime the plant immune system for augmented defense. β-aminobutyric acid (BABA) is a priming agent that provides broad-spectrum disease protection. However, BABA also suppresses plant growth when applied in high doses, which has hampered its application as a crop defense activator. Here we describe a mutant of Arabidopsis thaliana that is impaired in BABA-induced disease immunity (ibi1) but is hypersensitive to BABA-induced growth repression. IBI1 encodes an aspartyl-tRNA synthetase. Enantiomer-specific binding of the R enantiomer of BABA to IBI1 primed the protein for noncanonical defense signaling in the cytoplasm after pathogen attack. This priming was associated with aspartic acid accumulation and tRNA-induced phosphorylation of translation initiation factor eIF2α. However, mutation of eIF2α-phosphorylating GCN2 kinase did not affect BABA-induced immunity but relieved BABA-induced growth repression. Hence, BABA-activated IBI1 controls plant immunity and growth via separate pathways. Our results open new opportunities to separate broad-spectrum disease resistance from the associated costs on plant growth.
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Affiliation(s)
- Estrella Luna
- Department of Animal and Plant Sciences, The University of Sheffield, UK
| | | | | | - Oliver Berkowitz
- School of Plant Biology, University of Western Australia, Perth, Australia
| | - Ana López
- Department of Animal and Plant Sciences, The University of Sheffield, UK
| | - Pierre Pétriacq
- Department of Animal and Plant Sciences, The University of Sheffield, UK
| | | | - Beining Chen
- Department of Chemistry, The University of Sheffield, UK
| | - Mike Burrell
- Department of Animal and Plant Sciences, The University of Sheffield, UK
| | | | | | - Victor Flors
- Department of CAMN, University of Jaume I, Spain
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, The University of Sheffield, UK
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Zhao C, Nie H, Shen Q, Zhang S, Lukowitz W, Tang D. EDR1 physically interacts with MKK4/MKK5 and negatively regulates a MAP kinase cascade to modulate plant innate immunity. PLoS Genet 2014; 10:e1004389. [PMID: 24830651 PMCID: PMC4022593 DOI: 10.1371/journal.pgen.1004389] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/03/2014] [Indexed: 12/17/2022] Open
Abstract
Mitogen-activated protein (MAP) kinase signaling cascades play important roles in the regulation of plant defense. The Raf-like MAP kinase kinase kinase (MAPKKK) EDR1 negatively regulates plant defense responses and cell death. However, how EDR1 functions, and whether it affects the regulation of MAPK cascades, are not well understood. Here, we showed that EDR1 negatively regulates the MKK4/MKK5-MPK3/MPK6 kinase cascade in Arabidopsis. We found that edr1 mutants have highly activated MPK3/MPK6 kinase activity and higher levels of MPK3/MPK6 proteins than wild type. EDR1 physically interacts with MKK4 and MKK5, and this interaction requires the N-terminal domain of EDR1. EDR1 also negatively affects MKK4/MKK5 protein levels. In addition, the mpk3, mkk4 and mkk5 mutations suppress edr1-mediated resistance, and over-expression of MKK4 or MKK5 causes edr1-like resistance and mildew-induced cell death. Taken together, our data indicate that EDR1 physically associates with MKK4/MKK5 and negatively regulates the MAPK cascade to fine-tune plant innate immunity. Plant immunity must be tightly regulated, as over- or constitutive activation of plant defenses can cause detrimental effects, such as dwarf stature and enhanced cell death. EDR1, a Raf-like mitogen-activated protein kinase (MAPK) kinase kinase, negatively regulates defenses in Arabidopsis. The highly conserved MAPK cascades modulate diverse biological processes, including plant immunity. However, whether EDR1 affects the regulation of one of the MAPK pathways was not previously known. Here, we show that EDR1 physically associates with MKK4 and MKK5, two MAP kinase kinases, and negatively regulates the protein levels of MKK4, MKK5, MPK3 and MPK6. We further show that edr1-mediated disease resistance requires MKK4, MKK5 and MPK3 function. Over-expression of MKK4 or MKK5 in wild-type increased resistance to powdery mildew and caused mildew-induced cell death. Our study suggests that EDR1 negatively regulates defenses and directly modulates the MKK4/MKK5-MPK3/MPK6 cascade to fine-tune plant immunity.
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Affiliation(s)
- Chunzhao Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Haozhen Nie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Qiujing Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Shuqun Zhang
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Dingzhong Tang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice. PLoS One 2013; 8:e77261. [PMID: 24130868 PMCID: PMC3795056 DOI: 10.1371/journal.pone.0077261] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 08/30/2013] [Indexed: 12/13/2022] Open
Abstract
Plants are simultaneously exposed to multiple stresses resulting in enormous changes in the molecular landscape within the cell. Identification and characterization of the synergistic and antagonistic components of stress response mechanisms contributing to the cross talk between stresses is of high priority to explore and enhance multiple stress responses. To this end, we performed meta-analysis of drought (abiotic), bacterial (biotic) stress response in rice and Arabidopsis by analyzing a total of 386 microarray samples belonging to 20 microarray studies and identified approximately 3100 and 900 DEGs in rice and Arabidopsis, respectively. About 38.5% (1214) and 28.7% (272) DEGs were common to drought and bacterial stresses in rice and Arabidopsis, respectively. A majority of these common DEGs showed conserved expression status in both stresses. Gene ontology enrichment analysis clearly demarcated the response and regulation of various plant hormones and related biological processes. Fatty acid metabolism and biosynthesis of alkaloids were upregulated and, nitrogen metabolism and photosynthesis was downregulated in both stress conditions. WRKY transcription family genes were highly enriched in all upregulated gene sets while ‘CO-like’ TF family showed inverse relationship of expression between drought and bacterial stresses. Weighted gene co-expression network analysis divided DEG sets into multiple modules that show high co-expression and identified stress specific hub genes with high connectivity. Detection of consensus modules based on DEGs common to drought and bacterial stress revealed 9 and 4 modules in rice and Arabidopsis, respectively, with conserved and reversed co-expression patterns.
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Neupane A, Nepal MP, Piya S, Subramanian S, Rohila JS, Reese RN, Benson BV. Identification, nomenclature, and evolutionary relationships of mitogen-activated protein kinase (MAPK) genes in soybean. Evol Bioinform Online 2013; 9:363-86. [PMID: 24137047 PMCID: PMC3785387 DOI: 10.4137/ebo.s12526] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) genes in eukaryotes regulate various developmental and physiological processes including those associated with biotic and abiotic stresses. Although MAPKs in some plant species including Arabidopsis have been identified, they are yet to be identified in soybean. Major objectives of this study were to identify GmMAPKs, assess their evolutionary relationships, and analyze their functional divergence. We identified a total of 38 MAPKs, eleven MAPKKs, and 150 MAPKKKs in soybean. Within the GmMAPK family, we also identified a new clade of six genes: four genes with TEY and two genes with TQY motifs requiring further investigation into possible legume-specific functions. The results indicated the expansion of the GmMAPK families attributable to the ancestral polyploidy events followed by chromosomal rearrangements. The GmMAPK and GmMAPKKK families were substantially larger than those in other plant species. The duplicated GmMAPK members presented complex evolutionary relationships and functional divergence when compared to their counterparts in Arabidopsis. We also highlighted existing nomenclatural issues, stressing the need for nomenclatural consistency. GmMAPK identification is vital to soybean crop improvement, and novel insights into the evolutionary relationships will enhance our understanding about plant genome evolution.
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Affiliation(s)
- Achal Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings SD, USA
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The MAPKKK gene family in Gossypium raimondii: genome-wide identification, classification and expression analysis. Int J Mol Sci 2013; 14:18740-57. [PMID: 24030721 PMCID: PMC3794805 DOI: 10.3390/ijms140918740] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/22/2013] [Accepted: 08/26/2013] [Indexed: 11/17/2022] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are conserved signal transduction pathways in all eukaryotic organisms. MAPKKKs (MAPK kinase kinases) operate at the top levels of these cascades. Recently, this family of genes has been systematically investigated in Arabidopsis, rice and maize, but has not yet been characterized in cotton. In this study, we identified 78 putative MAPKKK genes in the genome of the diploid cotton, Gossypium raimondii. They were classified into three subfamilies, of which 12 were ZIK, 22 were MEKK and 44 were Raf. The ZIK and MEKK genes displayed a scattered genomic distribution across 11 of the 13 chromosomes, whereas Raf genes were distributed across the entire genome. Their conserved patterns observed for introns and additional domains were consistent with the evolutionary relationships inferred from the phylogenetic analysis within subfamily. Transcriptome sequencing data were used to investigate their transcript profiles in mature leaves, 0 day and 3 days post-anthesis (DPA) ovules. Sixty MAPKKK genes were expressed, of which 41 were strongly expressed in mature leaves. Twelve MAPKKK genes were more highly expressed in 3-DPA ovules than in 0-DPA ovules. Our results provide a foundation for future evolutionary and functional characterizations of MAPKKK genes in cotton and probably other Gossypium plants.
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Lehti-Shiu MD, Shiu SH. Diversity, classification and function of the plant protein kinase superfamily. Philos Trans R Soc Lond B Biol Sci 2012; 367:2619-39. [PMID: 22889912 DOI: 10.1098/rstb.2012.0003] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic protein kinases belong to a large superfamily with hundreds to thousands of copies and are components of essentially all cellular functions. The goals of this study are to classify protein kinases from 25 plant species and to assess their evolutionary history in conjunction with consideration of their molecular functions. The protein kinase superfamily has expanded in the flowering plant lineage, in part through recent duplications. As a result, the flowering plant protein kinase repertoire, or kinome, is in general significantly larger than other eukaryotes, ranging in size from 600 to 2500 members. This large variation in kinome size is mainly due to the expansion and contraction of a few families, particularly the receptor-like kinase/Pelle family. A number of protein kinases reside in highly conserved, low copy number families and often play broadly conserved regulatory roles in metabolism and cell division, although functions of plant homologues have often diverged from their metazoan counterparts. Members of expanded plant kinase families often have roles in plant-specific processes and some may have contributed to adaptive evolution. Nonetheless, non-adaptive explanations, such as kinase duplicate subfunctionalization and insufficient time for pseudogenization, may also contribute to the large number of seemingly functional protein kinases in plants.
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Affiliation(s)
- Melissa D Lehti-Shiu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
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