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Chen W, Tang L, Li Q, Cai Y, Ahmad S, Wang Y, Tang S, Guo N, Wei X, Tang S, Shao G, Jiao G, Xie L, Hu S, Sheng Z, Hu P. YGL3 Encoding an IPP and DMAPP Synthase Interacts with OsPIL11 to Regulate Chloroplast Development in Rice. RICE (NEW YORK, N.Y.) 2024; 17:8. [PMID: 38228921 DOI: 10.1186/s12284-024-00687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2024] [Indexed: 01/18/2024]
Abstract
As the source of isoprenoid precursors, the plastidial methylerythritol phosphate (MEP) pathway plays an essential role in plant development. Here, we report a novel rice (Oryza sativa L.) mutant ygl3 (yellow-green leaf3) that exhibits yellow-green leaves and lower photosynthetic efficiency compared to the wild type due to abnormal chloroplast ultrastructure and reduced chlorophyll content. Map-based cloning showed that YGL3, one of the major genes involved in the MEP pathway, encodes 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, which is localized in the thylakoid membrane. A single base substitution in ygl3 plants resulted in lower 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity and lower contents of isopentenyl diphosphate (IPP) compared to the wild type. The transcript levels of genes involved in the syntheses of chlorophyll and thylakoid membrane proteins were significantly reduced in the ygl3 mutant compared to the wild type. The phytochrome interacting factor-like gene OsPIL11 regulated chlorophyll synthesis during the de-etiolation process by directly binding to the promoter of YGL3 to activate its expression. The findings provides a theoretical basis for understanding the molecular mechanisms by which the MEP pathway regulate chloroplast development in rice.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Center for Rice, Nanchang, P. R. China
| | - Liqun Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Qianlong Li
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yicong Cai
- Key Labora tory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Ministry of Education/Collaboration Center for Double-season Rice Modernization Production, Jiangxi Agricultural University, Nanchang, Jiangxi Province, 330045, P. R. China
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Yakun Wang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Naihui Guo
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Lihong Xie
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Shikai Hu
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China.
| | - Peisong Hu
- State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice improvement Centre, National Rice Research Institute, Hangzhou, 310006, P. R. China.
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Yao G, Zhang H, Leng B, Cao B, Shan J, Yan Z, Guan H, Cheng W, Liu X, Mu C. A large deletion conferring pale green leaves of maize. BMC PLANT BIOLOGY 2023; 23:360. [PMID: 37452313 PMCID: PMC10347855 DOI: 10.1186/s12870-023-04360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND The structural basis of chloroplast and the regulation of chloroplast biogenesis remain largely unknown in maize. Gene mutations in these pathways have been linked to the abnormal leaf color phenotype observed in some mutants. Large scale structure variants (SVs) are crucial for genome evolution, but few validated SVs have been reported in maize and little is known about their functions though they are abundant in maize genomes. RESULTS In this research, a spontaneous maize mutant, pale green leaf-shandong (pgl-sd), was studied. Genetic analysis showed that the phenotype of pale green leaf was controlled by a recessive Mendel factor mapped to a 156.8-kb interval on the chromosome 1 delineated by molecular markers gy546 and gy548. There were 7 annotated genes in this interval. Reverse transcription quantitative PCR analysis, SV prediction, and de novo assembly of pgl-sd genome revealed that a 137.8-kb deletion, which was verified by Sanger sequencing, might cause the pgl-sd phenotype. This deletion contained 5 annotated genes, three of which, including Zm00001eb031870, Zm00001eb031890 and Zm00001eb031900, were possibly related to the chloroplast development. Zm00001eb031870, encoding a Degradation of Periplasmic Proteins (Deg) homolog, and Zm00001eb031900, putatively encoding a plastid pyruvate dehydrogenase complex E1 component subunit beta (ptPDC-E1-β), might be the major causative genes for the pgl-sd mutant phenotype. Plastid Degs play roles in protecting the vital photosynthetic machinery and ptPDCs provide acetyl-CoA and NADH for fatty acid biosynthesis in plastids, which were different from functions of other isolated maize leaf color associated genes. The other two genes in the deletion were possibly associated with DNA repair and disease resistance, respectively. The pgl-sd mutation decreased contents of chlorophyll a, chlorophyll b, carotenoids by 37.2%, 22.1%, and 59.8%, respectively, and led to abnormal chloroplast. RNA-seq revealed that the transcription of several other genes involved in the structure and function of chloroplast was affected in the mutant. CONCLUSIONS It was identified that a 137.8-kb deletion causes the pgl-sd phenotype. Three genes in this deletion were possibly related to the chloroplast development, which may play roles different from that of other isolated maize leaf color associated genes.
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Affiliation(s)
- Guoqi Yao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Hua Zhang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Bingying Leng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Bing Cao
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Juan Shan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Zhenwei Yan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Wen Cheng
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China
- National Maize Improvement Sub-Center, Jinan, 250100, China
| | - Xia Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China.
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China.
- National Maize Improvement Sub-Center, Jinan, 250100, China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
| | - Chunhua Mu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, 250100, China.
- National Engineering Laboratory of Wheat and Maize, Jinan, 250100, China.
- National Maize Improvement Sub-Center, Jinan, 250100, China.
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Trieu A, Belaffif MB, Hirannaiah P, Manjunatha S, Wood R, Bathula Y, Billingsley RL, Arpan A, Sacks EJ, Clemente TE, Moose SP, Reichert NA, Swaminathan K. Transformation and gene editing in the bioenergy grass Miscanthus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:148. [PMID: 36578060 PMCID: PMC9798709 DOI: 10.1186/s13068-022-02241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Miscanthus, a C4 member of Poaceae, is a promising perennial crop for bioenergy, renewable bioproducts, and carbon sequestration. Species of interest include nothospecies M. x giganteus and its parental species M. sacchariflorus and M. sinensis. Use of biotechnology-based procedures to genetically improve Miscanthus, to date, have only included plant transformation procedures for introduction of exogenous genes into the host genome at random, non-targeted sites. RESULTS We developed gene editing procedures for Miscanthus using CRISPR/Cas9 that enabled the mutation of a specific (targeted) endogenous gene to knock out its function. Classified as paleo-allopolyploids (duplicated ancient Sorghum-like DNA plus chromosome fusion event), design of guide RNAs (gRNAs) for Miscanthus needed to target both homeologs and their alleles to account for functional redundancy. Prior research in Zea mays demonstrated that editing the lemon white1 (lw1) gene, involved in chlorophyll and carotenoid biosynthesis, via CRISPR/Cas9 yielded pale green/yellow, striped or white leaf phenotypes making lw1 a promising target for visual confirmation of editing in other species. Using sequence information from both Miscanthus and sorghum, orthologs of maize lw1 were identified; a multi-step screening approach was used to select three gRNAs that could target homeologs of lw1. Embryogenic calli of M. sacchariflorus, M. sinensis and M. x giganteus were transformed via particle bombardment (biolistics) or Agrobacterium tumefaciens introducing the Cas9 gene and three gRNAs to edit lw1. Leaves on edited Miscanthus plants displayed the same phenotypes noted in maize. Sanger sequencing confirmed editing; deletions in lw1 ranged from 1 to 26 bp in length, and one deletion (433 bp) encompassed two target sites. Confocal microscopy verified lack of autofluorescence (chlorophyll) in edited leaves/sectors. CONCLUSIONS We developed procedures for gene editing via CRISPR/Cas9 in Miscanthus and, to the best of our knowledge, are the first to do so. This included five genotypes representing three Miscanthus species. Designed gRNAs targeted all copies of lw1 (homeologous copies and their alleles); results also confirmed lw1 made a good editing target in species other than Z. mays. The ability to target specific loci to enable endogenous gene editing presents a new avenue for genetic improvement of this important biomass crop.
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Affiliation(s)
- Anthony Trieu
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Mohammad B. Belaffif
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Pradeepa Hirannaiah
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Shilpa Manjunatha
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebekah Wood
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Yokshitha Bathula
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Rebecca L. Billingsley
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Anjali Arpan
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Erik J. Sacks
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Thomas E. Clemente
- grid.24434.350000 0004 1937 0060Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Stephen P. Moose
- grid.35403.310000 0004 1936 9991Department of Crop Sciences, E.R. Madigan Laboratory, University of Illinois Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Nancy A. Reichert
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, 295 Lee Blvd., Mississippi State, MS 39762 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
| | - Kankshita Swaminathan
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806 USA ,grid.35403.310000 0004 1936 9991DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801 USA
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Xu R, Ming Y, Li Y, Li S, Zhu W, Wang H, Guo J, Shi Z, Shu S, Xiong C, Cheng X, Wang L, You J, Wan D. Full-Length Transcriptomic Sequencing and Temporal Transcriptome Expression Profiling Analyses Offer Insights into Terpenoid Biosynthesis in Artemisia argyi. Molecules 2022; 27:molecules27185948. [PMID: 36144681 PMCID: PMC9501300 DOI: 10.3390/molecules27185948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Artemisiae argyi Folium is a traditional herbal medicine used for moxibustion heat therapy in China. The volatile oils in A.argyi leaves are closely related to its medicinal value. Records suggest that the levels of these terpenoids components within the leaves vary as a function of harvest time, with June being the optimal time for A. argyi harvesting, owing to the high levels of active ingredients during this month. However, the molecular mechanisms governing terpenoid biosynthesis and the time-dependent changes in this activity remain unclear. In this study, GC–MS analysis revealed that volatile oil levels varied across four different harvest months (April, May, June, and July) in A. argyi leaves, and the primarily terpenoids components (including both monoterpenes and sesquiterpenes) reached peak levels in early June. Through single-molecule real-time (SMRT) sequencing, corrected by Illumina RNA-sequencing (RNA-Seq), 44 full-length transcripts potentially involved in terpenoid biosynthesis were identified in this study. Differentially expressed genes (DEGs) exhibiting time-dependent expression patterns were divided into 12 coexpression clusters. Integrated chemical and transcriptomic analyses revealed distinct time-specific transcriptomic patterns associated with terpenoid biosynthesis. Subsequent hierarchical clustering and correlation analyses ultimately identified six transcripts that were closely linked to the production of these two types of terpenoid within A. argyi leaves, revealing that the structural diversity of terpenoid is related to the generation of the diverse terpene skeletons by prenyltransferase (TPS) family of enzymes. These findings can guide further studies of the molecular mechanisms underlying the quality of A. argyi leaves, aiding in the selection of optimal timing for harvests of A. argyi.
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Affiliation(s)
- Ran Xu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Yue Ming
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yongchang Li
- College of Osteopathic Medicine, Kansas City University of Medicine and Biosciences, Joplin, MO 64804, USA
| | - Shaoting Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Wenjun Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hongxun Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jie Guo
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
| | - Zhaohua Shi
- Key Laboratory of Chinese Medicine Resources and Compound Formula, Ministry of Education, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Shaohua Shu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Xiong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiang Cheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jingmao You
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
| | - Dingrong Wan
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China
- Correspondence: (R.X.); (J.Y.); (D.W.)
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Song H, Li Y, Wang Z, Duan Z, Wang Y, Yang E, Que Q, Chen X, Li P. Transcriptome profiling of Toona ciliata young stems in response to Hypsipyla robusta Moore. FRONTIERS IN PLANT SCIENCE 2022; 13:950945. [PMID: 36105698 PMCID: PMC9465623 DOI: 10.3389/fpls.2022.950945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Toona ciliata is a traditional woody plant that can be used as a medicinal material in China. The extracts of its roots, stems, leaves, and flowers all have a wide range of bioactive compounds. However, T. ciliata has been facing an unresolved pest problem caused by Hypsipyla robusta Moore (HRM), which seriously affects its growth and development. In this study, the expression level of TcMYB3 gene reached the maximum (28-fold) at 12 h and transcriptome sequencing of young stems eaten by HRM for 0, 3, 12, and 21 h were performed. A large number of differentially expressed genes (DEGs) were identified including jointly up-regulated genes (263) and down-regulated genes (378). JA synthesis and signaling transduction, terpene biosynthesis, and MAPKs signaling pathway were analyzed in depth and found that TcOPR3, TcJAR1, TcJAZs, and TcTPS9 genes possessed anti-insect potential. Moreover, MYB and ERF transcription factor (TF) families were significantly strengthened to the point that they may participate in induced defense mechanisms in T. ciliata. These data not only provide insights into the molecular mechanisms in resistance of T. ciliata to HRM but also helps to explore the new biocontrol strategies against insects in eco-friendly woody plants.
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Affiliation(s)
- Huiyun Song
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Yue Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Zhi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Zhihao Duan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Yueyang Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Endian Yang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Qingmin Que
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Pei Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, China
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Li Y, Sun W, Wang Z, Wan C, Zhang J, Qi X, Zhang J. SDG102, a H3K36-Methyltransferase-Encoding Gene, Plays Pleiotropic Roles in Growth and Development of Maize ( Zea mays L.). Int J Mol Sci 2022; 23:ijms23137458. [PMID: 35806471 PMCID: PMC9267571 DOI: 10.3390/ijms23137458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/01/2023] Open
Abstract
Although histone lysine methylation has been studied in thale cress (Arabidopsis thaliana (L.) Heynh.) and rice (Oryza sativa L.) in recent years, its function in maize (Zea mays L.) remains poorly characterized. To better understand the function of histone lysine methylation in maize, SDG102, a H3 lysine 36 (H3K36) methylase, was chosen for functional characterization using overexpressed and knockout transgenic plants. SDG102-deficiency in maize caused multiple phenotypes including yellow leaves in seedlings, late-flowering, and increased adult plant height, while the overexpression of SDG102 led to reduced adult plant height. The key flowering genes, ZCN8/ZCN7 and MADS4/MADA67, were downregulated in SDG102-deficient plants. Chromatin immunoprecipitation (ChIP) experiments showed that H3 lysine 36 trimethylation (H3K36me3) levels were reduced at these loci. Perturbation of SDG102 expression caused the misexpression of multiple genes. Interestingly, the overexpression or knockout of SDG102 also led to genome-wide decreases and increases in the H3K36me3 levels, respectively. Together, our results suggest that SDG102 is a methyltransferase that catalyzes the trimethylation of H3K36 of many genes across the maize genome, which are involved in multiple biological processes including those controlling flowering time.
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Affiliation(s)
- Yongjian Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
| | - Weifeng Sun
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
| | - Chang Wan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
| | - Xin Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
- Correspondence: (X.Q.); (J.Z.)
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (Y.L.); (W.S.); (C.W.); (Z.W.); (J.Z.)
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada
- Correspondence: (X.Q.); (J.Z.)
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7
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Li JY, Yang C, Tian YY, Liu JX. Regulation of Chloroplast Development and Function at Adverse Temperatures in Plants. PLANT & CELL PHYSIOLOGY 2022; 63:580-591. [PMID: 35141744 DOI: 10.1093/pcp/pcac022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The chloroplast is essential for photosynthesis, plant growth and development. As semiautonomous organelles, the biogenesis and development of chloroplasts need to be well-regulated during plant growth and stress responses. Low or high ambient temperatures are adverse environmental stresses that affect crop growth and productivity. As sessile organisms, plants regulate the development and function of chloroplasts in a fluctuating temperature environment to maintain normal photosynthesis. This review focuses on the molecular mechanisms and regulatory factors required for chloroplast biogenesis and development under cold or heat stress conditions and highlights the importance of chloroplast gene transcription, RNA metabolism, ribosome function and protein homeostasis essential for chloroplast development under adverse temperature conditions.
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Affiliation(s)
- Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Chuang Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Ying-Ying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
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8
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Lee YJ, Kim JK, Baek SA, Yu JS, You MK, Ha SH. Differential Regulation of an OsIspH1, the Functional 4-Hydroxy-3-Methylbut-2-Enyl Diphosphate Reductase, for Photosynthetic Pigment Biosynthesis in Rice Leaves and Seeds. FRONTIERS IN PLANT SCIENCE 2022; 13:861036. [PMID: 35498655 PMCID: PMC9044040 DOI: 10.3389/fpls.2022.861036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/10/2022] [Indexed: 06/02/2023]
Abstract
The methylerythritol 4-phosphate (MEP) pathway is responsible for providing common precursors for the biosynthesis of diverse plastidial terpenoids, including chlorophylls, carotenoids, and phytohormones, in plants. In rice (Oryza sativa), the last-step genes encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [HDR/isoprenoid synthesis H (IspH)] have been annotated in two genes (OsIspH1 and OsIspH2) in the rice genome. The spatial transcript levels indicated that OsIspH1 is highly expressed in all tissues at different developmental stages, whereas OsIspH2 is barely expressed due to an early stop in exon 1 caused by splicing error. OsIspH1 localized into plastids and osisph1, a T-DNA inserted knockout mutant, showed an albino phenotype, indicating that OsIspH1 is the only functional gene. To elucidate the role of OsIspH1 in the MEP pathway, we created two single (H145P and K407R) and double (H145P/K407R) mutations and performed complementation tests in two hdr mutants, including Escherichia coli DLYT1 strains and osisph1 rice plants. The results showed that every single mutation retained HDR function, but a double mutation lost it, proposing that the complementary relations of two residues might be important for enzyme activity but not each residue. When overexpressed in rice plants, the double-mutated gene, OsIspH1MUT , reduced chlorophyll and carotenoid biosynthesis in the leaves and seeds. It confirmed the crucial role of OsIspH1 in plastidic terpenoid biosynthesis, revealing organ-specific differential regulation of OsIspH1 in rice plants.
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Affiliation(s)
- Yeo Jin Lee
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Jae Kwang Kim
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Seung-A Baek
- Division of Life Sciences, Bio-Resource and Environmental Center, Incheon National University, Incheon, South Korea
| | - Ji-Su Yu
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Min Kyoung You
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
| | - Sun-Hwa Ha
- Department of Genetics and Biotechnology, Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, South Korea
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9
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Gupta P, Hirschberg J. The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:806184. [PMID: 35069664 PMCID: PMC8770946 DOI: 10.3389/fpls.2021.806184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.
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Affiliation(s)
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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10
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Movahedi A, Wei H, Pucker B, Ghaderi-Zefrehei M, Rasouli F, Kiani-Pouya A, Jiang T, Zhuge Q, Yang L, Zhou X. Isoprenoid biosynthesis regulation in poplars by methylerythritol phosphate and mevalonic acid pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:968780. [PMID: 36247639 PMCID: PMC9562105 DOI: 10.3389/fpls.2022.968780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
It is critical to develop plant isoprenoid production when dealing with human-demanded industries such as flavoring, aroma, pigment, pharmaceuticals, and biomass used for biofuels. The methylerythritol phosphate (MEP) and mevalonic acid (MVA) plant pathways contribute to the dynamic production of isoprenoid compounds. Still, the cross-talk between MVA and MEP in isoprenoid biosynthesis is not quite recognized. Regarding the rate-limiting steps in the MEP pathway through catalyzing 1-deoxy-D-xylulose5-phosphate synthase and 1-deoxy-D-xylulose5-phosphate reductoisomerase (DXR) and also the rate-limiting step in the MVA pathway through catalyzing 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), the characterization and function of HMGR from Populus trichocarpa (PtHMGR) were analyzed. The results indicated that PtHMGR overexpressors (OEs) displayed various MEP and MVA-related gene expressions compared to NT poplars. The overexpression of PtDXR upregulated MEP-related genes and downregulated MVA-related genes. The overexpression of PtDXR and PtHMGR affected the isoprenoid production involved in both MVA and MEP pathways. Here, results illustrated that the PtHMGR and PtDXR play significant roles in regulating MEP and MVA-related genes and derived isoprenoids. This study clarifies cross-talk between MVA and MEP pathways. It demonstrates the key functions of HMGR and DXR in this cross-talk, which significantly contribute to regulate isoprenoid biosynthesis in poplars.
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Affiliation(s)
- Ali Movahedi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong, China
| | - Boas Pucker
- Institute of Plant Biology and BRICS, TU Braunschweig, Braunschweig, Germany
| | | | - Fatemeh Rasouli
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS, Australia
| | - Ali Kiani-Pouya
- State Key Laboratory of Molecular Plant Genetics, Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, TAS, Australia
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qiang Zhuge
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- *Correspondence: Qiang Zhuge,
| | - Liming Yang
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Liming Yang,
| | - Xiaohong Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Xiaohong Zhou,
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11
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Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ. An epigenetic basis of inbreeding depression in maize. SCIENCE ADVANCES 2021; 7:7/35/eabg5442. [PMID: 34452913 PMCID: PMC8397266 DOI: 10.1126/sciadv.abg5442] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/07/2021] [Indexed: 05/12/2023]
Abstract
Inbreeding depression is widespread across plant and animal kingdoms and may arise from the exposure of deleterious alleles and/or loss of overdominant alleles resulting from increased homozygosity, but these genetic models cannot fully explain the phenomenon. Here, we report epigenetic links to inbreeding depression in maize. Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors control plant development. During successive inbreeding among inbred lines, thousands of genomic regions across TCP-binding sites (TBS) are hypermethylated through the H3K9me2-mediated pathway. These hypermethylated regions are accompanied by decreased chromatin accessibility, increased levels of the repressive histone marks H3K27me2 and H3K27me3, and reduced binding affinity of maize TCP-proteins to TBS. Consequently, hundreds of TCP-target genes involved in mitochondrion, chloroplast, and ribosome functions are down-regulated, leading to reduced growth vigor. Conversely, random mating can reverse corresponding hypermethylation sites and TCP-target gene expression, restoring growth vigor. These results support a unique role of reversible epigenetic modifications in inbreeding depression.
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Affiliation(s)
- Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Fang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Tieshan Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
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12
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Pu X, Dong X, Li Q, Chen Z, Liu L. An update on the function and regulation of methylerythritol phosphate and mevalonate pathways and their evolutionary dynamics. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1211-1226. [PMID: 33538411 DOI: 10.1111/jipb.13076] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
Isoprenoids are among the largest and most chemically diverse classes of organic compounds in nature and are involved in the processes of photosynthesis, respiration, growth, development, and plant responses to stress. The basic building block units for isoprenoid synthesis-isopentenyl diphosphate and its isomer dimethylallyl diphosphate-are generated by the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways. Here, we summarize recent advances on the roles of the MEP and MVA pathways in plant growth, development and stress responses, and attempt to define the underlying gene networks that orchestrate the MEP and MVA pathways in response to developmental or environmental cues. Through phylogenomic analysis, we also provide a new perspective on the evolution of the plant isoprenoid pathway. We conclude that the presence of the MVA pathway in plants may be associated with the transition from aquatic to subaerial and terrestrial environments, as lineages for its core components are absent in green algae. The emergence of the MVA pathway has acted as a key evolutionary event in plants that facilitated land colonization and subsequent embryo development, as well as adaptation to new and varied environments.
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Affiliation(s)
- Xiaojun Pu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Xiumei Dong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
| | - Qing Li
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Zexi Chen
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 434200, China
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, the Chinese Academy of Sciences, and Yunnan Key Laboratory for Wild Plant Resources, Kunming, 650201, China
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13
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Wang Y, Huang N, Ye N, Qiu L, Li Y, Ma H. An Efficient Virus-Induced Gene Silencing System for Functional Genomics Research in Walnut ( Juglans regia L.) Fruits. FRONTIERS IN PLANT SCIENCE 2021; 12:661633. [PMID: 34249033 PMCID: PMC8261060 DOI: 10.3389/fpls.2021.661633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
The Persian walnut (Juglans regia L.) is a leading source of woody oil in warm temperate regions and has high nutritional and medicinal values. It also provides both tree nuts and woody products. Nevertheless, incomplete characterization of the walnut genetic system limits the walnut gene function analysis. This study used the tobacco rattle virus (TRV) vector to construct an infectious pTRV-JrPDS recombinant clone. A co-culture inoculation method utilizing Agrobacterium was screened out from four inoculation methods and optimized to set up an efficient virus-induced gene silencing (VIGS) system for J. regia fruit. The optimized VIGS-TRV system induced complete photobleaching phenotype on the walnut fruits of four cultivars, and the JrPDS transcript levels decreased by up to 88% at 8 days post-inoculation (dpi). While those of browning-related J. regia polyphenol oxidase (PPO) genes JrPPO1 and JrPPO2 decreased by 67 and 80% at 8 dpi, respectively, accompanied by a significant reduction in fruit browning phenotype. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis screening and Western Blot showed that the PPO protein levels were significantly reduced. Moreover, a model of TRV-mediated VIGS system for inoculating J. regia fruit with efficient silence efficiency via co-culture was developed. These results indicate that the VIGS-TRV system is an efficient tool for rapid gene function analysis in J. regia fruits.
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14
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Yuchun RAO, Ran JIAO, Sheng WANG, Xianmei WU, Hanfei YE, Chenyang PAN, Sanfeng LI, Dedong X, Weiyong ZHOU, Gaoxing DAI, Juan HU, Deyong REN, Yuexing WANG. SPL36 Encodes a Receptor-like Protein Kinase that Regulates Programmed Cell Death and Defense Responses in Rice. RICE (NEW YORK, N.Y.) 2021; 14:34. [PMID: 33825994 PMCID: PMC8026784 DOI: 10.1186/s12284-021-00475-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/23/2021] [Indexed: 05/23/2023]
Abstract
Lesion mimic mutants spontaneously produce disease spots in the absence of biotic or abiotic stresses. Analyzing lesion mimic mutants' sheds light on the mechanisms underlying programmed cell death and defense-related responses in plants. Here, we isolated and characterized the rice (Oryza sativa) spotted leaf 36 (spl36) mutant, which was identified from an ethyl methanesulfonate-mutagenized japonica cultivar Yundao population. spl36 displayed spontaneous cell death and enhanced resistance to rice bacterial pathogens. Gene expression analysis suggested that spl36 functions in the disease response by upregulating the expression of defense-related genes. Physiological and biochemical experiments indicated that more cell death occurred in spl36 than the wild type and that plant growth and development were affected in this mutant. We isolated SPL36 by map-based cloning. A single base substitution was detected in spl36, which results in a cysteine-to-arginine substitution in SPL36. SPL36 is predicted to encode a receptor-like protein kinase containing leucine-rich domains that may be involved in stress responses in rice. spl36 was more sensitive to salt stress than the wild type, suggesting that SPL36 also negatively regulates the salt-stress response. These findings suggest that SPL36 regulates the disease resistance response in rice by affecting the expression of defense- and stress-related genes.
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Affiliation(s)
- R A O Yuchun
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China.
| | - J I A O Ran
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - W A N G Sheng
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - W U Xianmei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Y E Hanfei
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - P A N Chenyang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - L I Sanfeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xin Dedong
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - Z H O U Weiyong
- Guangxi Academy of Agricultural Sciences, Nanning, 530000, China
| | - D A I Gaoxing
- Guangxi Academy of Agricultural Sciences, Nanning, 530000, China
| | - H U Juan
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua, 321004, China
| | - R E N Deyong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - W A N G Yuexing
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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15
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Yuan G, Li Y, Chen B, He H, Wang Z, Shi J, Yang Y, Zou C, Pan G. Identification and fine mapping of a recessive gene controlling zebra leaf phenotype in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:9. [PMID: 37309474 PMCID: PMC10236063 DOI: 10.1007/s11032-021-01202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/07/2021] [Indexed: 06/14/2023]
Abstract
Leaf color mutant is an important resource for studying chlorophyll biosynthesis and chloroplast development in maize. Here, a novel mutant zebra crossband 9 (zb9) with transverse green-/yellow-striped leaves appeared from ten-leaf stage until senescence was identified from mutant population derived from the maize inbred line RP125. The yellow section of the zb9 mutant displays a reduction of chlorophyll and carotenoid contents, as well as impaired chloroplast structure. Genetic analysis showed that the zb9 mutant phenotype was caused by a single recessive gene. Map-based cloning demonstrated that the zb9 locus was delimited into a 648 kb region on chromosome 1 covering thirteen open reading frames (ORFs). Among them, a point mutation (G to A) in exon 2 of the gene Zm00001d029151, named Zmzb9, was identified based on sequencing analysis. The causal gene Zmzb9 encodes UDP-glucose-4-epimerase 4 (UGE4), a key enzyme involved in chloroplast development and was considered as the only candidate gene controlling the mutant phenotype. Expression patterns indicated that the causal gene was abundantly expressed in the leaves and sheaths, as well as significantly downregulated in the mutant compared to that in the wild type. Subcellular localization showed that ZmZB9 was localized in chloroplasts and implied the putative gene involved in chloroplast development. Taken together, we propose that the causal gene Zmzb9 tightly associated with the zebra leaf phenotype, and the obtained gene here will help to uncover the regulatory mechanism of pigment biosynthesis and chloroplast development in maize. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01202-7.
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Affiliation(s)
- Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yucui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Benfang Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Hui He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Zhiying Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jiahao Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yan Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 China
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16
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Liu X, Cao PH, Huang QQ, Yang YR, Tao DD. Disruption of a Rice Chloroplast-Targeted Gene OsHMBPP Causes a Seedling-Lethal Albino Phenotype. RICE (NEW YORK, N.Y.) 2020; 13:51. [PMID: 32712772 PMCID: PMC7382669 DOI: 10.1186/s12284-020-00408-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/06/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Chloroplast development is coordinately regulated by plastid- and nuclear-encoding genes. Although many regulators have been reported to be involved in chloroplast development, new factors remain to be identified, given the complexity of this process. RESULTS In this study, we characterized a rice mutant lethal albinic seedling 1(las1)form of a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (OsHMBPP) that was targeted to the chloroplasts. The LAS1 mutation caused the albino lethal phenotype in seedlings. Transmission electron microscopy indicated that las1 were defective in early chloroplast development. LAS1 is preferentially expressed in leaves, implying its role in controlling chloroplast development. The expression levels of many chloroplast-encoded genes were altered significantly in las1. The expression levels of nuclear-encoded gene involved in Chl biosynthesis were also decreased in las1. We further investigated plastidic RNA editing in las1 and found that the edit efficiency of four chloroplast genes were markly altered. Compared with WT, las1 exhibited defective in biogenesis of chloroplast ribosomes. CONCLUSIONS Our results show that LAS1/OsHMBPP plays an essential role in the early chloroplast development in rice.
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Affiliation(s)
- X Liu
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China.
| | - P H Cao
- Suzhou Academy of Agricultural Sciences, Suzhou, 215155, China
| | - Q Q Huang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - Y R Yang
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
| | - D D Tao
- Key Laboratory of Eco-Agricultural Biotechnology around Hongze Lake, Regional Cooperative Innovation Center for Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian, 223300, China
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17
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Feng C, Su H, Bai H, Wang R, Liu Y, Guo X, Liu C, Zhang J, Yuan J, Birchler JA, Han F. High-efficiency genome editing using a dmc1 promoter-controlled CRISPR/Cas9 system in maize. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1848-1857. [PMID: 29569825 PMCID: PMC6181213 DOI: 10.1111/pbi.12920] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 05/13/2023]
Abstract
Previous studies revealed that the promoters for driving both Cas9 and sgRNAs are quite important for efficient genome editing by CRISPR/Cas9 in plants. Here, we report our results of targeted genome editing using the maize dmc1 gene promoter combined with the U3 promoter for Cas9 and sgRNA, respectively. Three loci in the maize genome were selected for targeting. The T0 plants regenerated were highly efficiently edited at the target sites with homozygous or bi-allelic mutants accounting for about 66%. The mutations in T0 plants could be stably transmitted to the T1 generation, and new mutations could be generated in gametes or zygotes. Whole-genome resequencing indicated that no off-target mutations could be detected in the predicted loci with sequence similarity to the targeted site. Our results show that the dmc1 promoter-controlled (DPC) CRISPR/Cas9 system is highly efficient in maize and provide further evidence that the optimization of the promoters used for the CRISPR/Cas9 system is important for enhancing the efficiency of targeted genome editing in plants. The evolutionary conservation of the dmc1 gene suggests its potential for use in other plant species.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Handong Su
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Han Bai
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Rui Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yalin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | | | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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18
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Fang J, Zhu X, Wang C, Shangguan L. Applications of DNA Technologies in Agriculture. Curr Genomics 2016; 17:379-86. [PMID: 27499686 PMCID: PMC4955036 DOI: 10.2174/1389202917666160331203224] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 11/22/2022] Open
Abstract
With the development of molecular biology, some DNA-based technologies have showed great potentiality in promoting the efficiency of crop breeding program, protecting germplasm resources, improving the quality and outputs of agricultural products, and protecting the eco-environment etc., making their roles in modern agriculture more and more important. To better understand the application of DNA technologies in agriculture, and achieve the goals to promote their utilities in modern agriculture, this paper describes, in some different way, the applications of molecular markers, transgenic engineering and gene's information in agriculture. Some corresponding anticipations for their development prospects are also made.
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Affiliation(s)
- Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
| | - Lingfei Shangguan
- College of Horticulture, Nanjing Agricultural University, Nanjing,P.R. China
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19
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Lipko A, Swiezewska E. Isoprenoid generating systems in plants - A handy toolbox how to assess contribution of the mevalonate and methylerythritol phosphate pathways to the biosynthetic process. Prog Lipid Res 2016; 63:70-92. [PMID: 27133788 DOI: 10.1016/j.plipres.2016.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/07/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022]
Abstract
Isoprenoids comprise an astonishingly diverse group of metabolites with numerous potential and actual applications in medicine, agriculture and the chemical industry. Generation of efficient platforms producing isoprenoids is a target of numerous laboratories. Such efforts are generally enhanced if the native biosynthetic routes can be identified, and if the regulatory mechanisms responsible for the biosynthesis of the compound(s) of interest can be determined. In this review a critical summary of the techniques applied to establish the contribution of the two alternative routes of isoprenoid production operating in plant cells, the mevalonate and methylerythritol pathways, with a focus on their co-operation (cross-talk) is presented. Special attention has been paid to methodological aspects of the referred studies, in order to give the reader a deeper understanding for the nuances of these powerful techniques. This review has been designed as an organized toolbox, which might offer the researchers comments useful both for project design and for interpretation of results obtained.
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Affiliation(s)
- Agata Lipko
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
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20
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Wang R, Yang X, Wang N, Liu X, Nelson RS, Li W, Fan Z, Zhou T. An efficient virus-induced gene silencing vector for maize functional genomics research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:102-15. [PMID: 26921244 DOI: 10.1111/tpj.13142] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/01/2016] [Accepted: 02/08/2016] [Indexed: 05/02/2023]
Abstract
Maize is a major crop whose rich genetic diversity provides an advanced resource for genetic research. However, a tool for rapid transient gene function analysis in maize that may be utilized in most maize cultivars has been lacking, resulting in reliance on time-consuming stable transformation and mutation studies to obtain answers. We developed an efficient virus-induced gene silencing (VIGS) vector for maize based on a naturally maize-infecting cucumber mosaic virus (CMV) strain, ZMBJ-CMV. An infectious clone of ZMBJ-CMV was constructed, and a vascular puncture inoculation method utilizing Agrobacterium was optimized to improve its utility for CMV infection of maize. ZMBJ-CMV was then modified to function as a VIGS vector. The ZMBJ-CMV vector induced mild to moderate symptoms in many maize lines, making it useful for gene function studies in critically important maize cultivars, such as the sequenced reference inbred line B73. Using this CMV VIGS system, expression of two endogenous genes, ZmPDS and ZmIspH, was found to be decreased by 75% and 78%, respectively, compared with non-silenced tissue. Inserts with lengths of 100-300 bp produced the most complete transcriptional and visual silencing phenotypes. Moreover, genes related to autophagy, ZmATG3 and ZmATG8a, were also silenced, and it was found that they function in leaf starch degradation. These results indicate that our ZMBJ-CMV VIGS vector provides a tool for rapid and efficient gene function studies in maize.
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Affiliation(s)
- Rong Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xinxin Yang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Nian Wang
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xuedong Liu
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Richard S Nelson
- Plant Biology Division, The Samuel Roberts Noble Foundation Inc., 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
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21
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Feng C, Yuan J, Wang R, Liu Y, Birchler JA, Han F. Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System. J Genet Genomics 2015; 43:37-43. [PMID: 26842992 DOI: 10.1016/j.jgg.2015.10.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/14/2015] [Accepted: 10/20/2015] [Indexed: 12/18/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, which is a newly developed technology for targeted genome modification, has been successfully used in a number of species. In this study, we applied this technology to carry out targeted genome modification in maize. A marker gene Zmzb7 was chosen for targeting. The sgRNA-Cas9 construct was transformed into maize protoplasts, and indel (insertion and deletion) mutations could be detected. A mutant seedling with an expected albino phenotype was obtained from screening 120 seedlings generated from 10 callus events. Mutation efficiency in maize heterochromatic regions was also investigated. Twelve sites with different expression levels in maize centromeres or pericentromere regions were selected. The sgRNA-Cas9 constructs were transformed into protoplasts followed by sequencing the transformed protoplast genomic DNA. The results show that the genes in heterochromatic regions could be targeted by the CRISPR/Cas9 system efficiently, no matter whether they are expressed or not. Meanwhile, off-target mutations were not found in the similar sites having no PAM (protospacer adjacent motif) or having more than two mismatches. Together, our results show that the CRISPR/Cas9 system is a robust and efficient tool for genome modification in both euchromatic and heterochromatic regions in maize.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. BMC Genomics 2015; 16:838. [PMID: 26494145 PMCID: PMC4619012 DOI: 10.1186/s12864-015-2015-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/06/2015] [Indexed: 11/28/2022] Open
Abstract
Background Leaf color variations are common in plants. Herein we describe a natural mutant of barley cultivar Edamai No.6, whs18, whose leaf color showed stable and inheritable stage-green-revertible-albino under field condition. Methods Bulked Segregant Analysis (BSA) based on SSR assay and Specific Length Amplified Fragment Sequencing (SLAF-seq) was used to map the candidate gene for this trait. Results We found that leaf color of whs18 was green at seedling stage, while the seventh or eighth leaf began to show etiolation, and albino leaves emerged after a short period. The newly emerged leaves began to show stripe white before jointing stage, and normal green leaves emerged gradually. The duration of whs18 with abnormal leaf color lasted for about 3 months, which had some negative impacts on yield-related-traits. Further investigations showed that the variation was associated with changes in chlorophyII content and chloroplast development. Genetic analysis revealed that the trait was controlled by a single recessive nuclear gene, and was designed as HvSGRA in this study. Based on the F2 population derived from Edamai No.9706 and whs18, we initially mapped the HvSGRA gene on the short arm of chromosome 2H using SSR and BSA. GBMS247 on 2HS showed co-segregation with HvSGRA. The genetic distance between the other marker GBM1187 and HvSGRA was 1.2 cM. Further analysis using BSA with SLAF-seq also identified this region as candidate region. Finally, HvSGRA interval was narrowed to 0.4 cM between morex_contig_160447 and morex_contig_92239, which were anchored to two adjacent FP contigs, contig_34437 and contig_46434, respectively. Furthermore, six putative genes with high-confidence in this interval were identified by POPSEQ. Further analysis showed that the substitution from C to A in the third exon of fructokinase-1-like gene generated a premature stop codon in whs18, which may lead to loss function of this gene. Conclusions Using SSR and SLAF-seq in conjunction with BSA, we mapped HvSGRA within two adjacent FP contigs of barley. The mutation of fructokinase-1-like gene in whs18 may cause the stage green-revertible albino of barley. The current study lays foundation for hierarchical map-based cloning of HvSGRA and utilizing the gene/trait as a visualized maker in molecular breeding in future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2015-1) contains supplementary material, which is available to authorized users.
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23
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Tong Y, Su P, Zhao Y, Zhang M, Wang X, Liu Y, Zhang X, Gao W, Huang L. Molecular Cloning and Characterization of DXS and DXR Genes in the Terpenoid Biosynthetic Pathway of Tripterygium wilfordii. Int J Mol Sci 2015; 16:25516-35. [PMID: 26512659 PMCID: PMC4632813 DOI: 10.3390/ijms161025516] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF sizes of 2154 bp (TwDXS1, GenBank accession no.KM879187), 2148 bp (TwDXS2, GenBank accession no.KM879186), 1410 bp (TwDXR, GenBank accession no.KM879185). And, the TwDXS1, TwDXS2 and TwDXR were characterized by color complementation in lycopene accumulating strains of Escherichia coli, which indicated that they encoded functional proteins and promoted lycopene pathway flux. TwDXS1 and TwDXS2 are constitutively expressed in the roots, stems and leaves and the expression level showed an order of roots > stems > leaves. After the suspension cells were induced by methyl jasmonate, the mRNA expression level of TwDXS1, TwDXS2, and TwDXR increased, and triptophenolide was rapidly accumulated to 149.52 µg·g−1, a 5.88-fold increase compared with the control. So the TwDXS1, TwDXS2, and TwDXR could be important genes involved in terpenoid biosynthesis in Tripterygium wilfordii Hook. f.
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Affiliation(s)
- Yuru Tong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Ping Su
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujun Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Meng Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xiujuan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Yujia Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Xianan Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China.
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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24
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Belcher S, Williams-Carrier R, Stiffler N, Barkan A. Large-scale genetic analysis of chloroplast biogenesis in maize. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1004-16. [PMID: 25725436 DOI: 10.1016/j.bbabio.2015.02.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/16/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Chloroplast biogenesis involves a collaboration between several thousand nuclear genes and ~100 genes in the chloroplast. Many of the nuclear genes are of cyanobacterial ancestry and continue to perform their ancestral function. However, many others evolved subsequently and comprise a diverse set of proteins found specifically in photosynthetic eucaryotes. Genetic approaches have been key to the discovery of nuclear genes that participate in chloroplast biogenesis, especially those lacking close homologs outside the plant kingdom. SCOPE OF REVIEW This article summarizes contributions from a genetic resource in maize, the Photosynthetic Mutant Library (PML). The PML collection consists of ~2000 non-photosynthetic mutants induced by Mu transposons. We include a summary of mutant phenotypes for 20 previously unstudied maize genes, including genes encoding chloroplast ribosomal proteins, a PPR protein, tRNA synthetases, proteins involved in plastid transcription, a putative ribosome assembly factor, a chaperonin 60 isoform, and a NifU-domain protein required for Photosystem I biogenesis. MAJOR CONCLUSIONS Insertions in 94 maize genes have been linked thus far to visible and molecular phenotypes with the PML collection. The spectrum of chloroplast biogenesis genes that have been genetically characterized in maize is discussed in the context of related efforts in other organisms. This comparison shows how distinct organismal attributes facilitate the discovery of different gene classes, and reveals examples of functional divergence between monocot and dicot plants. GENERAL SIGNIFICANCE These findings elucidate the biology of an organelle whose activities are fundamental to agriculture and the biosphere. This article is part of a Special Issue entitled: Chloroplast Biogenesis.
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Affiliation(s)
- Susan Belcher
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | | | - Nicholas Stiffler
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
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25
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Hsieh WY, Sung TY, Wang HT, Hsieh MH. Functional evidence for the critical amino-terminal conserved domain and key amino acids of Arabidopsis 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE. PLANT PHYSIOLOGY 2014; 166:57-69. [PMID: 25037211 PMCID: PMC4149731 DOI: 10.1104/pp.114.243642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The plant 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE (HDR) catalyzes the last step of the methylerythritol phosphate pathway to synthesize isopentenyl diphosphate and its allyl isomer dimethylallyl diphosphate, which are common precursors for the synthesis of plastid isoprenoids. The Arabidopsis (Arabidopsis thaliana) genomic HDR transgene-induced gene-silencing lines are albino, variegated, or pale green, confirming that HDR is essential for plants. We used Escherichia coli isoprenoid synthesis H (Protein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabidopsis HDR. The predicted model reveals that cysteine (Cys)-122, Cys-213, and Cys-350 are involved in iron-sulfur cluster formation and that histidine (His)-152, His-241, glutamate (Glu)-242, Glu-243, threonine (Thr)-244, Thr-312, serine-379, and asparagine-381 are related to substrate binding or catalysis. Glu-242 and Thr-244 are conserved only in cyanobacteria, green algae, and land plants, whereas the other key amino acids are absolutely conserved from bacteria to plants. We used site-directed mutagenesis and complementation assay to confirm that these amino acids, except His-152 and His-241, were critical for Arabidopsis HDR function. Furthermore, the Arabidopsis HDR contains an extra amino-terminal domain following the transit peptide that is highly conserved from cyanobacteria, and green algae to land plants but not existing in the other bacteria. We demonstrated that the amino-terminal conserved domain was essential for Arabidopsis and cyanobacterial HDR function. Further analysis of conserved amino acids in the amino-terminal conserved domain revealed that the tyrosine-72 residue was critical for Arabidopsis HDR. These results suggest that the structure and reaction mechanism of HDR evolution have become specific for oxygen-evolving photosynthesis organisms and that HDR probably evolved independently in cyanobacteria versus other prokaryotes.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Ying Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Tzu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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