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Thuy NT, Kim H, Hong S. Antagonistic functions of CTL1 and SUH1 mediate cell wall assembly in Arabidopsis. PLANT DIRECT 2024; 8:e580. [PMID: 38525472 PMCID: PMC10960159 DOI: 10.1002/pld3.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/06/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024]
Abstract
Plant genomes contain numerous genes encoding chitinase-like (CTL) proteins, which have a similar protein structure to chitinase belonging to the glycoside hydrolase (GH) family but lack the chitinolytic activity to cleave the β-1,4-glycosidic bond in chitins, polymers of N-acetylglucosamine. CTL1 mutations found in rice and Arabidopsis have caused pleiotropic developmental defects, including altered cell wall composition and decreased abiotic stress tolerance, likely due to reduced cellulose content. In this study, we identified suppressor of hot2 1 (suh1) as a genetic suppressor of the ctl1 hot2-1 mutation in Arabidopsis. The mutation in SUH1 restored almost all examined ctl1 hot2-1 defects to nearly wild-type levels or at least partially. SUH1 encodes a Golgi-located type II membrane protein with glycosyltransferase (GT) activity, and its mutations lead to a reduction in cellulose content and hypersensitivity to cellulose biosynthesis inhibitors, although to a lesser extent than ctl1 hot2-1 mutation. The SUH1 promoter fused with the GUS reporter gene exhibited GUS activity in interfascicular fibers and xylem in stems; meanwhile, the ctl1 hot2-1 mutation significantly increased this activity. Our findings provide genetic and molecular evidence that the antagonistic activities of CTL1 and SUH1 play an essential role in assembling the cell wall in Arabidopsis.
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Affiliation(s)
- Nguyen Thi Thuy
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Hyun‐Jung Kim
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Suk‐Whan Hong
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
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2
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Ogden M, Whitcomb SJ, Khan GA, Roessner U, Hoefgen R, Persson S. Cellulose biosynthesis inhibitor isoxaben causes nutrient-dependent and tissue-specific Arabidopsis phenotypes. PLANT PHYSIOLOGY 2024; 194:612-617. [PMID: 37823413 PMCID: PMC10828196 DOI: 10.1093/plphys/kiad538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/07/2023] [Accepted: 09/24/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Michael Ogden
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C 1871, Denmark
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Cereal Crops Research Unit, USDA-ARS, Madison, WI 53726, USA
| | - Ghazanfar Abbas Khan
- Department of Animal, Plant and Soil Sciences, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2600, Australia
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Staffan Persson
- Copenhagen Plant Science Center, Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg C 1871, Denmark
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Xuan C, Feng M, Li X, Hou Y, Wei C, Zhang X. Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection. Int J Mol Sci 2024; 25:638. [PMID: 38203810 PMCID: PMC10779513 DOI: 10.3390/ijms25010638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses.
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Affiliation(s)
- Changqing Xuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Mengjiao Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Xianyang 712100, China; (C.X.); (M.F.); (X.L.); (Y.H.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
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Zhou YY, Wang YS, Sun CC, Fei J. Cloning and Expression of Class I Chitinase Genes from Four Mangrove Species under Heavy Metal Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2772. [PMID: 37570926 PMCID: PMC10421288 DOI: 10.3390/plants12152772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 08/13/2023]
Abstract
Chitinases are believed to act as defense proteins when plants are exposed to heavy metal stress. Typical Class I chitinase genes were cloned from Bruguiera gymnorrhiza, Rhizophora stylosa, Kandelia obovata, and Avicennia marina using the methods of reverse-transcription-polymerase chain reaction and rapid amplification of cDNA ends. All four cDNA sequences of chitinase from the mangrove plants were 1092 bp in length and consisted of an open reading frame of 831 bp, encoding 276 amino acids. However, there were differences in the sequences among the four mangrove species. Four gene proteins have a signal peptide, are located in the vacuole, and belong to the GH19 chitinase family. The sequence of chitinase was highly similar to the protein sequences of Camellia fraternal chitinases. A real-time polymerase chain reaction was used to analyze the chitinase expressions of the above four mangrove species exposed to different concentrations of heavy metal at different times. The gene expression of chitinase was higher in Bruguiera gymnorrhiza leaves than in other mangrove plant species. With an increase in heavy metal stress, the expression level of Bruguiera gymnorrhiza increased continuously. These results suggest that chitinase plays an important role in improving the heavy metal tolerance of mangrove plants.
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Affiliation(s)
- Yue-Yue Zhou
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (Y.-Y.Z.); (C.-C.S.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (Y.-Y.Z.); (C.-C.S.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (Y.-Y.Z.); (C.-C.S.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (Y.-Y.Z.); (C.-C.S.)
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen 518121, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
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Xu Z, Dai J, Liang L, Zhang Y, He Y, Xing L, Ma J, Zhang D, Zhao C. Chitinase-Like Protein PpCTL1 Contributes to Maintaining Fruit Firmness by Affecting Cellulose Biosynthesis during Peach Development. Foods 2023; 12:2503. [PMID: 37444241 DOI: 10.3390/foods12132503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
The firmness of the flesh fruit is a very important feature in the eating process. Peach fruit is very hard during development, but its firmness slightly decreases in the later stages of development. While there has been extensive research on changes in cell wall polysaccharides during fruit ripening, little is known about the changes that occur during growth and development. In this study, we investigated the modifications in cell wall components throughout the development and ripening of peach fruit, as well as its impact on firmness. Our findings revealed a significant positive correlation between fruit firmness and cellulose content at development stage. However, the correlation was lost during the softening process, suggesting that cellulose might be responsible for the fruit firmness during development. Members of the chitinase-like protein (CTL) group are of interest because of their possible role in plant cell wall biosynthesis. Here, two CTL homologous genes, PpCTL1 and PpCTL2, were identified in peach. Spatial and temporal expression patterns of PpCTLs revealed that PpCTL1 exhibited high expression abundance in the fruit and followed a similar trend to cellulose during fruit growth. Furthermore, silencing PpCTL1 expression resulted in reduced cellulose content at 5 DAI (days after injection), this change that would have a negative effect on fruit firmness. Our results indicate that PpCTL1 plays an important role in cellulose biosynthesis and the maintenance of peach firmness during development.
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Affiliation(s)
- Ze Xu
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Jieyu Dai
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Liping Liang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Yonglan Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Yaojun He
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Libo Xing
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Juanjuan Ma
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Dong Zhang
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
| | - Caiping Zhao
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Xianyang 712100, China
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [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: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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De Pessemier J, Moturu TR, Nacry P, Ebert R, De Gernier H, Tillard P, Swarup K, Wells DM, Haseloff J, Murray SC, Bennett MJ, Inzé D, Vincent CI, Hermans C. Root system size and root hair length are key phenes for nitrate acquisition and biomass production across natural variation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3569-3583. [PMID: 35304891 DOI: 10.1093/jxb/erac118] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The role of root phenes in nitrogen (N) acquisition and biomass production was evaluated in 10 contrasting natural accessions of Arabidopsis thaliana L. Seedlings were grown on vertical agar plates with two different nitrate supplies. The low N treatment increased the root to shoot biomass ratio and promoted the proliferation of lateral roots and root hairs. The cost of a larger root system did not impact shoot biomass. Greater biomass production could be achieved through increased root length or through specific root hair characteristics. A greater number of root hairs may provide a low-resistance pathway under elevated N conditions, while root hair length may enhance root zone exploration under low N conditions. The variability of N uptake and the expression levels of genes encoding nitrate transporters were measured. A positive correlation was found between root system size and high-affinity nitrate uptake, emphasizing the benefits of an exploratory root organ in N acquisition. The expression levels of NRT1.2/NPF4.6, NRT2.2, and NRT1.5/NPF7.3 negatively correlated with some root morphological traits. Such basic knowledge in Arabidopsis demonstrates the importance of root phenes to improve N acquisition and paves the way to design eudicot ideotypes.
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Affiliation(s)
- Jérôme De Pessemier
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Taraka Ramji Moturu
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
| | - Philippe Nacry
- Institute of Plant Science Montpellier, Université de Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Rebecca Ebert
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Hugues De Gernier
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Pascal Tillard
- Institute of Plant Science Montpellier, Université de Montpellier, CNRS, INRAE, Institut Agro, 34060 Montpellier, France
| | - Kamal Swarup
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Christopher I Vincent
- Citrus Research and Education Center, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Christian Hermans
- Crop Production and Biostimulation Laboratory, Interfacultary School of Bioengineers, Université libre de Bruxelles, B-1050 Brussels, Belgium
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Mesara SN, Dave KP, Subramanian RB. Comparative transcriptome analysis elucidates positive physiological effects of foliar application of pyraclostrobin on tomato ( Solanum lycopersicum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:971-986. [PMID: 35722521 PMCID: PMC9203623 DOI: 10.1007/s12298-022-01191-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 05/03/2023]
Abstract
Strobilurins, including pyraclostrobin have frequently been reported showing positive physiological effects in various agricultural crops apart from fungicidal activity. Present study elucidates comparative transcriptome analysis of control and pyraclostrobin treated tomato leaf and identifies metabolic pathways and key genes responsible for positive effects of pyraclostrobin on tomato. Pair-end raw reads, generated by Illumina Hi-seq platform were pre-processed and good quality reads were mapped onto tomato reference genome using HISAT2 alignment programme. Transcript assembly and quantification were performed using StringTie assembler. Differential Gene Expression analysis by DESeq2 identified 1,952 upregulated genes including genes encoding pathogenesis related proteins and 835 downregulated genes. RT-PCR study showed increase in expression of RBCs (2.5-fold), GA20o (3-fold), and NR (1.4-fold) genes, which are the key genes of photosynthesis, gibberellic acid synthesis, and nitrogen assimilation pathways respectively identified in KEGG pathway analysis. Pyraclostrobin treated plants showed 1.6-folds increase in plant height, 3.3-folds increase in number of leaves, and 2.8-folds increase in number of flowers. Total protein content increased 1.7, 1.4, 1.2, 1.2, and 1.4 folds at 1 day after application (DAA), 4DAA, 7DAA, 10DAA, and 13DAA respectively in treated plants. Moreover, content of phenol also increased 1.14, 1.5, 2.4, and 1.5 folds in 4DAA, 7DAA, 10DAA, and 13DAA respectively. Nitrate reductase activity increased 2-fold, 1.8-fold, 1.5-fold and 1.15-fold in 1DAA, 7DAA, 10DAA and 13DAA respectively. Carbohydrate decreased in treated plants up to 7DAA. The present study is the first report of transcriptome analysis elucidating positive physiological effects of strobilurin on plant. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01191-7.
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Affiliation(s)
- Sureshkumar N. Mesara
- Department of Biosciences, Sardar Patel University, Satellite campus, Bakrol-Vadtal road, Bakrol, Anand, Gujarat 388315 India
| | - Kirtan P. Dave
- Indukaka Ipcowala Centre of Interdisciplinary Studies in Science and Technology–IICISST, Sardar Patel University, Vallabh Vidyanagar, Anand, Gujarat 388120 India
| | - Ramalingam B. Subramanian
- Department of Biosciences, Sardar Patel University, Satellite campus, Bakrol-Vadtal road, Bakrol, Anand, Gujarat 388315 India
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Oilseed Rape Cultivars Show Diversity of Root Morphologies with the Potential for Better Capture of Nitrogen. NITROGEN 2021. [DOI: 10.3390/nitrogen2040033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The worldwide demand for vegetable oils is rising. Oilseed rape (Brassica napus) diversifies cereal dominated crop rotations but requires important nitrogen input. Yet, the root organ is offering an untapped opportunity to improve the nitrogen capture in soil. This study evaluates three culture systems in controlled environment, to observe root morphology and to identify root attributes for superior biomass production and nitrogen use. The phenotypic diversity in a panel of 55 modern winter oilseed rape cultivars was screened in response to two divergent nitrate supplies. Upon in vitro and hydroponic cultures, a large variability for root morphologies was observed. Root biomass and morphological traits positively correlated with shoot biomass or leaf area. The activities of high-affinity nitrate transport systems correlated negatively with the leaf area, while the combined high- and low-affinity systems positively with the total root length. The X-ray computed tomography permitted to visualize the root system in pipes filled with soil. The in vitro root phenotype at germination stage was indicative of lateral root deployment in soil-grown plants. This study highlights great genetic potential in oilseed rape, which could be manipulated to optimize crop root characteristics and nitrogen capture with substantial implications for agricultural production.
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DeMott L, Oblessuc PR, Pierce A, Student J, Melotto M. Spatiotemporal regulation of JAZ4 expression and splicing contribute to ethylene- and auxin-mediated responses in Arabidopsis roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1266-1282. [PMID: 34562337 DOI: 10.1111/tpj.15508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Jasmonic acid (JA) signaling controls several processes related to plant growth, development, and defense, which are modulated by the transcription regulator and receptor JASMONATE-ZIM DOMAIN (JAZ) proteins. We recently discovered that a member of the JAZ family, JAZ4, has a prominent function in canonical JA signaling as well as other mechanisms. Here, we discovered the existence of two naturally occurring splice variants (SVs) of JAZ4 in planta, JAZ4.1 and JAZ4.2, and employed biochemical and pharmacological approaches to determine protein stability and repression capability of these SVs within JA signaling. We then utilized quantitative and qualitative transcriptional studies to determine spatiotemporal expression and splicing patterns in vivo, which revealed developmental-, tissue-, and organ-specific regulation. Detailed phenotypic and expression analyses suggest a role of JAZ4 in ethylene (ET) and auxin signaling pathways differentially within the zones of root development in seedlings. These results support a model in which JAZ4 functions as a negative regulator of ET signaling and auxin signaling in root tissues above the apex. However, in the root apex JAZ4 functions as a positive regulator of auxin signaling possibly independently of ET. Collectively, our data provide insight into the complexity of spatiotemporal regulation of JAZ4 and how this impacts hormone signaling specificity and diversity in Arabidopsis roots.
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Affiliation(s)
- Logan DeMott
- Department of Plant Sciences, University of California, Davis, CA, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, USA
| | - Paula R Oblessuc
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Alice Pierce
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Joseph Student
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA, USA
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11
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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12
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Menna A, Dora S, Sancho-Andrés G, Kashyap A, Meena MK, Sklodowski K, Gasperini D, Coll NS, Sánchez-Rodríguez C. A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. BMC Biol 2021; 19:161. [PMID: 34404410 PMCID: PMC8371875 DOI: 10.1186/s12915-021-01100-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/16/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cell walls (CWs) are protein-rich polysaccharide matrices essential for plant growth and environmental acclimation. The CW constitutes the first physical barrier as well as a primary source of nutrients for microbes interacting with plants, such as the vascular pathogen Fusarium oxysporum (Fo). Fo colonizes roots, advancing through the plant primary CWs towards the vasculature, where it grows causing devastation in many crops. The pathogenicity of Fo and other vascular microbes relies on their capacity to reach and colonize the xylem. However, little is known about the root-microbe interaction before the pathogen reaches the vasculature and the role of the plant CW during this process. RESULTS Using the pathosystem Arabidopsis-Fo5176, we show dynamic transcriptional changes in both fungus and root during their interaction. One of the earliest plant responses to Fo5176 was the downregulation of primary CW synthesis genes. We observed enhanced resistance to Fo5176 in Arabidopsis mutants impaired in primary CW cellulose synthesis. We confirmed that Arabidopsis roots deposit lignin in response to Fo5176 infection, but we show that lignin-deficient mutants were as susceptible as wildtype plants to Fo5176. Genetic impairment of jasmonic acid biosynthesis and signaling did not alter Arabidopsis response to Fo5176, whereas impairment of ethylene signaling did increase vasculature colonization by Fo5176. Abolishing ethylene signaling attenuated the observed resistance while maintaining the dwarfism observed in primary CW cellulose-deficient mutants. CONCLUSIONS Our study provides significant insights on the dynamic root-vascular pathogen interaction at the transcriptome level and the vital role of primary CW cellulose during defense response to these pathogens. These findings represent an essential resource for the generation of plant resistance to Fo that can be transferred to other vascular pathosystems.
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Affiliation(s)
- Alexandra Menna
- Department of Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Susanne Dora
- Department of Biology, ETH Zürich, 8092, Zürich, Switzerland
| | | | - Anurag Kashyap
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain
| | - Mukesh Kumar Meena
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | | | - Debora Gasperini
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120, Halle (Saale), Germany
| | - Nuria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193, Barcelona, Spain
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13
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Allelign Ashagre H, Zaltzman D, Idan-Molakandov A, Romano H, Tzfadia O, Harpaz-Saad S. FASCICLIN-LIKE 18 Is a New Player Regulating Root Elongation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:645286. [PMID: 33897736 PMCID: PMC8058476 DOI: 10.3389/fpls.2021.645286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/19/2021] [Indexed: 05/26/2023]
Abstract
The plasticity of root development represents a key trait that enables plants to adapt to diverse environmental cues. The pattern of cell wall deposition, alongside other parameters, affects the extent, and direction of root growth. In this study, we report that FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 18 (FLA18) plays a role during root elongation in Arabidopsis thaliana. Using root-specific co-expression analysis, we identified FLA18 to be co-expressed with a sub-set of genes required for root elongation. FLA18 encodes for a putative extra-cellular arabinogalactan protein from the FLA-gene family. Two independent T-DNA insertion lines, named fla18-1 and fla18-2, display short and swollen lateral roots (LRs) when grown on sensitizing condition of high-sucrose containing medium. Unlike fla4/salt overly sensitive 5 (sos5), previously shown to display short and swollen primary root (PR) and LRs under these conditions, the PR of the fla18 mutants is slightly longer compared to the wild-type. Overexpression of the FLA18 CDS complemented the fla18 root phenotype. Genetic interaction between either of the fla18 alleles and sos5 reveals a more severe perturbation of anisotropic growth in both PR and LRs, as compared to the single mutants and the wild-type under restrictive conditions of high sucrose or high-salt containing medium. Additionally, under salt-stress conditions, fla18sos5 had a small, chlorotic shoot phenotype, that was not observed in any of the single mutants or the wild type. As previously shown for sos5, the fla18-1 and fla18-1sos5 root-elongation phenotype is suppressed by abscisic acid (ABA) and display hypersensitivity to the ABA synthesis inhibitor, Fluridon. Last, similar to other cell wall mutants, fla18 root elongation is hypersensitive to the cellulose synthase inhibitor, Isoxaben. Altogether, the presented data assign a new role for FLA18 in the regulation of root elongation. Future studies of the unique vs. redundant roles of FLA proteins during root elongation is anticipated to shed a new light on the regulation of root architecture during plant adaptation to different growth conditions.
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Affiliation(s)
- Hewot Allelign Ashagre
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Zaltzman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Idan-Molakandov
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hila Romano
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Tzfadia
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Jerusalem, Israel
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14
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Friis G, Vizueta J, Smith EG, Nelson DR, Khraiwesh B, Qudeimat E, Salehi-Ashtiani K, Ortega A, Marshell A, Duarte CM, Burt JA. A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina. G3 (BETHESDA, MD.) 2021; 11:jkaa025. [PMID: 33561229 PMCID: PMC8022769 DOI: 10.1093/g3journal/jkaa025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/19/2020] [Indexed: 11/17/2022]
Abstract
The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4-10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4-1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.
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Affiliation(s)
- Guillermo Friis
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08007, Spain
| | - Edward G Smith
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - David R Nelson
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Basel Khraiwesh
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Enas Qudeimat
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Alejandra Ortega
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alyssa Marshell
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - John A Burt
- Center for Genomics and Systems Biology, New York University - Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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15
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Valadares RBS, Perotto S, Lucheta AR, Santos EC, Oliveira RM, Lambais MR. Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature. J Fungi (Basel) 2020; 6:E148. [PMID: 32858792 PMCID: PMC7558880 DOI: 10.3390/jof6030148] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 01/05/2023] Open
Abstract
Orchids form endomycorrhizal associations with fungi mainly belonging to basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchanges imply a modulation of gene expression. Here, we used proteomics and transcriptomics to identify changes in the steady-state levels of proteins and transcripts in the roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed, and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways. Overall, proteomics and transcriptomics revealed, in mycorrhizal roots, increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggested that plant defense was reduced in O. maculata mycorrhizal roots sampled in nature. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.
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Affiliation(s)
- Rafael B. S. Valadares
- Escola Superior de Agricultura “Luiz de Queiroz”, Depto de Ciência do Solo, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba 13418-900, Brazil;
- Instituto Tecnológico Vale. Rua Boaventura da Silva 955, Belém 66050-000, Brazil;
| | - Silvia Perotto
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino e IPSP-CNR, Viale Mattioli 25, 10125 Torino, Italy
| | - Adriano R. Lucheta
- SENAI Innovation Institute for Mineral Technologies, Avenida Brás de Aguiar, 548, Belém 66035-405, Brazil;
| | - Eder C. Santos
- Universidade Tecnológica Federal do Paraná, Linha Santa Bárbara, Francisco Beltrão 85601-970, Brazil;
| | - Renato M. Oliveira
- Instituto Tecnológico Vale. Rua Boaventura da Silva 955, Belém 66050-000, Brazil;
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Belo Horizonte 31270-901, Brazil
| | - Marcio R. Lambais
- Escola Superior de Agricultura “Luiz de Queiroz”, Depto de Ciência do Solo, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba 13418-900, Brazil;
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16
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Aguado E, García A, Iglesias-Moya J, Romero J, Wehner TC, Gómez-Guillamón ML, Picó B, Garcés-Claver A, Martínez C, Jamilena M. Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches. FRONTIERS IN PLANT SCIENCE 2020; 11:1243. [PMID: 32973825 PMCID: PMC7466658 DOI: 10.3389/fpls.2020.01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/29/2020] [Indexed: 05/11/2023]
Abstract
The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.
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Affiliation(s)
- Encarnación Aguado
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Alicia García
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jonathan Romero
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Todd C. Wehner
- Departament of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | | | - Belén Picó
- COMAV—Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Cecilia Martínez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
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17
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Jiao S, Hazebroek JP, Chamberlin MA, Perkins M, Sandhu AS, Gupta R, Simcox KD, Yinghong L, Prall A, Heetland L, Meeley RB, Multani DS. Chitinase-like1 Plays a Role in Stalk Tensile Strength in Maize. PLANT PHYSIOLOGY 2019; 181:1127-1147. [PMID: 31492738 PMCID: PMC6836851 DOI: 10.1104/pp.19.00615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/29/2019] [Indexed: 05/22/2023]
Abstract
Stalk lodging in maize (Zea mays) causes significant yield losses due to breaking of stalk tissue below the ear node before harvest. Here, we identified the maize brittle stalk4 (bk4) mutant in a Mutator F2 population. This mutant was characterized by highly brittle aerial parts that broke easily from mechanical disturbance or in high-wind conditions. The bk4 plants displayed a reduction in average stalk diameter and mechanical strength, dwarf stature, senescence at leaf tips, and semisterility of pollen. Histological studies demonstrated a reduction in lignin staining of cells in the bk4 mutant leaves and stalk, and deformation of vascular bundles in the stalk resulting in the loss of xylem and phloem tissues. Biochemical characterization showed a significant reduction in p-coumaric acid, Glc, Man, and cellulose contents. The candidate gene responsible for bk4 phenotype is Chitinase-like1 protein (Ctl1), which is expressed at its highest levels in elongated internodes. Expression levels of secondary cell wall cellulose synthase genes (CesA) in the bk4 single mutant, and phenotypic observations in double mutants combining bk4 with bk2 or null alleles for two CesA genes, confirmed interaction of ZmCtl1 with CesA genes. Overexpression of ZmCtl1 enhanced mechanical stalk strength without affecting plant stature, senescence, or fertility. Biochemical characterization of ZmCtl1 overexpressing lines supported a role for ZmCtl1 in tensile strength enhancement. Conserved identity of CTL1 peptides across plant species and analysis of Arabidopsis (Arabidopsis thaliana) ctl1-1 ctl2-1 double mutants indicated that Ctl1 might have a conserved role in plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alan Prall
- Corteva Agriscience, Johnston, Iowa 50131
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18
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Štajner N, Radišek S, Mishra AK, Nath VS, Matoušek J, Jakše J. Evaluation of Disease Severity and Global Transcriptome Response Induced by Citrus bark cracking viroid, Hop latent viroid, and Their Co-Infection in Hop ( Humulus lupulus L.). Int J Mol Sci 2019; 20:E3154. [PMID: 31261625 PMCID: PMC6651264 DOI: 10.3390/ijms20133154] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/10/2023] Open
Abstract
Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery. Humulus lupulus (hop) plants are hosts to several viroids among which Hop latent viroid (HLVd) and Citrus bark cracking viroid (CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.
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Affiliation(s)
- Nataša Štajner
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Plant Protection Department, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Vishnu Sukumari Nath
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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Gu SY, Wang LC, Cheuh CM, Lo WS. CHITINASE LIKE1 Regulates Root Development of Dark-Grown Seedlings by Modulating Ethylene Biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:600. [PMID: 31156671 PMCID: PMC6530356 DOI: 10.3389/fpls.2019.00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/24/2019] [Indexed: 05/07/2023]
Abstract
The plant hormone ethylene plays a regulatory role in development in light- and dark-grown seedlings. We previously isolated a group of small-molecule compounds with a quinazolinone backbone, which were named acsinones (for ACC synthase inhibitor quinazolinones), that act as uncompetitive inhibitors of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS). Thus, the triple response phenotype, which consists of shortened hypocotyls and roots, radial swelling of hypocotyls and exaggerated curvature of apical hooks, was suppressed by acsinones in dark-grown (etiolated) ethylene overproducer (eto) seedlings. Here, we describe our isolation and characterization of an Arabidopsis revert to eto1 9 (ret9) mutant, which showed reduced sensitivity to acsinones in etiolated eto1 seedlings. Map-based cloning of RET9 revealed an amino acid substitution in CHITINASE LIKE1 (CTL1), which is required for cell wall biogenesis and stress resistance in Arabidopsis. Etiolated seedlings of ctl1ret9 showed short hypocotyls and roots, which were augmented in combination with eto1-4. Consistently, ctl1ret9 seedlings showed enhanced sensitivity to exogenous ACC to suppress primary root elongation as compared with the wild type. After introducing ctl1ret9 to mutants completely insensitive to ethylene, genetic analysis indicated that an intact ethylene response pathway is essential for the alterations in root and apical hook but not hypocotyl in etiolated ctl1ret9 seedlings. Furthermore, a mild yet significantly increased ethylene level in ctl1 mutants was related to elevated mRNA level and activity of ACC oxidase (ACO). Moreover, genes associated with ethylene biosynthesis (ACO1 and ACO2) and response (ERF1 and EDF1) were upregulated in etiolated ctl1ret9 seedlings. By characterizing a new recessive allele of CTL1, we reveal that CTL1 negatively regulates ACO activity and the ethylene response, which thus contributes to understanding a role for ethylene in root elongation in response to perturbed cell wall integrity.
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Affiliation(s)
- Shin-Yuan Gu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Central University, Taoyuan City, Taiwan
| | - Long-Chi Wang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chiao-Mei Cheuh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Li P, Liu Y, Tan W, Chen J, Zhu M, Lv Y, Liu Y, Yu S, Zhang W, Cai H. Brittle Culm 1 Encodes a COBRA-Like Protein Involved in Secondary Cell Wall Cellulose Biosynthesis in Sorghum. PLANT & CELL PHYSIOLOGY 2019; 60:788-801. [PMID: 30590744 DOI: 10.1093/pcp/pcy246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/20/2018] [Indexed: 05/08/2023]
Abstract
Plant mechanical strength contributes to lodging resistance and grain yield, making it an agronomically important trait in sorghum (Sorghum bicolor). In this study, we isolated the brittle culm 1 (bc1) mutant and identified SbBC1 through map-based cloning. SbBC1, a homolog of rice OsBC1 and Arabidopsis thaliana AtCOBL4, encodes a COBRA-like protein that exhibits typical structural features of a glycosylphosphatidylinositol-anchored protein. A single-nucleotide mutation in SbBC1 led to reduced mechanical strength, decreased cellulose content, and increased lignin content without obviously altering plant morphology. Transmission electron microscopy revealed reduced cell wall thickness in sclerenchyma cells of the bc1 mutant. SbBC1 is primarily expressed in developing sclerenchyma cells and vascular bundles in sorghum. RNA-seq analysis further suggested a possible mechanism by which SbBC1 mediates cellulose biosynthesis and cell wall remodeling. Our results demonstrate that SbBC1 participates in the biosynthesis of cellulose in the secondary cell wall and affects the mechanical strength of sorghum plants, providing additional genetic evidence for the roles of COBRA-like genes in cellulose biosynthesis in grasses.
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Affiliation(s)
- Pan Li
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops North China, Ministry of Agriculture, Beijing, China
| | - Yanrong Liu
- Department of Grassland Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Wenqing Tan
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
| | - Jun Chen
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
| | - Mengjiao Zhu
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
| | - Ya Lv
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
| | - Yishan Liu
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops North China, Ministry of Agriculture, Beijing, China
| | - Wanjun Zhang
- Department of Grassland Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Hongwei Cai
- Department of Plant Genetics Breeding and Seed Science, China Agricultural University; Beijing Key Laboratory of Crop Genetic Improvement; Laboratory of Crop Heterosis and Utilization, MOE, Beijing, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi, Japan
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21
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Cao J, Tan X. Comprehensive Analysis of the Chitinase Family Genes in Tomato ( Solanum lycopersicum). PLANTS 2019; 8:plants8030052. [PMID: 30823433 PMCID: PMC6473868 DOI: 10.3390/plants8030052] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.
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Affiliation(s)
- Jun Cao
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
| | - Xiaona Tan
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
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22
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Zheng M, Liu X, Lin J, Liu X, Wang Z, Xin M, Yao Y, Peng H, Zhou DX, Ni Z, Sun Q, Hu Z. Histone acetyltransferase GCN5 contributes to cell wall integrity and salt stress tolerance by altering the expression of cellulose synthesis genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:587-602. [PMID: 30394596 DOI: 10.1111/tpj.14144] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 05/22/2023]
Abstract
Excess soluble salts in soil are harmful to the growth and development of most plants. Evidence is emerging that the plant cell wall is involved in sensing and responding to salt stress, but the underlying mechanisms are not well understood. We reveal that the histone acetyltransferase General control non-repressed protein 5 (GCN5) is required for the maintenance of cell wall integrity and salt stress tolerance. The levels of GCN5 mRNA are increased in response to salt stress. The gcn5 mutants exhibited severe growth inhibition and defects in cell wall integrity under salt stress conditions. Combining RNA sequencing and chromatin immunoprecipitation assays, we identified the chitinase-like gene CTL1, polygalacturonase involved in expansion-3 (PGX3) and MYB domain protein-54 (MYB54) as direct targets of GCN5. Acetylation of H3K9 and H3K14 mediated by GCN5 is associated with activation of CTL1, PGX3 and MYB54 under salt stress. Moreover, constitutive expression of CTL1 in the gcn5 mutant restores salt tolerance and cell wall integrity. In addition, the expression of the wheat TaGCN5 gene in Arabidopsis gcn5 mutant plants complemented the salt tolerance and cell wall integrity phenotypes, suggesting that GCN5-mediated salt tolerance is conserved between Arabidopsis and wheat. Taken together, our data indicate that GCN5 plays a key role in the preservation of salt tolerance via versatile regulation in plants.
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Affiliation(s)
- Mei Zheng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Xingbei Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Jingchen Lin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Zhouying Wang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay, Université Paris Sud, 91405, Orsay, France
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, 100193, China
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23
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Feeding the Walls: How Does Nutrient Availability Regulate Cell Wall Composition? Int J Mol Sci 2018; 19:ijms19092691. [PMID: 30201905 PMCID: PMC6164997 DOI: 10.3390/ijms19092691] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/12/2023] Open
Abstract
Nutrients are critical for plants to grow and develop, and nutrient depletion severely affects crop yield. In order to optimize nutrient acquisition, plants adapt their growth and root architecture. Changes in growth are determined by modifications in the cell walls surrounding every plant cell. The plant cell wall, which is largely composed of complex polysaccharides, is essential for plants to attain their shape and to protect cells against the environment. Within the cell wall, cellulose strands form microfibrils that act as a framework for other wall components, including hemicelluloses, pectins, proteins, and, in some cases, callose, lignin, and suberin. Cell wall composition varies, depending on cell and tissue type. It is governed by synthesis, deposition and remodeling of wall components, and determines the physical and structural properties of the cell wall. How nutrient status affects cell wall synthesis and organization, and thus plant growth and morphology, remains poorly understood. In this review, we aim to summarize and synthesize research on the adaptation of root cell walls in response to nutrient availability and the potential role of cell walls in nutrient sensing.
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24
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Yıldırım K, Yağcı A, Sucu S, Tunç S. Responses of grapevine rootstocks to drought through altered root system architecture and root transcriptomic regulations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:256-268. [PMID: 29627732 DOI: 10.1016/j.plaphy.2018.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
Roots are the major interface between the plant and various stress factors in the soil environment. Alteration of root system architecture (RSA) (root length, spread, number and length of lateral roots) in response to environmental changes is known to be an important strategy for plant adaptation and productivity. In light of ongoing climate changes and global warming predictions, the breeding of drought-tolerant grapevine cultivars is becoming a crucial factor for developing a sustainable viticulture. Root-trait modeling of grapevine rootstock for drought stress scenarios, together with high-throughput phenotyping and genotyping techniques, may provide a valuable background for breeding studies in viticulture. Here, tree grafted grapevine rootstocks (110R, 5BB and 41B) having differential RSA regulations and drought tolerance were investigated to define their drought dependent root characteristics. Root area, root length, ramification and number of root tips reduced less in 110R grafted grapevines compared to 5BB and 41B grafted ones during drought treatment. Root relative water content as well as total carbohydrate and nitrogen content were found to be much higher in the roots of 110R than it was in the roots of other rootstocks under drought. Microarray-based root transcriptome profiling was also conducted on the roots of these rootstocks to identify their gene regulation network behind drought-dependent RSA alterations. Transcriptome analysis revealed totally 2795, 1196 and 1612 differentially expressed transcripts at the severe drought for the roots of 110R, 5BB and 41B, respectively. According to this transcriptomic data, effective root elongation and enlargement performance of 110R were suggested to depend on three transcriptomic regulations. First one is the drought-dependent induction in sugar and protein transporters genes (SWEET and NRT1/PTR) in the roots of 110R to facilitate carbohydrate and nitrogen accumulation. In the roots of the same rootstock, expression increase in osmolyte producer genes revealed another transcriptomic regulation enabling effective root osmotic adjustment under drought stress. The third mechanism was linked to root suberization with upregulation of transcripts functional in wax producing enzymes (Caffeic acid 3-O-methyltransferase, Eceriferum3, 3-ketoacyl-CoAsynthase). These three transcriptomic regulations were suggested to provide essential energy and water preservation to the roots of 110R for its effective RSA regulation under drought. This phenotypic and genotypic knowledge could be used to develop root-dependent drought tolerant grapevines in breeding programs and could facilitate elucidation of genetic regulations behind RSA alteration in other plants.
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Affiliation(s)
- Kubilay Yıldırım
- Gaziosmanpaşa University, Department of Bioengineering, Tokat, Turkey.
| | - Adem Yağcı
- Department of Agriculture, Tokat, Turkey
| | - Seda Sucu
- Department of Agriculture, Tokat, Turkey
| | - Sümeyye Tunç
- Gaziosmanpaşa University, Department of Bioengineering, Tokat, Turkey
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25
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A Phenotyping Method of Giant Cells from Root-Knot Nematode Feeding Sites by Confocal Microscopy Highlights a Role for CHITINASE-LIKE 1 in Arabidopsis. Int J Mol Sci 2018; 19:ijms19020429. [PMID: 29389847 PMCID: PMC5855651 DOI: 10.3390/ijms19020429] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/19/2018] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
Most effective nematicides for the control of root-knot nematodes are banned, which demands a better understanding of the plant-nematode interaction. Understanding how gene expression in the nematode-feeding sites relates to morphological features may assist a better characterization of the interaction. However, nematode-induced galls resulting from cell-proliferation and hypertrophy hinders such observation, which would require tissue sectioning or clearing. We demonstrate that a method based on the green auto-fluorescence produced by glutaraldehyde and the tissue-clearing properties of benzyl-alcohol/benzyl-benzoate preserves the structure of the nematode-feeding sites and the plant-nematode interface with unprecedented resolution quality. This allowed us to obtain detailed measurements of the giant cells’ area in an Arabidopsis line overexpressing CHITINASE-LIKE-1 (CTL1) from optical sections by confocal microscopy, assigning a role for CTL1 and adding essential data to the scarce information of the role of gene repression in giant cells. Furthermore, subcellular structures and features of the nematodes body and tissues from thick organs formed after different biotic interactions, i.e., galls, syncytia, and nodules, were clearly distinguished without embedding or sectioning in different plant species (Arabidopsis, cucumber or Medicago). The combination of this method with molecular studies will be valuable for a better understanding of the plant-biotic interactions.
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26
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Wen D, Xu H, Xie L, He M, Hou H, Zhang C. A loose endosperm structure of wheat seed produced under low nitrogen level promotes early germination by accelerating water uptake. Sci Rep 2017; 7:3116. [PMID: 28596607 PMCID: PMC5465190 DOI: 10.1038/s41598-017-03333-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/26/2017] [Indexed: 02/01/2023] Open
Abstract
Water uptake is the fundamental requirement for the initiation and completion of seed germination that is a vital phase in the life cycle of seed plants. We found that seeds produced under four nitrogen levels showed significantly different germination speed. The objective of this study was to study the mechanism of rapid seed germination and explore which pathways and genes play critical roles in radicle protrusion. Anatomical data revealed that seed protein content affected endosperm structure of seeds. Moreover, scanning electron microscope maps showed that faster germinated seeds had a looser endosperm structure compared with other seeds. Subsequently, high throughout RNA-seq data were used to compare the transcriptomes of imbibed seeds with different germination speed. Gene ontology (GO) term enrichment analysis revealed that cell wall metabolism related genes significantly up-regulated in faster germinated seeds. In these genes, the top four were chitinase that had about fourfold higher expression in faster germinated seeds. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that faster germinated seeds had enhanced expression in glutathione metabolism. By combining these results, we propose a model for nitrogen fertilizer affects germination speed of wheat seed, which provide new insights into seed germination.
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Affiliation(s)
- Daxing Wen
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Haicheng Xu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Liuyong Xie
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Mingrong He
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Hongcun Hou
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China
| | - Chunqing Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Tai'an, Shandong Province, 271018, P.R. China.
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27
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Fu C, Wang F, Liu W, Liu D, Li J, Zhu M, Liao Y, Liu Z, Huang H, Zeng X, Ma X. Transcriptomic Analysis Reveals New Insights into High-Temperature-Dependent Glume-Unclosing in an Elite Rice Male Sterile Line. FRONTIERS IN PLANT SCIENCE 2017; 8:112. [PMID: 28261226 PMCID: PMC5306291 DOI: 10.3389/fpls.2017.00112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/19/2017] [Indexed: 05/23/2023]
Abstract
Glume-unclosing after anthesis is a widespread phenomenon in hybrid rice and also a maternal hereditary trait. The character of Glume-unclosing in rice male sterile lines also seriously influences germination rate and the commercial quality of hybrid rice seeds. We validated that the type of glume-unclosing after anthesis in the elite rice thermo-sensitive genic male sterile (TGMS) line RGD-7S was caused by high temperature. Transcriptomic sequencing of rice panicles was performed to explore the change of transcript profiles under four conditions: pre- and post-anthesis under high temperature (HRGD0 and HRGD1), and pre- and post-anthesis under low temperature (LRGD0 and LRGD1). We identified a total of 14,540 differentially expressed genes (DEGs) including some heat shock factors (HSFs) across the four samples. We found that more genes were up-regulated than down-regulated in the sample pair HRGD1vsHRGD0. These up-regulated genes were significantly enriched in the three biological processes of carbohydrate metabolism, response to water and cell wall macromolecular metabolism. Simultaneously, we also found that the HSF gene OsHsfB1 was specially up-regulated in HRGD1vsHRGD0. However, the down-regulated DEGs in LRGD1vsLRGD0 were remarkably clustered in the biological process of carbohydrate metabolism. This suggests that carbohydrate metabolism may play a key role in regulation of glume-unclosing under high temperature in RGD-7S. We also analyzed the expression pattern of genes enriched in carbohydrate metabolism and several HSF genes under different conditions and provide new insights into the cause of rice glume-unclosing.
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Affiliation(s)
- Chongyun Fu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Feng Wang
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Wuge Liu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Jinhua Li
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Manshan Zhu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Yilong Liao
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Zhenrong Liu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
| | - Huijun Huang
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Xueqin Zeng
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
| | - Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of New Technology in Rice BreedingGuangzhou, China
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28
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Chen W, Li J, Zhu H, Xu P, Chen J, Yao Q. Arbuscular Mycorrhizal Fungus Enhances Lateral Root Formation in Poncirus trifoliata (L.) as Revealed by RNA-Seq Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:2039. [PMID: 29238356 PMCID: PMC5713035 DOI: 10.3389/fpls.2017.02039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/14/2017] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbiosis with most terrestrial plants, and greatly regulate lateral root (LR) formation. Phosphorus (P), sugar, and plant hormones are proposed being involved in this regulation, however, no global evidence regarding these factors is available so far, especially in woody plants. In this study, we inoculated trifoliate orange seedlings (Poncirus trifoliata L. Raf) with an AMF isolate, Rhizophagus irregularis BGC JX04B. After 4 months of growth, LR formation was characterized, and sugar contents in roots were determined. RNA-Seq analysis was performed to obtain the transcriptomes of LR root tips from non-mycorrhizal and mycorrhizal seedlings. Quantitative real time PCR (qRT-PCR) of selected genes was also conducted for validation. The results showed that AMF significantly increased LR number, as well as plant biomass and shoot P concentration. The contents of glucose and fructose in primary root, and sucrose content in LR were also increased. A total of 909 differentially expressed genes (DEGs) were identified in response to AMF inoculation, and qRT-PCR validated the transcriptomic data. The numbers of DEGs related to P, sugar, and plant hormones were 31, 32, and 25, respectively. For P metabolism, the most up-regulated DEGs mainly encoded phosphate transporter, and the most down-regulated DEGs encoded acid phosphatase. For sugar metabolism, the most up-regulated DEGs encoded polygalacturonase and chitinase. For plant hormones, the most up-regulated DEGs were related to auxin signaling, and the most down-regulated DEGs were related to ethylene signaling. PLS-SEM analysis indicates that P metabolism was the most important pathway by which AMF regulates LR formation in this study. These data reveal the changes of genome-wide gene expression in responses to AMF inoculation in trifoliate orange and provide a solid basis for the future identification and characterization of key genes involved in LR formation induced by AMF.
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Affiliation(s)
- Weili Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Juan Li
- Department of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China
| | - Pengyang Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiezhong Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
- *Correspondence: Qing Yao
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29
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Zhang M, Wei F, Guo K, Hu Z, Li Y, Xie G, Wang Y, Cai X, Peng L, Wang L. A Novel FC116/ BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1366. [PMID: 27708650 PMCID: PMC5030303 DOI: 10.3389/fpls.2016.01366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/29/2016] [Indexed: 05/11/2023]
Abstract
We report isolation and characterization of a fragile culm mutant fc116 that displays reduced mechanical strength caused by decreased cellulose content and altered cell wall structure in rice. Map-based cloning revealed that fc116 was a base substitution mutant (G to A) in a putative beta-1,6-N-acetylglucosaminyltransferase (C2GnT) gene (LOC_Os05g07790, allelic to BC10). This mutation resulted in one amino acid missing within a newly-identified protein motif "R, RXG, RA." The FC116/BC10 gene was lowly but ubiquitously expressed in the all tissues examined across the whole life cycle of rice, and slightly down-regulated during secondary growth. This mutant also exhibited a significant increase in the content of hemicelluloses and lignins, as well as the content of pentoses (xylose and arabinose). But the content of hexoses (glucose, mannose, and galactose) was decreased in both cellulosic and non-cellulosic (pectins and hemicelluloses) fractions of the mutant. Transcriptomic analysis indicated that the typical genes in the fc116 mutant were up-regulated corresponding to xylan biosynthesis, as well as lignin biosynthesis including p-hydroxyphenyl (H), syringyl (S), and guaiacyl (G). Our results indicate that FC116 has universal function in regulation of the cell wall polymers in rice.
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Affiliation(s)
- Mingliang Zhang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Feng Wei
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Kai Guo
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yuyang Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xiwen Cai
- Department of Plant Science, North Dakota State UniversityFargo, ND, USA
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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De Gernier H, De Pessemier J, Xu J, Cristescu SM, Van Der Straeten D, Verbruggen N, Hermans C. A Comparative Study of Ethylene Emanation upon Nitrogen Deficiency in Natural Accessions of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2016; 7:70. [PMID: 26904047 PMCID: PMC4748056 DOI: 10.3389/fpls.2016.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/15/2016] [Indexed: 05/07/2023]
Abstract
An original approach to develop sustainable agriculture with less nitrogen fertilizer inputs is to tackle the cross-talk between nitrogen nutrition and plant growth regulators. In particular the gaseous hormone, ethylene, is a prime target for that purpose. The variation of ethylene production in natural accessions of the model species Arabidopsis thaliana was explored in response to the nitrate supply. Ethylene was measured with a laser-based photoacoustic detector. First, experimental conditions were established with Columbia-0 (Col-0) accession, which was grown in vitro on horizontal plates across a range of five nitrate concentrations (0.5, 1, 2.5, 5, or 10 mM). The concentrations of 1 and 10 mM nitrate were retained for further characterization. Along with a decrease of total dry biomass and higher biomass allocation to the roots, the ethylene production was 50% more important at 1 mM than at 10 mM nitrate. The total transcript levels of 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASES (ACS) in roots and those of ACC OXIDASES (ACO) in shoots increased by 100% between the same treatments. This was mainly due to higher transcript levels of ACS6 and of ACO2 and ACO4 respectively. The assumption was that during nitrogen deficiency, the greater biomass allocation in favor of the roots was controlled by ethylene being released in the shoots after conversion of ACC originating from the roots. Second, biomass and ethylene productions were measured in 20 additional accessions. Across all accessions, the total dry biomass and ethylene production were correlated negatively at 1 mM but positively at 10 mM nitrate. Furthermore, polymorphism was surveyed in ACC and ethylene biosynthesis genes and gene products among accessions. Very few substitutions modifying the amino acids properties in conserved motifs of the enzymes were found in the accessions. Natural variation of ethylene production could be further explored to improve Nitrogen Use Efficiency (NUE), in particular by manipulating features like the biomass production and the timing of senescence upon nitrogen limitation.
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Affiliation(s)
- Hugues De Gernier
- Laboratory of Plant Physiology and Molecular Genetics, Interfacultary School of Bioengineers, Université Libre de BruxellesBrussels, Belgium
| | - Jérôme De Pessemier
- Laboratory of Plant Physiology and Molecular Genetics, Interfacultary School of Bioengineers, Université Libre de BruxellesBrussels, Belgium
| | - Jiajia Xu
- Laboratory of Plant Physiology and Molecular Genetics, Interfacultary School of Bioengineers, Université Libre de BruxellesBrussels, Belgium
| | - Simona M. Cristescu
- Trace Gas Research Group, Department of Molecular and Laser Physics, Institute for Molecules and Materials, Radboud UniversityNijmegen, Netherlands
| | - Dominique Van Der Straeten
- Unit Hormone Signalling and Bio-Imaging, Laboratory of Functional Plant Biology, Department of Physiology, Ghent UniversityGhent, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Interfacultary School of Bioengineers, Université Libre de BruxellesBrussels, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Interfacultary School of Bioengineers, Université Libre de BruxellesBrussels, Belgium
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31
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Wang T, McFarlane HE, Persson S. The impact of abiotic factors on cellulose synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:543-52. [PMID: 26552883 DOI: 10.1093/jxb/erv488] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
As sessile organisms, plants require mechanisms to sense and respond to changes in their environment, including both biotic and abiotic factors. One of the most common plant adaptations to environmental changes is differential regulation of growth, which results in growth either away from adverse conditions or towards more favorable conditions. As cell walls shape plant growth, this differential growth response must be accompanied by alterations to the plant cell wall. Here, we review the impact of four abiotic factors (osmotic conditions, ionic stress, light, and temperature) on the synthesis of cellulose, an important component of the plant cell wall. Understanding how different abiotic factors influence cellulose production and addressing key questions that remain in this field can provide crucial information to cope with the need for increased crop production under the mounting pressures of a growing world population and global climate change.
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Affiliation(s)
- Ting Wang
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam, Germany
| | | | - Staffan Persson
- ARC Centre of Excellence in Plant Cell Walls, School of Biosciences, University of Melbourne, 3010, Melbourne, Australia
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Yang QS, Gao J, He WD, Dou TX, Ding LJ, Wu JH, Li CY, Peng XX, Zhang S, Yi GJ. Comparative transcriptomics analysis reveals difference of key gene expression between banana and plantain in response to cold stress. BMC Genomics 2015; 16:446. [PMID: 26059100 PMCID: PMC4461995 DOI: 10.1186/s12864-015-1551-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/17/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Banana and plantain (Musa spp.) comprise an important part of diets for millions of people around the globe. Low temperature is one of the key environmental stresses which greatly affects the global banana production. To understand the molecular mechanism of the cold-tolerance in plantain we used RNA-Seq based comparative transcriptomics analyses for both cold-sensitive banana and cold-tolerant plantain subjected to the cold stress for 0, 3 and 6 h. RESULTS The cold-response genes at early stage are identified and grouped in both species by GO analysis. The results show that 10 and 68 differentially expressed genes (DEGs) are identified for 3 and 6 h of cold stress respectively in plantain, while 40 and 238 DEGs are identified respectively in banana. GO classification analyses show that the majority of DEGs identified in both banana and plantain belong to 11 categories including regulation of transcription, response to stress signal transduction, etc. A similar profile for 28 DEGs was found in both banana and plantain for 6 h of cold stress, suggesting both share some common adaptation processes in response to cold stress. There are 17 DEGs found uniquely in cold-tolerance plantain, which were involved in signal transduction, abiotic stress, copper ion equilibrium, photosynthesis and photorespiration, sugar stimulation, protein modifications etc. Twelve early responsive genes including ICE1 and MYBS3 were selected and further assessed and confirmed by qPCR in the extended time course experiments (0, 3, 6, 24 and 48 h), which revealed significant expression difference of key genes in response to cold stress, especially ICE1 and MYBS3 between cold-sensitive banana and cold-tolerant plantain. CONCLUSIONS We found that the cold-tolerance pathway appears selectively activated by regulation of ICE1 and MYBS3 expression in plantain under different stages of cold stress. We conclude that the rapid activation and selective induction of ICE1 and MYBS3 cold tolerance pathways in plantain, along with expression of other cold-specific genes, may be one of the main reasons that plantain has higher cold resistance than banana.
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Affiliation(s)
- Qiao-Song Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China.
| | - Jie Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510640, China.
| | - Wei-Di He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China. .,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Tong-Xin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510640, China.
| | - Li-Jie Ding
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510640, China.
| | - Jun-Hua Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510640, China.
| | - Chun-Yu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China.
| | - Xin-Xiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510640, China.
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, 14853-2703, USA.
| | - Gan-Jun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, 80 Dafeng 2nd street, Tianhe District, Guangzhou, Guangdong Province, 510640, China. .,Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, 510640, China.
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Lyons R, Stiller J, Powell J, Rusu A, Manners JM, Kazan K. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS One 2015; 10:e0121902. [PMID: 25849296 PMCID: PMC4388846 DOI: 10.1371/journal.pone.0121902] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/05/2015] [Indexed: 11/19/2022] Open
Abstract
Some of the most devastating agricultural diseases are caused by root-infecting pathogens, yet the majority of studies on these interactions to date have focused on the host responses of aerial tissues rather than those belowground. Fusarium oxysporum is a root-infecting pathogen that causes wilt disease on several plant species including Arabidopsis thaliana. To investigate and compare transcriptional changes triggered by F. oxysporum in different Arabidopsis tissues, we infected soil-grown plants with F. oxysporum and subjected root and leaf tissue harvested at early and late timepoints to RNA-seq analyses. At least half of the genes induced or repressed by F. oxysporum showed tissue-specific regulation. Regulators of auxin and ABA signalling, mannose binding lectins and peroxidases showed strong differential expression in root tissue. We demonstrate that ARF2 and PRX33, two genes regulated in the roots, promote susceptibility to F. oxysporum. In the leaves, defensins and genes associated with the response to auxin, cold and senescence were strongly regulated while jasmonate biosynthesis and signalling genes were induced throughout the plant.
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Affiliation(s)
- Rebecca Lyons
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
- * E-mail:
| | - Jiri Stiller
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Jonathan Powell
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Anca Rusu
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - John M. Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, ACT, Australia
| | - Kemal Kazan
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture & Food Innovation (QAAFI), The University of Queensland, St Lucia, Brisbane, Queensland, 4067, Australia
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Baxter I. Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits? JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2127-31. [PMID: 25711709 PMCID: PMC4986723 DOI: 10.1093/jxb/erv040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/12/2014] [Accepted: 01/12/2015] [Indexed: 05/18/2023]
Abstract
It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400,000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches.
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Affiliation(s)
- Ivan Baxter
- United States Department of Agriculture-Agricultural Research Service Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
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35
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Martínez-Caballero S, Cano-Sánchez P, Mares-Mejía I, Díaz-Sánchez AG, Macías-Rubalcava ML, Hermoso JA, Rodríguez-Romero A. Comparative study of two GH19 chitinase-like proteins fromHevea brasiliensis, one exhibiting a novel carbohydrate-binding domain. FEBS J 2014; 281:4535-54. [DOI: 10.1111/febs.12962] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/12/2014] [Accepted: 08/06/2014] [Indexed: 10/24/2022]
Affiliation(s)
| | - Patricia Cano-Sánchez
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | - Israel Mares-Mejía
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | - Angel G. Díaz-Sánchez
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
| | | | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural; Instituto de Química-Física ‘Rocasolano’; CSIC Madrid Spain
| | - Adela Rodríguez-Romero
- Instituto de Química; Universidad Nacional Autónoma de México; Ciudad Universitaria México
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36
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Mokshina N, Gorshkova T, Deyholos MK. Chitinase-like (CTL) and cellulose synthase (CESA) gene expression in gelatinous-type cellulosic walls of flax (Linum usitatissimum L.) bast fibers. PLoS One 2014; 9:e97949. [PMID: 24918577 PMCID: PMC4053336 DOI: 10.1371/journal.pone.0097949] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/26/2014] [Indexed: 11/19/2022] Open
Abstract
Plant chitinases (EC 3.2.1.14) and chitinase-like (CTL) proteins have diverse functions including cell wall biosynthesis and disease resistance. We analyzed the expression of 34 chitinase and chitinase-like genes of flax (collectively referred to as LusCTLs), belonging to glycoside hydrolase family 19 (GH19). Analysis of the transcript expression patterns of LusCTLs in the stem and other tissues identified three transcripts (LusCTL19, LusCTL20, LusCTL21) that were highly enriched in developing bast fibers, which form cellulose-rich gelatinous-type cell walls. The same three genes had low relative expression in tissues with primary cell walls and in xylem, which forms a xylan type of secondary cell wall. Phylogenetic analysis of the LusCTLs identified a flax-specific sub-group that was not represented in any of other genomes queried. To provide further context for the gene expression analysis, we also conducted phylogenetic and expression analysis of the cellulose synthase (CESA) family genes of flax, and found that expression of secondary wall-type LusCESAs (LusCESA4, LusCESA7 and LusCESA8) was correlated with the expression of two LusCTLs (LusCTL1, LusCTL2) that were the most highly enriched in xylem. The expression of LusCTL19, LusCTL20, and LusCTL21 was not correlated with that of any CESA subgroup. These results defined a distinct type of CTLs that may have novel functions specific to the development of the gelatinous (G-type) cellulosic walls.
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Affiliation(s)
- Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Michael K. Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress. PLoS One 2014; 9:e97878. [PMID: 24837971 PMCID: PMC4023963 DOI: 10.1371/journal.pone.0097878] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/24/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Salt stress interferes with plant growth and production. Plants have evolved a series of molecular and morphological adaptations to cope with this abiotic stress, and overexpression of salt response genes reportedly enhances the productivity of various crops. However, little is known about the salt responsive genes in the energy plant physic nut (Jatropha curcas L.). Thus, excavate salt responsive genes in this plant are informative in uncovering the molecular mechanisms for the salt response in physic nut. METHODOLOGY/PRINCIPAL FINDINGS We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of physic nut plants (roots and leaves) 2 hours, 2 days and 7 days after the onset of salt stress. A total of 1,504 and 1,115 genes were significantly up and down-regulated in roots and leaves, respectively, under salt stress condition. Gene ontology (GO) analysis of physiological process revealed that, in the physic nut, many "biological processes" were affected by salt stress, particular those categories belong to "metabolic process", such as "primary metabolism process", "cellular metabolism process" and "macromolecule metabolism process". The gene expression profiles indicated that the associated genes were responsible for ABA and ethylene signaling, osmotic regulation, the reactive oxygen species scavenging system and the cell structure in physic nut. CONCLUSIONS/SIGNIFICANCE The major regulated genes detected in this transcriptomic data were related to trehalose synthesis and cell wall structure modification in roots, while related to raffinose synthesis and reactive oxygen scavenger in leaves. The current study shows a comprehensive gene expression profile of physic nut under salt stress. The differential expression genes detected in this study allows the underling the salt responsive mechanism in physic nut with the aim of improving its salt resistance in the future.
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Roycewicz PS, Malamy JE. Cell wall properties play an important role in the emergence of lateral root primordia from the parent root. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2057-69. [PMID: 24619997 PMCID: PMC3991740 DOI: 10.1093/jxb/eru056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants adapt to their unique soil environments by altering the number and placement of lateral roots post-embryonic. Mutants were identified in Arabidopsis thaliana that exhibit increased lateral root formation. Eight mutants were characterized in detail and were found to have increased lateral root formation due to at least three distinct mechanisms. The causal mutation in one of these mutants was found in the XEG113 gene, recently shown to be involved in plant cell wall biosynthesis. Lateral root primordia initiation is unaltered in this mutant. In contrast, synchronization of lateral root initiation demonstrated that mutation of XEG113 increases the rate at which lateral root primordia develop and emerge to form lateral roots. The effect of the XEG113 mutation was specific to the root system and had no apparent effect on shoot growth. Screening of 17 additional cell wall mutants, altering a myriad of cell wall components, revealed that many (but not all) types of cell wall defects promote lateral root formation. These results suggest that proper cell wall biosynthesis is necessary to constrain lateral root primordia emergence. While previous reports have shown that lateral root emergence is accompanied by active remodelling of cell walls overlying the primordia, this study is the first to demonstrate that alteration of the cell wall is sufficient to promote lateral root formation. Therefore, inherent cell wall properties may play a previously unappreciated role in regulation of root system architecture.
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Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N. Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2014; 201:810-824. [PMID: 24134393 DOI: 10.1111/nph.12554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/16/2013] [Indexed: 05/23/2023]
Abstract
The exposure of plants to high concentrations of trace metallic elements such as copper involves a remodeling of the root system, characterized by a primary root growth inhibition and an increase in the lateral root density. These characteristics constitute easy and suitable markers for screening mutants altered in their response to copper excess. A forward genetic approach was undertaken in order to discover novel genetic factors involved in the response to copper excess. A Cu(2+) -sensitive mutant named copper modified resistance1 (cmr1) was isolated and a causative mutation in the CMR1 gene was identified by using positional cloning and next-generation sequencing. CMR1 encodes a plant-specific protein of unknown function. The analysis of the cmr1 mutant indicates that the CMR1 protein is required for optimal growth under normal conditions and has an essential role in the stress response. Impairment of the CMR1 activity alters root growth through aberrant activity of the root meristem, and modifies potassium concentration and hormonal balance (ethylene production and auxin accumulation). Our data support a putative role for CMR1 in cell division regulation and meristem maintenance. Research on the role of CMR1 will contribute to the understanding of the plasticity of plants in response to changing environments.
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Affiliation(s)
- Michal Juraniec
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Hélène Lequeux
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Christian Hermans
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Glenda Willems
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Pietrino Salis
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Maud Vromant
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
| | - Stanley Lutts
- Groupe de Recherche en Physiologie Végétale, Earth and Life Institute, Université catholique de Louvain, 5 bte13, Croix du Sud, 1348, Louvain-La-Neuve, Belgium
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, 1050, Brussels, Belgium
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40
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Li S, Bashline L, Lei L, Gu Y. Cellulose synthesis and its regulation. THE ARABIDOPSIS BOOK 2014; 12:e0169. [PMID: 24465174 PMCID: PMC3894906 DOI: 10.1199/tab.0169] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cellulose, the most abundant biopolymer synthesized on land, is made of linear chains of ß (1-4) linked D-glucose. As a major structural component of the cell wall, cellulose is important not only for industrial use but also for plant growth and development. Cellulose microfibrils are tethered by other cell wall polysaccharides such as hemicellulose, pectin, and lignin. In higher plants, cellulose is synthesized by plasma membrane-localized rosette cellulose synthase complexes. Despite the recent advances using a combination of molecular genetics, live cell imaging, and spectroscopic tools, many aspects of the cellulose synthesis remain a mystery. In this chapter, we highlight recent research progress towards understanding the mechanism of cellulose synthesis in Arabidopsis.
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Affiliation(s)
- Shundai Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Logan Bashline
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Lei Lei
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Ying Gu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
- Address correspondence to
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Szymanowska-Pułka J. Form matters: morphological aspects of lateral root development. ANNALS OF BOTANY 2013; 112:1643-54. [PMID: 24190952 PMCID: PMC3838556 DOI: 10.1093/aob/mct231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 08/13/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND The crucial role of roots in plant nutrition, and consequently in plant productivity, is a strong motivation to study the growth and functioning of various aspects of the root system. Numerous studies on lateral roots, as a major determinant of the root system architecture, mostly focus on the physiological and molecular bases of developmental processes. Unfortunately, little attention is paid either to the morphological changes accompanying the formation of a lateral root or to morphological defects occurring in lateral root primordia. The latter are observed in some mutants and occasionally in wild-type plants, but may also result from application of external factors. SCOPE AND CONCLUSIONS In this review various morphological aspects of lateral branching in roots are analysed. Morphological events occurring during the formation of a typical lateral root are described. This process involves dramatic changes in the geometry of the developing organ that at early stages are associated with oblique cell divisions, leading to breaking of the symmetry of the cell pattern. Several types of defects in the morphology of primordia are indicated and described. Computer simulations show that some of these defects may result from an unstable field of growth rates. Significant changes in both primary and lateral root morphology may also be a consequence of various mutations, some of which are auxin-related. Examples reported in the literature are considered. Finally, lateral root formation is discussed in terms of mechanics. In this approach the primordium is considered as a physical object undergoing deformation and is characterized by specific mechanical properties.
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Adrangi S, Faramarzi MA. From bacteria to human: a journey into the world of chitinases. Biotechnol Adv 2013; 31:1786-95. [PMID: 24095741 DOI: 10.1016/j.biotechadv.2013.09.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/26/2013] [Accepted: 09/28/2013] [Indexed: 12/28/2022]
Abstract
Chitinases, the enzymes responsible for the biological degradation of chitin, are found in a wide range of organisms from bacteria to higher plants and animals. They participate in numerous physiological processes such as nutrition, parasitism, morphogenesis and immunity. Many organisms, in addition to chitinases, produce inactive chitinase-like lectins that despite lacking enzymatic activity are involved in several regulatory functions. Most known chitinases belong to families 18 and 19 of glycosyl hydrolases, however a few chitinases that belong to families 23 and 48 have also been identified in recent years. In this review, different aspects of chitinases and chi-lectins from bacteria, fungi, insects, plants and mammals are discussed.
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Affiliation(s)
- Sina Adrangi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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43
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Xia H, Zhao C, Hou L, Li A, Zhao S, Bi Y, An J, Zhao Y, Wan S, Wang X. Transcriptome profiling of peanut gynophores revealed global reprogramming of gene expression during early pod development in darkness. BMC Genomics 2013; 14:517. [PMID: 23895441 PMCID: PMC3765196 DOI: 10.1186/1471-2164-14-517] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 07/23/2013] [Indexed: 12/12/2022] Open
Abstract
Background After the zygote divides few times, the development of peanut pre-globular embryo and fruit is arrested under white or red light. Embryo development could be resumed in dark condition after gynophore is buried in soil. It is interesting to study the mechanisms of gynophore development and pod formation in peanut. Results In this study, transcriptome analysis of peanut gynophore was performed using Illumina HiSeq™ 2000 to understand the mechanisms of geocarpy. More than 13 million short sequences were assembled into 72527 unigenes with average size of 394 bp. A large number of genes that were not identified previously in peanut EST projects were identified in this study, including most genes involved in plant circadian rhythm, intra-cellular transportation, plant spliceosome, eukaryotes basal transcription factors, genes encoding ribosomal proteins, brassinosteriod biosynthesis, light-harvesting chlorophyll protein complex, phenylpropanoid biosynthesis and TCA cycle. RNA-seq based gene expression profiling results showed that before and after gynophore soil penetration, the transcriptional level of a large number of genes changed significantly. Genes encoding key enzymes for hormone metabolism, signaling, photosynthesis, light signaling, cell division and growth, carbon and nitrogen metabolism as well as genes involved in stress responses were high lighted. Conclusions Transcriptome analysis of peanut gynophore generated a large number of unigenes which provide useful information for gene cloning and expression study. Digital gene expression study suggested that gynophores experience global changes and reprogram from light to dark grown condition to resume embryo and fruit development.
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44
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Sahoo DK, Stork J, DeBolt S, Maiti IB. Manipulating cellulose biosynthesis by expression of mutant Arabidopsis proM24::CESA3(ixr1-2) gene in transgenic tobacco. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:362-72. [PMID: 23527628 DOI: 10.1111/pbi.12024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/04/2012] [Accepted: 10/05/2012] [Indexed: 05/19/2023]
Abstract
Manipulation of the cellulose biosynthetic machinery in plants has the potential to provide insight into plant growth, morphogenesis and to create modified cellulose for anthropogenic use. Evidence exists that cellulose microfibril structure and its recalcitrance to enzymatic digestion can ameliorated via mis-sense mutation in the primary cell wall-specific gene AtCELLULOSE SYNTHASE (CESA)3. This mis-sense mutation has been identified based on conferring drug resistance to the cellulose inhibitory herbicide isoxaben. To examine whether it would be possible to introduce mutant CESA alleles via a transgenic approach, we overexpressed a modified version of CESA3, AtCESA3(ixr1-2) derived from Arabidopsis thaliana L. Heynh into a different plant family, the Solanceae dicotyledon tobacco (Nicotiana tabacum L. variety Samsun NN). Specifically, a chimeric gene construct of CESA3(ixr1-2) , codon optimized for tobacco, was placed between the heterologous M24 promoter and the rbcSE9 gene terminator. The results demonstrated that the tobacco plants expressing M24-CESA3(ixr1-2) displayed isoxaben resistance, consistent with functionality of the mutated AtCESA3(ixr1-2) in tobacco. Secondly, during enzymatic saccharification, transgenic leaf- and stem-derived cellulose is 54%-66% and 40%-51% more efficient, respectively, compared to the wild type, illustrating translational potential of modified CESA loci. Moreover, the introduction of M24-AtCESA3(ixr1-2) caused aberrant spatial distribution of lignified secondary cell wall tissue and a reduction in the zone occupied by parenchyma cells.
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Affiliation(s)
- Dipak K Sahoo
- KTRDC, College of Agriculture, University of Kentucky, Lexington, KY, USA
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45
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Li G, Li B, Dong G, Feng X, Kronzucker HJ, Shi W. Ammonium-induced shoot ethylene production is associated with the inhibition of lateral root formation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1413-1425. [PMID: 23382554 DOI: 10.1093/jxb/ert019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Foliar NH4(+) exposure is linked to inhibition of lateral root (LR) formation. Here, the role of shoot ethylene in NH4(+)-induced inhibition of LR formation in Arabidopsis was investigated using wild-type and mutant lines that show either blocked ethylene signalling (etr1) or enhanced ethylene synthesis (eto1, xbat32). NH4(+) exposure of wild-type Arabidopsis led to pronounced inhibition of LR production chiefly in the distal root, and triggered ethylene evolution and enhanced activity of the ethylene reporter EBS:GUS in the shoot. It is shown that shoot contact with NH4(+) is necessary to stimulate shoot ethylene evolution. The ethylene antagonists Ag(+) and aminoethoxyvinylglycine (AVG) mitigated LR inhibition under NH4(+) treatment. The decrease in LR production was significantly greater for eto1-1 and xbat32 and significantly less for etr1-3. Enhanced shoot ethylene synthesis/signalling blocked recovery of LR production when auxin was applied in the presence of NH4(+) and negatively impacted shoot AUX1 expression. The findings highlight the important role of shoot ethylene evolution in NH4(+)-mediated inhibition of LR formation.
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Affiliation(s)
- Guangjie Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No. 71 East Beijing Road, Nanjing 210008, China
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46
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Day A, Fénart S, Neutelings G, Hawkins S, Rolando C, Tokarski C. Identification of cell wall proteins in the flax (Linum usitatissimum
) stem. Proteomics 2013; 13:812-25. [DOI: 10.1002/pmic.201200257] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Revised: 10/08/2012] [Accepted: 11/14/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Arnaud Day
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Stéphane Fénart
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Godfrey Neutelings
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Simon Hawkins
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV); INRA UMR 1281, Villeneuve d'Ascq France
| | - Christian Rolando
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP); USR CNRS 3290; Villeneuve d'Ascq; France
| | - Caroline Tokarski
- Université de Lille 1 Sciences et Technologies and Protéomique; Modifications Post-traductionnelles et Glycobiologie IFR 147, Villeneuve d'Ascq France
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP); USR CNRS 3290; Villeneuve d'Ascq; France
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Wu B, Zhang B, Dai Y, Zhang L, Shang-Guan K, Peng Y, Zhou Y, Zhu Z. Brittle culm15 encodes a membrane-associated chitinase-like protein required for cellulose biosynthesis in rice. PLANT PHYSIOLOGY 2012; 159:1440-1452. [PMID: 22665444 DOI: 10.1016/j.biombioe.2016.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant chitinases, a class of glycosyl hydrolases, participate in various aspects of normal plant growth and development, including cell wall metabolism and disease resistance. The rice (Oryza sativa) genome encodes 37 putative chitinases and chitinase-like proteins. However, none of them has been characterized at the genetic level. In this study, we report the isolation of a brittle culm mutant, bc15, and the map-based cloning of the BC15/OsCTL1 (for chitinase-like1) gene affected in the mutant. The gene encodes the rice chitinase-like protein BC15/OsCTL1. Mutation of BC15/OsCTL1 causes reduced cellulose content and mechanical strength without obvious alterations in plant growth. Bioinformatic analyses indicated that BC15/OsCTL1 is a class II chitinase-like protein that is devoid of both an amino-terminal cysteine-rich domain and the chitinase activity motif H-E-T-T but possesses an amino-terminal transmembrane domain. Biochemical assays demonstrated that BC15/OsCTL1 is a Golgi-localized type II membrane protein that lacks classical chitinase activity. Quantitative real-time polymerase chain reaction and β-glucuronidase activity analyses indicated that BC15/OsCTL1 is ubiquitously expressed. Investigation of the global expression profile of wild-type and bc15 plants, using Illumina RNA sequencing, further suggested a possible mechanism by which BC15/OsCTL1 mediates cellulose biosynthesis and cell wall remodeling. Our findings provide genetic evidence of a role for plant chitinases in cellulose biosynthesis in rice, which appears to differ from their roles as revealed by analysis of Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
- Bin Wu
- Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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48
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Wu B, Zhang B, Dai Y, Zhang L, Shang-Guan K, Peng Y, Zhou Y, Zhu Z. Brittle culm15 encodes a membrane-associated chitinase-like protein required for cellulose biosynthesis in rice. PLANT PHYSIOLOGY 2012; 159:1440-52. [PMID: 22665444 PMCID: PMC3425189 DOI: 10.1104/pp.112.195529] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/02/2012] [Indexed: 05/19/2023]
Abstract
Plant chitinases, a class of glycosyl hydrolases, participate in various aspects of normal plant growth and development, including cell wall metabolism and disease resistance. The rice (Oryza sativa) genome encodes 37 putative chitinases and chitinase-like proteins. However, none of them has been characterized at the genetic level. In this study, we report the isolation of a brittle culm mutant, bc15, and the map-based cloning of the BC15/OsCTL1 (for chitinase-like1) gene affected in the mutant. The gene encodes the rice chitinase-like protein BC15/OsCTL1. Mutation of BC15/OsCTL1 causes reduced cellulose content and mechanical strength without obvious alterations in plant growth. Bioinformatic analyses indicated that BC15/OsCTL1 is a class II chitinase-like protein that is devoid of both an amino-terminal cysteine-rich domain and the chitinase activity motif H-E-T-T but possesses an amino-terminal transmembrane domain. Biochemical assays demonstrated that BC15/OsCTL1 is a Golgi-localized type II membrane protein that lacks classical chitinase activity. Quantitative real-time polymerase chain reaction and β-glucuronidase activity analyses indicated that BC15/OsCTL1 is ubiquitously expressed. Investigation of the global expression profile of wild-type and bc15 plants, using Illumina RNA sequencing, further suggested a possible mechanism by which BC15/OsCTL1 mediates cellulose biosynthesis and cell wall remodeling. Our findings provide genetic evidence of a role for plant chitinases in cellulose biosynthesis in rice, which appears to differ from their roles as revealed by analysis of Arabidopsis (Arabidopsis thaliana).
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Affiliation(s)
| | | | | | - Lei Zhang
- Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Keke Shang-Guan
- Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Peng
- Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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De Pessemier J, Chardon F, Juraniec M, Delaplace P, Hermans C. Natural variation of the root morphological response to nitrate supply in Arabidopsis thaliana. Mech Dev 2012; 130:45-53. [PMID: 22683348 DOI: 10.1016/j.mod.2012.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 05/16/2012] [Accepted: 05/29/2012] [Indexed: 01/24/2023]
Abstract
Nitrogen fertilization increases crop yield but excessive nitrate use can be a major environmental problem due to soil leaching or greenhouse gas emission. Root traits have been seldom considered as selection criteria to improve Nitrogen Use Efficiency of crops, due to the difficulty of measuring root traits under field conditions. Nonetheless, learning about mechanisms of lateral root (LR) growth stimulation or repression by nitrate availability could help to redesign root system architecture (RSA), a strategy aimed at developing plants with a dense and profound root system and with higher N uptake efficiency. Here, we explored the genetic diversity provided by natural populations of the model species Arabidopsis thaliana to identify potentially adaptive differences in biomass production and root morphology in response to nitrate availability. A core collection of 24 accessions that maximizes the genetic diversity within the species and Col-0 (the reference accession) were grown vertically on agar medium at moderate (N+) nitrate level for 6 days and then transferred to the same condition or to low (N-) nitrate concentration for 7 days. There was a major nutritional effect on the shoot biomass and root to shoot biomass ratio. The variation of the root biomass and RSA traits (primary root length, LRs number, LR mean length, total LRs length and LR densities) was primarily genetically determined. Differences in RSA traits between accessions were somewhat more pronounced at N-. Some accessions produced almost no visible LRs (Pyl-1, N13) at N-, while other produced up to a dozen (Kn-0). Taken together our data illustrate that natural variation exists within Arabidopsis for the studied traits. The identification of RSA ideotypes in the N response will facilitate further analysis of quantitative traits for root morphology.
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Affiliation(s)
- Jérôme De Pessemier
- Lab. of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Campus Plaine CP 242, Bd du Triomphe, 1050 Brussels, Belgium.
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50
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Roycewicz P, Malamy JE. Dissecting the effects of nitrate, sucrose and osmotic potential on Arabidopsis root and shoot system growth in laboratory assays. Philos Trans R Soc Lond B Biol Sci 2012; 367:1489-500. [PMID: 22527391 PMCID: PMC3321681 DOI: 10.1098/rstb.2011.0230] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Studying the specific effects of water and nutrients on plant development is difficult because changes in a single component can often trigger multiple response pathways. Such confounding issues are prevalent in commonly used laboratory assays. For example, increasing the nitrate concentration in growth media alters both nitrate availability and osmotic potential. In addition, it was recently shown that a change in the osmotic potential of media alters the plant's ability to take up other nutrients such as sucrose. It can also be difficult to identify the initial target tissue of a particular environmental cue because there are correlated changes in development of many organs. These growth changes may be coordinately regulated, or changes in development of one organ may trigger changes in development of another organ as a secondary effect. All these complexities make analyses of plant responses to environmental factors difficult to interpret. Here, we review the literature on the effects of nitrate, sucrose and water availability on root system growth and discuss the mechanisms underlying these effects. We then present experiments that examine the impact of nitrate, sucrose and water on root and shoot system growth in culture using an approach that holds all variables constant except the one under analysis. We found that while all three factors also alter root system size, changes in sucrose and osmotic potential also altered shoot system size. In contrast, we found that, when osmotic effects are controlled, nitrate specifically inhibits root system growth while having no effect on shoot system growth. This effectively decreases the root : shoot ratio. Alterations in root : shoot ratio have been widely observed in response to nitrogen starvation, where root growth is selectively increased, but the present results suggest that alterations in this ratio can be triggered across a wide spectrum of nitrate concentrations.
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Affiliation(s)
| | - Jocelyn E. Malamy
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences W519, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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