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Long S, Xie W, Zhao W, Liu D, Wang P, Zhao L. Effects of acid and aluminum stress on seed germination and physiological characteristics of seedling growth in Sophora davidii. PLANT SIGNALING & BEHAVIOR 2024; 19:2328891. [PMID: 38506438 PMCID: PMC10956626 DOI: 10.1080/15592324.2024.2328891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
Sophora davidii, a vital forage species, predominantly thrives in the subtropical karst mountains of Southwest China. Its resilience to poor soil conditions and arid environments renders it an ideal pioneer species for ecological restoration in these regions. This study investigates the influence of acidic, aluminum-rich local soil on the germination and seedling growth physiology of S. davidii. Experiments were conducted under varying degrees of acidity and aluminum stress, employing three pH levels (3.5 to 5.5) and four aluminum concentrations (0.5 to 2.0 mmol·L-1). The results showed that germination rate, germination index, and vigor index of S. davidii seeds were decreased but not significantly under slightly acidic conditions (pH 4.5-5.5), while strong acid (pH = 3.5) significantly inhibited the germination rate, germination index, and vigor index of white spurge seeds compared with the control group. Aluminum stress (≥0.5 mmol·L-1) significantly inhibited the germination rate, germination index, and vigor index of S. davidii seed. Moreover, the seedlings' root systems were sensitive to the changes of aluminum concentration, evident from significant root growth inhibition, characterized by root shortening and color deepening. Notably, under aluminum stress (pH = 4.3), the levels of malondialdehyde and proline in S. davidii escalated with increasing aluminum concentration, while antioxidant enzyme activities demonstrated an initial increase followed by a decline. The study underscores the pivotal role of cellular osmoregulatory substances and protective enzymes in combating aluminum toxicity in S. davidii, a key factor exacerbating growth inhibition in acidic environments. These findings offer preliminary theoretical insights for the practical agricultural utilization of S. davidii in challenging soil conditions.
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Affiliation(s)
- Sisi Long
- College of Animal Science, Guizhou University, Guiyang, China
| | - Wenhui Xie
- College of Animal Science, Guizhou University, Guiyang, China
| | - Wenwu Zhao
- College of Animal Science, Guizhou University, Guiyang, China
| | - Danyang Liu
- College of Forestry, Guizhou University, Guiyang, China
| | - Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Lili Zhao
- College of Animal Science, Guizhou University, Guiyang, China
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2
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Liu C, Cheng H, Wang S, Yu D, Wei Y. Physiological and Transcriptomic Analysis Reveals That Melatonin Alleviates Aluminum Toxicity in Alfalfa ( Medicago sativa L.). Int J Mol Sci 2023; 24:17221. [PMID: 38139053 PMCID: PMC10743983 DOI: 10.3390/ijms242417221] [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: 11/02/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Aluminum (Al) toxicity is the most common factor limiting the growth of alfalfa in acidic soil conditions. Melatonin (MT), a significant pleiotropic molecule present in both plants and animals, has shown promise in mitigating Al toxicity in various plant species. This study aims to elucidate the underlying mechanism by which melatonin alleviates Al toxicity in alfalfa through a combined physiological and transcriptomic analysis. The results reveal that the addition of 5 μM melatonin significantly increased alfalfa root length by 48% and fresh weight by 45.4% compared to aluminum treatment alone. Moreover, the 5 μM melatonin application partially restored the enlarged and irregular cell shape induced by aluminum treatment, resulting in a relatively compact arrangement of alfalfa root cells. Moreover, MT application reduces Al accumulation in alfalfa roots and shoots by 28.6% and 27.6%, respectively. Additionally, MT plays a crucial role in scavenging Al-induced excess H2O2 by enhancing the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), consequently reducing malondialdehyde (MDA) levels. More interestingly, the RNA-seq results reveal that MT application significantly upregulates the expression of xyloglucan endotransglucosylase/hydrolase (XTH) and carbon metabolism-related genes, including those involved in the glycolysis process, as well as sucrose and starch metabolism, suggesting that MT application may mitigate Al toxicity by facilitating the binding of Al to the cell walls, thereby reducing intracellular Al accumulation, and improving respiration and the content of sucrose and trehalose. Taken together, our study demonstrates that MT alleviates Al toxicity in alfalfa by reducing Al accumulation and restoring redox homeostasis. These RNA-seq results suggest that the alleviation of Al toxicity by MT may occur through its influence on cell wall composition and carbon metabolism. This research advances our understanding of the mechanisms underlying MT's effectiveness in mitigating Al toxicity, providing a clear direction for our future investigations into the underlying mechanisms by which MT alleviates Al toxicity in alfalfa.
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Affiliation(s)
| | | | | | - Dashi Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (C.L.); (H.C.); (S.W.)
| | - Yunmin Wei
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (C.L.); (H.C.); (S.W.)
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Xu YX, Lei YS, Huang SX, Zhang J, Wan ZY, Zhu XT, Jin SH. Combined de novo transcriptomic and physiological analyses reveal RyALS3-mediated aluminum tolerance in Rhododendron yunnanense Franch. FRONTIERS IN PLANT SCIENCE 2022; 13:951003. [PMID: 36035662 PMCID: PMC9399778 DOI: 10.3389/fpls.2022.951003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Rhododendron (Ericaceae) not only has ornamental value, but also has great medicinal and edible values. Many Rhododendron species are native to acid soils where aluminum (Al) toxicity limits plant productivity and species distribution. However, it remains unknown how Rhododendron adapts to acid soils. Here, we investigated the physiological and molecular mechanisms of Al tolerance in Rhododendron yunnanense Franch. We found that the shoots of R. yunnanense Franch did not accumulate Al after exposure of seedlings to 50 μM Al for 7 days but predominantly accumulated in roots, suggesting that root Al immobilization contributes to its high Al tolerance. Whole-genome de novo transcriptome analysis was carried out for R. yunnanense Franch root apex in response to 6 h of 50 μM Al stress. A total of 443,639 unigenes were identified, among which 1,354 and 3,413 were up- and down-regulated, respectively, by 6 h of 50 μM Al treatment. Both Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that genes involved in "ribosome" and "cytoskeleton" are overrepresented. Additionally, we identified Al-tolerance homologous genes including a tonoplast-localized ABC transporter RyALS3; 1. Overexpression of RyALS3; 1 in tobacco plants confers transgenic plants higher Al tolerance. However, root Al content was not different between wild-type plants and transgenic plants, suggesting that RyALS3; 1 is responsible for Al compartmentalization within vacuoles. Taken together, integrative transcriptome, physiological, and molecular analyses revealed that high Al tolerance in R. yunnanense Franch is associated with ALS3; 1-mediated Al immobilization in roots.
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Affiliation(s)
- Yan-Xia Xu
- Jiyang College, Zhejiang A&F University, Zhuji, China
- Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Lin’an, China
| | - Yun-Sheng Lei
- Jiyang College, Zhejiang A&F University, Zhuji, China
| | | | - Jing Zhang
- Jiyang College, Zhejiang A&F University, Zhuji, China
| | - Zi-Yun Wan
- Jiyang College, Zhejiang A&F University, Zhuji, China
| | - Xiang-Tao Zhu
- Jiyang College, Zhejiang A&F University, Zhuji, China
| | - Song-Heng Jin
- Jiyang College, Zhejiang A&F University, Zhuji, China
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin’an, China
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Ranjan A, Sinha R, Sharma TR, Pattanayak A, Singh AK. Alleviating aluminum toxicity in plants: Implications of reactive oxygen species signaling and crosstalk with other signaling pathways. PHYSIOLOGIA PLANTARUM 2021; 173:1765-1784. [PMID: 33665830 DOI: 10.1111/ppl.13382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Aluminum (Al) toxicity is a major limiting factor for plant growth and productivity in acidic soil. At pH lower than 5.0 (pH < 5.0), the soluble and toxic form of Al (Al3+ ions) enters root cells and inhibits root growth and uptake of water and nutrients. The organic acids malate, citrate, and oxalate are secreted by the roots and chelate Al3+ to form a non-toxic Al-OA complex, which decreases the entry of Al3+ into the root cells. When Al3+ enters, it leads to the production of reactive oxygen species (ROS) in cells, which are toxic and cause damage to biomolecules like lipids, carbohydrates, proteins, and nucleic acids. When ROS levels rise beyond the threshold, plants activate an antioxidant defense system that comprises of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione S-transferase (GST), ascorbic acid (ASA), phenolics and alkaloids etc., which protect plant cells from oxidative damage by scavenging and neutralizing ROS. Besides, ROS also play an important role in signal transduction and influence many molecular and cellular process like hormone signaling, gene expression, cell wall modification, cell cycle, programed cell death (PCD), and development. In the present review, the mechanisms of Al-induced ROS generation, ROS signaling, and crosstalk with other signaling pathways helping to combat Al toxicity have been summarized, which will help researchers to understand the intricacies of Al-induced plant response at cellular level and plan research for developing Al-toxicity tolerant crops for sustainable agriculture in acid soil-affected regions of the world.
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Affiliation(s)
- Alok Ranjan
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Ragini Sinha
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Tilak Raj Sharma
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | | | - Anil Kumar Singh
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
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Zheng Y, Xiao J, Zheng K, Ma J, He M, Li J, Li M. Transcriptome Profiling Reveals the Effects of Nitric Oxide on the Growth and Physiological Characteristics of Watermelon under Aluminum Stress. Genes (Basel) 2021; 12:genes12111735. [PMID: 34828340 PMCID: PMC8622656 DOI: 10.3390/genes12111735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Excessive aluminum ions (Al3+) in acidic soil can have a toxic effect on watermelons, restricting plant growth and reducing yield and quality. In this study, we found that exogenous application of nitric oxide (NO) could increase the photochemical efficiency of watermelon leaves under aluminum stress by promoting closure of leaf stomata, reducing malondialdehyde and superoxide anion in leaves, and increasing POD and CAT activity. These findings showed that the exogenous application of NO improved the ability of watermelon to withstand aluminum stress. To further reveal the mitigation mechanism of NO on watermelons under aluminum stress, the differences following different types of treatments—normal growth, Al, and Al + NO—were shown using de novo sequencing of transcriptomes. In total, 511 differentially expressed genes (DEGs) were identified between the Al + NO and Al treatment groups. Significantly enriched biological processes included nitrogen metabolism, phenylpropane metabolism, and photosynthesis. We selected 23 genes related to antioxidant enzymes and phenylpropane metabolism for qRT-PCR validation. The results showed that after exogenous application of NO, the expression of genes encoding POD and CAT increased, consistent with the results of the physiological indicators. The expression patterns of genes involved in phenylpropanoid metabolism were consistent with the transcriptome expression abundance. These results indicate that aluminum stress was involved in the inhibition of the photosynthetic pathway, and NO could activate the antioxidant enzyme defense system and phenylpropane metabolism to protect cells and scavenge reactive oxygen species. This study improves our current understanding by comprehensively analyzing the molecular mechanisms underlying NO-induced aluminum stress alleviation in watermelons.
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Ding ZJ, Shi YZ, Li GX, Harberd NP, Zheng SJ. Tease out the future: How tea research might enable crop breeding for acid soil tolerance. PLANT COMMUNICATIONS 2021; 2:100182. [PMID: 34027395 PMCID: PMC8132122 DOI: 10.1016/j.xplc.2021.100182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/28/2021] [Accepted: 03/23/2021] [Indexed: 05/15/2023]
Abstract
Unlike most crops, in which soil acidity severely limits productivity, tea (Camellia sinensis) actually prefers acid soils (pH 4.0-5.5). Specifically, tea is very tolerant of acidity-promoted aluminum (Al) toxicity, a major factor that limits the yield of most other crops, and it even requires Al for optimum growth. Understanding tea Al tolerance and Al-stimulatory mechanisms could therefore be fundamental for the future development of crops adapted to acid soils. Here, we summarize the Al-tolerance mechanisms of tea plants, propose possible mechanistic explanations for the stimulation of tea growth by Al based on recent research, and put forward ideas for future crop breeding for acid soils.
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Affiliation(s)
- Zhong Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan Zhi Shi
- Tea Research Institute, Chinese Academy of Agriculture Sciences, Key Laboratory for Tea Plant Biology and Resource Utilization, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Gui Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nicholas P. Harberd
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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Wang P, Dong Y, Zhu L, Hao Z, Hu L, Hu X, Wang G, Cheng T, Shi J, Chen J. The role of γ-aminobutyric acid in aluminum stress tolerance in a woody plant, Liriodendron chinense × tulipifera. HORTICULTURE RESEARCH 2021; 8:80. [PMID: 33790239 PMCID: PMC8012378 DOI: 10.1038/s41438-021-00517-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 05/26/2023]
Abstract
The aluminum (Al) cation Al3+ in acidic soil shows severe rhizotoxicity that inhibits plant growth and development. Most woody plants adapted to acidic soils have evolved specific strategies against Al3+ toxicity, but the underlying mechanism remains elusive. The four-carbon amino acid gamma-aminobutyric acid (GABA) has been well studied in mammals as an inhibitory neurotransmitter; GABA also controls many physiological responses during environmental or biotic stress. The woody plant hybrid Liriodendron (L. chinense × tulipifera) is widely cultivated in China as a horticultural tree and provides high-quality timber; studying its adaptation to high Al stress is important for harnessing its ecological and economic potential. Here, we performed quantitative iTRAQ (isobaric tags for relative and absolute quantification) to study how protein expression is altered in hybrid Liriodendron leaves subjected to Al stress. Hybrid Liriodendron shows differential accumulation of several proteins related to cell wall biosynthesis, sugar and proline metabolism, antioxidant activity, cell autophagy, protein ubiquitination degradation, and anion transport in response to Al damage. We observed that Al stress upregulated glutamate decarboxylase (GAD) and its activity, leading to increased GABA biosynthesis. Additional GABA synergistically increased Al-induced antioxidant enzyme activity to efficiently scavenge ROS, enhanced proline biosynthesis, and upregulated the expression of MATE1/2, which subsequently promoted the efflux of citrate for chelation of Al3+. We also showed similar effects of GABA on enhanced Al3+ tolerance in Arabidopsis. Thus, our findings suggest a function of GABA signaling in enhancing hybrid Liriodendron tolerance to Al stress through promoting organic acid transport and sustaining the cellular redox and osmotic balance.
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Affiliation(s)
- Pengkai Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China
| | - Yini Dong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Liming Zhu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - LingFeng Hu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Liu H, Chen H, Ding G, Li K, Ren Q. Identification of candidate genes conferring tolerance to aluminum stress in Pinus massoniana inoculated with ectomycorrhizal fungus. BMC PLANT BIOLOGY 2020; 20:521. [PMID: 33198640 PMCID: PMC7667757 DOI: 10.1186/s12870-020-02719-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/25/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Pinus massoniana Lamb. is an important afforestation tree species with high economic, ecological and medicinal values. Aluminum (Al) toxicity driven by soil acidification causes dieback of P. massoniana plantations. Previous studies showed that ectomycorrhizal fungi alleviate Al stress damages in Pinus, but the underlying molecular mechanisms and key genes induced by ectomycorrhizal fungi inoculation under Al stress in Pinus have not been explored. Herein, we applied Al stress for 60 days to P. massoniana seedlings inoculated with Suillus luteus (SL) and those non-inoculated. Then, we compared their growth parameters and transcriptome in order to detect candidate genes induced by SL conferring Al tolerance in P. massoniana. RESULT Our results showed that SL inoculation confers Al stress tolerance in P. massoniana through improved growth performance, strong antioxidant enzyme activities and reduced malondialdehyde accumulation as compared to non-inoculated seedlings. Transcriptome sequencing further supported these findings as very few genes (51 genes) were transcriptionally altered by Al in SL inoculated plants as compared to non-inoculated plants (2140 genes). We identified three core genes (cox1, cox3 and Nd1) that were strongly up-regulated by Al in the SL inoculated plants but were down-regulated in the non-inoculated plants. We also identified 42 genes specifically regulated by SL inoculated plants under Al stress, which are involved in a wide range of biological processes such as antioxidative response, transporters, hormone signaling and plant pathogen infection responses. CONCLUSIONS Altogether, our data suggest that SL inoculation induces priming of key stress response pathways and triggers specific genes that efficiently alleviate Al stress effects in P. massoniana. The candidate genes resources generated in this study are of utmost importance for functional characterization and molecular studies aiming at improving Al tolerance in plants.
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Affiliation(s)
- Haiyan Liu
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
- Guizhou Botanical Garden, Guiyang, 550004, Guizhou, China
| | - Houying Chen
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
| | - Guijie Ding
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China.
| | - Kuaifen Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang, 550025, Guizhou, China
| | - Qifei Ren
- Guizhou Botanical Garden, Guiyang, 550004, Guizhou, China
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Ma Z, Lin S. Transcriptomic Revelation of Phenolic Compounds Involved in Aluminum Toxicity Responses in Roots of Cunninghamia lanceolata (Lamb.) Hook. Genes (Basel) 2019; 10:genes10110835. [PMID: 31652726 PMCID: PMC6896160 DOI: 10.3390/genes10110835] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/09/2019] [Accepted: 10/18/2019] [Indexed: 11/17/2022] Open
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often inhibited by aluminum (Al) toxicity in acidic soils of South China. Understanding the molecular mechanisms of Chinese fir root responses to Al toxicity might help to further increase its productivity. Here we used the Illumina Hiseq4000 platform to carry out transcriptome analysis of Chinese fir roots subjected to Al toxicity conditions. A total of 88.88 Gb of clean data was generated from 12 samples and assembled into 105,732 distinct unigenes. The average length and N50 length of these unigenes were 839 bp and 1411 bp, respectively. Among them, 58362 unigenes were annotated through searches of five public databases (Nr: NCBI non-redundant protein sequences, Swiss-Prot: A manually annotated and reviewed protein sequence database, GO: Gene Ontology, KOG/COG: Clusters of Orthologous Groups of proteins, and KEGG: the Kyoto Encyclopedia of Genes and Genomes database), which led to association of unigenes with 44 GO terms. Plus, 1615 transcription factors (TFs) were functionally classified. Then, differentially expressed genes (DEGs, |log2(fold change)| ≥ 1 and FDR ≤ 0.05) were identified in comparisons labelled TC1 (CK-72 h/CK-1 h) and TC2 (Al-72 h/Al-1 h). A large number of TC2 DEGs group were identified, with most being down-regulated under Al stress, while TC1 DEGs were primarily up-regulated. Combining GO, KEGG, and MapMan pathway analysis indicated that many DEGs are involved in primary metabolism, including cell wall metabolism and lipid metabolism, while other DEGs are associated with signaling pathways and secondary metabolism, including flavonoids and phenylpropanoids metabolism. Furthermore, TFs identified in TC1 and TC2 DEGs represented 21 and 40 transcription factor families, respectively. Among them, expression of bHLH, C2H2, ERF, bZIP, GRAS, and MYB TFs changed considerably under Al stress, which suggests that these TFs might play crucial roles in Chinese fir root responses to Al toxicity. These differentially expressed TFs might act in concert with flavonoid and phenylpropanoid pathway genes in fulfilling of key roles in Chinese fir roots responding to Al toxicity.
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Affiliation(s)
- Zhihui Ma
- Institute for Forest Resources and Environment of Guizhou,Guizhou University,Guiyang 550025, China.
| | - Sizu Lin
- State Forestry Administration Engineering Research Center of Chinese Fir, Fuzhou 350002, China.
- College of Forestry, Fujian Agricultural and Forestry University, Fuzhou 350002, China.
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Cardoso TB, Pinto RT, Paiva LV. Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp. PLoS One 2019; 14:e0223217. [PMID: 31600239 PMCID: PMC6786596 DOI: 10.1371/journal.pone.0223217] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/16/2019] [Indexed: 11/23/2022] Open
Abstract
The adaptation of crops to acid soils is needed for the maintenance of food security in a sustainable way, as decreasing fertilizers use and mechanical interventions in the soil would favor the reduction of agricultural practices' environmental impact. Phosphate deficiency and the presence of reactive aluminum affect vital processes to the plant in this soil, mostly water and nutrient absorption. From this, the understanding of the molecular response to these stresses can foster strategies for genetic improvement, so the aim was to broadly analyze the transcriptional variations in Poupulus spp. in response to these abiotic stresses, as a plant model for woody crops. A co-expression network was constructed among 3,180 genes differentially expressed in aluminum-stressed plants with 34,988 connections. Of this total, 344 genes presented two-fold transcriptional variation and the group of genes associated with those regulated after 246 hours of stress had higher number of connections per gene, with some already characterized genes related to this stress as main hubs. Another co-expression network was made up of 8,380 connections between 550 genes regulated by aluminum stress and phosphate deficiency, in which 380 genes had similar profile in both stresses and only eight with transcriptional variation higher than 20%. All the transcriptomic data are presented here with functional enrichment and homology comparisons with already characterized genes in another species that are related to the explored stresses, in order to provide a broad analysis of the co-opted responses for both the stresses as well as some specificity. This approach improves our understanding regarding the plants adaptation to acid soils and may contribute to strategies of crop genetic improvement for this condition that is widely present in regions of high agricultural activity.
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Affiliation(s)
- Thiago Bergamo Cardoso
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Renan Terassi Pinto
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil
| | - Luciano Vilela Paiva
- Central Laboratory of Molecular Biology, Department of Chemistry, Federal University of Lavras, Lavras, Brazil
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Aluminum stress differentially affects physiological performance and metabolic compounds in cultivars of highbush blueberry. Sci Rep 2019; 9:11275. [PMID: 31375763 PMCID: PMC6677737 DOI: 10.1038/s41598-019-47569-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 07/18/2019] [Indexed: 11/08/2022] Open
Abstract
Aluminum (Al) toxicity is one of the major factors that limit the growth and production of crops in acid soils. Highbush blueberry (Vaccinium corymbosum L.) cultivars differing in resistance to Al toxicity regarding root growth and photosynthetic performance were used. In this study, we compared the physiological and metabolic strategies to cope with Al toxicity among the highbush blueberry cultivars [two new ones (Camellia and Cargo) and three established ones (Brigitta (Al-resistant), Star and Duke)]. Aluminum concentration in roots and leaves increased in all cultivars after 24 and 48 h of exposure to Al, but less so in roots of cultivar Camellia and leaves of cultivar Cargo. These two cultivars displayed minor effects of Al exposure in terms of photosynthetic activity in comparison with the established cultivars. Furthermore, Cargo did not vary fluorescence parameters, whereas Camellia exhibited a decrease in effective quantum yield (ΦPSII) and electron transport rate (ETR) and a change in non-photochemical quenching (NPQ) and maximum quantum yield (Fv/Fm) under Al after 48 h. The Al treatment increased total phenols in leaves of Brigitta, Cargo, and Camellia, whereas antioxidant activity increased in Star and Cargo after 48 h. Aluminum exposure decreased malate concentration in roots of all cultivars, but no change was noted in fumarate concentration. The antioxidant activity correlated with photosynthetic performance and the total phenol concentration in the leaves of new cultivars exposed to Al, suggesting enhanced resistance in the short-term experiment. The principal component analysis separated the new from the established cultivars. In conclusion, the new cultivars appear to be more Al-resistant than the established ones, with Star being most Al-sensitive. Regarding the Al-resistance mechanisms of the new cultivars, it is suggested that Camellia could have a root Al-exclusion mechanism under Al toxicity. This mechanism could be explained by low Al concentration in roots, suggesting that this cultivar could exude organic acid, allowing to chelate Al in the rhizosphere. Nonetheless, further researches are needed to confirm this assumption.
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Böhlenius H, Asp H, Hjelm K. Differences in Al sensitivity affect establishment of Populus genotypes on acidic forest land. PLoS One 2018; 13:e0204461. [PMID: 30256819 PMCID: PMC6157885 DOI: 10.1371/journal.pone.0204461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/07/2018] [Indexed: 11/19/2022] Open
Abstract
Forest lands hold great potential for Populus plantations, but in native boreal forests, soils normally have low pH and thus higher levels of aluminum ions (Al3+ and hydroxides). Aluminum (Al) is one of the major factors limiting plant growth on these soils by inhibiting root growth, thus reducing water and nutrient uptake and slowing growth. There is a large variation in Al resistance both among and within species. In this study, growth responses of greenhouse-grown hybrid aspen (P. tremula × tremuloides) and poplar (P. trichocarpa hybrids) were monitored in relation to changes in Al concentrations. In quartz sand, hybrid aspen was more tolerant to exogenous application of Al than P. trichocarpa hybrids. This difference in Al-tolerance was further confirmed by hematoxylin staining of the roots, with hybrid aspen displaying less staining after Al treatment than poplar clones. When planted on forest land with low pH, hybrid aspen increased growth after planting and showed low mortality. This was not the case for poplar clones; plant height decreased after planting and mortality increased. Together, our results suggest that differences in initial growth and survival on forest land among hybrid aspen and the tested poplar clones may be connected to differences in Al tolerance. Our findings that staining with hematoxylin can identify Al-tolerant Populus genotypes may help identify Al-tolerant genotypes suitable for forest land.
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Affiliation(s)
- Henrik Böhlenius
- Swedish University of Agricultural Sciences, Department of Southern Swedish Forest Research Centre, Alnarp, Sweden
- * E-mail:
| | - Håkan Asp
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Alnarp, Sweden
| | - Karin Hjelm
- The Forestry Research Institute of Sweden (Skogforsk), Ekebo 2250, Svalöv, Sweden
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Zhu J, Yu Z, He L, Cao X, Liu S, Song X. Molecular Mechanism of Modified Clay Controlling the Brown Tide Organism Aureococcus anophagefferens Revealed by Transcriptome Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7006-7014. [PMID: 29768919 DOI: 10.1021/acs.est.7b05172] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The data and experiences in mitigating harmful algal blooms (HABs) by modified clay (MC) show that a bloom does not continue after the dispersal of the MC, even though the density of the residual cells in the water is still high, at 20-30% of the initial cell density. This interesting phenomenon indicates that in addition to flocculation, MC has an additional control mechanism. Here, transcriptome sequencing technology was used to study the molecular mechanism of MC in controlling HABs. In residual cells treated with MC, the photosynthetic light reaction was the most affected physiological process. Some genes related to the light harvesting complex, photosystem (PS) I and PS II, were significantly up-regulated ( p < 0.05), and several transcripts increased by as much as 6-fold. In contrast, genes associated with the dark reaction did not significantly change. In addition to genes associated with photosynthesis, numerous genes related to energy metabolism, stress adaptation, cytoskeletal functioning, and cell division also responded to MC treatment. These results indicated that following treatment with MC, the normal physiological processes of algal cells were disrupted, which inhibited cell proliferation and growth. Thus, these findings provide scientific proof that HABs are controlled by MC.
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Affiliation(s)
- Jianan Zhu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- Functional Laboratory of Marine Ecology and Environmental Science , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- Functional Laboratory of Marine Ecology and Environmental Science , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- Functional Laboratory of Marine Ecology and Environmental Science , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology , Chinese Academy of Sciences , Qingdao 266071 , China
- Functional Laboratory of Marine Ecology and Environmental Science , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266237 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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Li N, Meng H, Xing H, Liang L, Zhao X, Luo K. Genome-wide analysis of MATE transporters and molecular characterization of aluminum resistance in Populus. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5669-5683. [PMID: 29099944 PMCID: PMC5853298 DOI: 10.1093/jxb/erx370] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/28/2017] [Indexed: 05/21/2023]
Abstract
Ionic aluminum (Al) in acidic soils, comprising approximately 50% of arable land globally, is highly toxic to most plant species. Populus grow naturally in acidic soils and tolerate high concentrations of Al. Multidrug and toxic compound extrusion (MATE) family genes in plants are involved in responses to Al tolerance. To date, however, the functional roles of the MATE genes in Populus remain unclear. In the present study, 71 putative MATE transporters were predicted in the genome of Populus trichocarpa. The chromosome distribution, phylogenetic relationships, and expression level analysis revealed that four candidate MATE genes belonging to subgroup IIIc might contribute to high Al tolerance in poplar. Further, the expression levels of two subgroup IIIc members, PtrMATE1 and PtrMATE2, were induced by Al stress. Transient expression in onion epidermal cells showed that PtrMATE1 was localized to the plasma membrane. Overexpression of PtrMATE1 increased Al-induced secretion of citrate from the root apex of transgenic plants. Al-induced inhibition of root growths were alleviated in both PtrMATE1 overexpression lines in Populus and in Arabidopsis compared with wild-type plants. In addition, PtrMATE1 expression was induced at 12 h after exposure to Al stress whereas PtrMATE2 expression was induced at 24 h, indicating that these proteins coordinately function in response to Al stress in poplar. Taken together, these results provide important insights into the molecular mechanisms involved in Al tolerance in poplar.
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Affiliation(s)
- Nannan Li
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
- College of Resources and Environment, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hongjun Meng
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Haitao Xing
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Lan Liang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Xin Zhao
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
| | - Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, China
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15
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Kusunoki K, Nakano Y, Tanaka K, Sakata Y, Koyama H, Kobayashi Y. Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance. PLANT, CELL & ENVIRONMENT 2017; 40:249-263. [PMID: 27861992 DOI: 10.1111/pce.12866] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 10/28/2016] [Accepted: 10/30/2016] [Indexed: 05/10/2023]
Abstract
Differences in the expression levels of aluminium (Al) tolerance genes are a known determinant of Al tolerance among plant varieties. We combined transcriptomic analysis of six Arabidopsis thaliana accessions with contrasting Al tolerance and a reverse genetic approach to identify Al-tolerance genes responsible for differences in Al tolerance between accession groups. Gene expression variation increased in the signal transduction process under Al stress and in growth-related processes in the absence of stress. Co-expression analysis and promoter single nucleotide polymorphism searching suggested that both trans-acting polymorphisms of Al signal transduction pathway and cis-acting polymorphisms in the promoter sequences caused the variations in gene expression associated with Al tolerance. Compared with the wild type, Al sensitivity increased in T-DNA knockout (KO) lines for five genes, including TARGET OF AVRB OPERATION1 (TAO1) and an unannotated gene (At5g22530). These were identified from 53 Al-inducible genes showing significantly higher expression in tolerant accessions than in sensitive accessions. These results indicate that the difference in transcriptional signalling is partly associated with the natural variation in Al tolerance in Arabidopsis. Our study also demonstrates the feasibility of comparative transcriptome analysis by using natural genetic variation for the identification of genes responsible for Al stress tolerance.
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Affiliation(s)
- Kazutaka Kusunoki
- Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yuki Nakano
- Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Yoichi Sakata
- Department of BioScience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Hiroyuki Koyama
- Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yuriko Kobayashi
- Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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Bojórquez-Quintal E, Escalante-Magaña C, Echevarría-Machado I, Martínez-Estévez M. Aluminum, a Friend or Foe of Higher Plants in Acid Soils. FRONTIERS IN PLANT SCIENCE 2017; 8:1767. [PMID: 29075280 PMCID: PMC5643487 DOI: 10.3389/fpls.2017.01767] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 09/27/2017] [Indexed: 05/11/2023]
Abstract
Aluminum (Al) is the most abundant metal in the earth's crust, but its availability depends on soil pH. Despite this abundance, Al is not considered an essential element and so far no experimental evidence has been put forward for a biological role. In plants and other organisms, Al can have a beneficial or toxic effect, depending on factors such as, metal concentration, the chemical form of Al, growth conditions and plant species. Here we review recent advances in the study of Al in plants at physiological, biochemical and molecular levels, focusing mainly on the beneficial effect of Al in plants (stimulation of root growth, increased nutrient uptake, the increase in enzyme activity, and others). In addition, we discuss the possible mechanisms involved in improving the growth of plants cultivated in soils with acid pH, as well as mechanisms of tolerance to the toxic effect of Al.
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Affiliation(s)
- Emanuel Bojórquez-Quintal
- CONACYT-Laboratorio de Análisis y Diagnóstico del Patrimonio, El Colegio de Michoacán, La Piedad, Mexico
| | - Camilo Escalante-Magaña
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Ileana Echevarría-Machado
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Manuel Martínez-Estévez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Manuel Martínez-Estévez,
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Li H, Du H, Huang K, Chen X, Liu T, Gao S, Liu H, Tang Q, Rong T, Zhang S. Identification, and Functional and Expression Analyses of the CorA/MRS2/MGT-Type Magnesium Transporter Family in Maize. PLANT & CELL PHYSIOLOGY 2016; 57:1153-68. [PMID: 27084594 DOI: 10.1093/pcp/pcw064] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 03/22/2016] [Indexed: 05/24/2023]
Abstract
Magnesium (Mg(2+)) is an essential macronutrient for plant growth and development, and the CorA/MRS2/MGT-type Mg(2+) transporters play important roles in maintaining Mg(2+) homeostasis in plants. Although the MRS2/MGT genes have been identified in two model plant species, Arabidopsis and rice, a comprehensive analysis of the MRS2/MGT gene family in other plants is lacking. In this work, 12 putative MRS2/MGT genes (ZmMGT1- ZmMGT12) were identified in maize and all of them were classified into five distinct subfamilies by phylogenetic analysis. A complementation assay in the Salmonella typhimurium MM281 strain showed that five representatives of the 12 members possess Mg(2+) transport abilities. Inhibition of ZmMGT protein activity using the hexaamminecobalt (III) (Co-Hex) inhibitor indicated that the ZmMGT protein mediated both low-affinity and high-affinity Mg(2+) transport in maize. A semi-quantitative reverse transcription-PCR (RT-PCR) analysis revealed that eight genes were constitutively expressed in all of the detected tissues, with one being specifically expressed in roots and three having no detectable expression signals. A quantitative RT-PCR analysis showed that some ZmMGT members displayed differential responses to Mg(2+) deficiency and aluminum (Al) stress. Furthermore, root growth inhibition and Mg(2+) accumulation analyses in two maize inbred lines, which conferred different levels of Al tolerance, revealed that ZmMGT proteins contributed to the Al resistance of the Al tolerance genotype. We hypothesize that ZmMGT family members function as Mg(2+) transporters and may play a role in linking Mg(2+) deficiency and Al stress responses. Our results will be valuable in a further analysis of the important biological functions of ZmMGT members in maize.
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Affiliation(s)
- Hongyou Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hanmei Du
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kaifeng Huang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Chen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianyu Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hailan Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Qilin Tang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingzhao Rong
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Suzhi Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest China of Agricultural Department, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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Larsen PE, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke LJ, Collart FR. Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. FRONTIERS IN PLANT SCIENCE 2016; 6:1061. [PMID: 26834754 PMCID: PMC4717292 DOI: 10.3389/fpls.2015.01061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/16/2015] [Indexed: 05/29/2023]
Abstract
In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root-mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree) and Laccaria bicolor (mycorrhizal fungi) interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with 15 transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.
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Affiliation(s)
- Peter E. Larsen
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Avinash Sreedasyam
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Geetika Trivedi
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Shalaka Desai
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at ChicagoChicago IL, USA
| | - Leland J. Cseke
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences DivisionLemont, IL, USA
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Wang Y, Xu L, Tang M, Jiang H, Chen W, Zhang W, Wang R, Liu L. Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure. FRONTIERS IN PLANT SCIENCE 2016; 7:1871. [PMID: 28018404 PMCID: PMC5156831 DOI: 10.3389/fpls.2016.01871] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/28/2016] [Indexed: 05/22/2023]
Abstract
Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L-1(Pb500) and 1000 mg L-1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included "cell wall," "apoplast," "response to metal ion," "vacuole," and "peroxidase activity," and the critical enriched pathways were involved in "citric acid (TCA) cycle and respiratory electron transport," "pyruvate metabolism," "phenylalanine metabolism," "phenylpropanoid biosynthesis," and "carbon metabolism." Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)-glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.
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Gould B, McCouch S, Geber M. De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment. PLoS One 2015; 10:e0124424. [PMID: 26148203 PMCID: PMC4493143 DOI: 10.1371/journal.pone.0124424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 03/13/2015] [Indexed: 11/18/2022] Open
Abstract
Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.
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Affiliation(s)
- Billie Gould
- Department of Plant Biology, Plant Biology Laboratories, Michigan State University, East Lansing, MI 48824, United States of America
| | - Susan McCouch
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall Tower Rd, Ithaca, NY 14853, United States of America
| | - Monica Geber
- Department of Plant Breeding and Genetics, Cornell University, Emerson Hall Tower Rd, Ithaca, NY 14853, United States of America
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Zhou XX, Yang LT, Qi YP, Guo P, Chen LS. Mechanisms on boron-induced alleviation of aluminum-toxicity in Citrus grandis seedlings at a transcriptional level revealed by cDNA-AFLP analysis. PLoS One 2015; 10:e0115485. [PMID: 25747450 PMCID: PMC4352013 DOI: 10.1371/journal.pone.0115485] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/24/2014] [Indexed: 11/18/2022] Open
Abstract
The physiological and biochemical mechanisms on boron (B)-induced alleviation of aluminum (B)-toxicity in plants have been examined in some details, but our understanding of the molecular mechanisms underlying these processes is very limited. In this study, we first used the cDNA-AFLP to investigate the gene expression patterns in Citrus grandis roots responsive to B and Al interactions, and isolated 100 differentially expressed genes. Results showed that genes related to detoxification of reactive oxygen species (ROS) and aldehydes (i.e., glutathione S-transferase zeta class-like isoform X1, thioredoxin M-type 4, and 2-alkenal reductase (NADP+-dependent)-like), metabolism (i.e., carboxylesterases and lecithin-cholesterol acyltransferase-like 4-like, nicotianamine aminotransferase A-like isoform X3, thiosulfate sulfurtransferase 18-like isoform X1, and FNR, root isozyme 2), cell transport (i.e., non-specific lipid-transfer protein-like protein At2g13820-like and major facilitator superfamily protein), Ca signal and hormone (i.e., calcium-binding protein CML19-like and IAA-amino acid hydrolase ILR1-like 4-like), gene regulation (i.e., Gag-pol polyprotein) and cell wall modification (i.e., glycosyl hydrolase family 10 protein) might play a role in B-induced alleviation of Al-toxicity. Our results are useful not only for our understanding of molecular processes associated with B-induced alleviation of Al-toxicity, but also for obtaining key molecular genes to enhance Al-tolerance of plants in the future.
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Affiliation(s)
- Xin-Xing Zhou
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin-Tong Yang
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical Sciences, Fuzhou 350001, China
| | - Peng Guo
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li-Song Chen
- College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Horticultural Plant Physiology, Biochemistry and Molecular Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory for Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- * E-mail:
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Ariani A, Di Baccio D, Romeo S, Lombardi L, Andreucci A, Lux A, Horner DS, Sebastiani L. RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc. PLoS One 2015; 10:e0117571. [PMID: 25671786 PMCID: PMC4324836 DOI: 10.1371/journal.pone.0117571] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/28/2014] [Indexed: 11/19/2022] Open
Abstract
Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE) genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated) and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO) terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1) probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS) that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.
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Affiliation(s)
- Andrea Ariani
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Daniela Di Baccio
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Stefania Romeo
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
| | - Lara Lombardi
- Department of Biology, Università degli Studi di Pisa, I-56126 Pisa, Italy
| | - Andrea Andreucci
- Department of Biology, Università degli Studi di Pisa, I-56126 Pisa, Italy
| | - Alexander Lux
- Department of Plant Physiology, Faculty of Natural Science, Comenius University in Bratislava, Bratislava, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Luca Sebastiani
- BioLabs-Institute of Life Sciences, Scuola Superiore Sant'Anna, I-56127 Pisa, Italy
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Rengel Z, Bose J, Chen Q, Tripathi BN. Magnesium alleviates plant toxicity of aluminium and heavy metals. CROP AND PASTURE SCIENCE 2015; 66:1298. [PMID: 0 DOI: 10.1071/cp15284] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Magnesium (Mg) is an essential nutrient that can alleviate soilborne toxicity of many ions. This review paper critically assesses the literature on interactions and mechanisms influencing Mg alleviation of aluminium (Al) and heavy metal toxicity. Hydrated radii of Mg2+ and Al3+ are similar; therefore, these two ions compete for binding to ion transporters and other important biological molecules. In monocotyledonous species such as rice and wheat, millimolar concentrations of Mg alleviate Al toxicity, mainly by decreasing Al saturation and activity at cell wall and plasma membrane binding sites. In dicotyledonous legume species such as soybean (Glycine max), rice bean (Vigna umbellata) and broad bean (Vicia faba), micromolar concentrations of Mg may enhance biosynthesis of organic ligands and thus underpin alleviation of Al toxicity. Resistance to Al may be enhanced by increased expression of the genes coding for Mg transporters, as well as by upregulation of activity of Mg-transport proteins; intracellular Mg2+ activity may thus be increased under Al stress, which may increase the activity of H+-ATPases. In Vicia faba, Mg-related enhancement in the activity of plasma membrane H+-ATPase under Al stress was found to be due to post-translational modification (increased phosphorylation of the penultimate threonine as well as association with regulatory 14-3-3 proteins), resulting in increased resistance to Al stress. Magnesium can alleviate heavy metal stress by decreasing negative electrical potential and thus metal ion activities at the plasma membrane surface (physico-chemical competition), by enhancing activities of enzymes involved in biosynthesis of organic ligands, and by increasing vacuolar sequestration of heavy metals via increasing H+-pumping activity at the tonoplast. Future work should concentrate on characterising the role of intracellular Mg2+ homeostasis and Mg transporters in alleviating metal stress as well as in transcriptional, translational and post-translational regulation of H+-pumps and enzymes involved in biosynthesis and exudation of organic ligands.
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Arenhart RA, Bai Y, Valter de Oliveira LF, Bucker Neto L, Schunemann M, Maraschin FDS, Mariath J, Silverio A, Sachetto-Martins G, Margis R, Wang ZY, Margis-Pinheiro M. New insights into aluminum tolerance in rice: the ASR5 protein binds the STAR1 promoter and other aluminum-responsive genes. MOLECULAR PLANT 2014; 7:709-21. [PMID: 24253199 PMCID: PMC3973494 DOI: 10.1093/mp/sst160] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 11/05/2013] [Indexed: 05/18/2023]
Abstract
Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. Here, we perform genome-wide analyses to identify ASR5-dependent Al-responsive genes in rice. Based on ASR5_RNAi silencing in plants, a global transcriptome analysis identified a total of 961 genes that were responsive to Al treatment in wild-type rice roots. Of these genes, 909 did not respond to Al in the ASR5_RNAi plants, indicating a central role for ASR5 in Al-responsive gene expression. Under normal conditions, without Al treatment, the ASR5_RNAi plants expressed 1.756 genes differentially compared to the wild-type plants, and 446 of these genes responded to Al treatment in the wild-type plants. Chromatin immunoprecipitation followed by deep sequencing identified 104 putative target genes that were directly regulated by ASR5 binding to their promoters, including the STAR1 gene, which encodes an ABC transporter required for Al tolerance. Motif analysis of the binding peak sequences revealed the binding motif for ASR5, which was confirmed via in vitro DNA-binding assays using the STAR1 promoter. These results demonstrate that ASR5 acts as a key transcription factor that is essential for Al-responsive gene expression and Al tolerance in rice.
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Affiliation(s)
- Rafael Augusto Arenhart
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
| | - Yang Bai
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Luiz Felipe Valter de Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
| | - Lauro Bucker Neto
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
| | - Mariana Schunemann
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
| | | | - Jorge Mariath
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Adriano Silverio
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | | | - Rogerio Margis
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brasil
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Marcia Margis-Pinheiro
- Programa de Pós-Graduação em Genética e Biologia Molecular Avenida Bento Gonçalves 9500, Departamento de Genética, sala 207, prédio 43312, Universidade Federal do Rio Grande do Sul, 91501–970, Porto Alegre, Brasil
- To whom correspondence should be addressed. E-mail , fax 55-51-3308-7311, tel. 55 (51) 3308–9814
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Wang ZQ, Xu XY, Gong QQ, Xie C, Fan W, Yang JL, Lin QS, Zheng SJ. Root proteome of rice studied by iTRAQ provides integrated insight into aluminum stress tolerance mechanisms in plants. J Proteomics 2014; 98:189-205. [PMID: 24412201 DOI: 10.1016/j.jprot.2013.12.023] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 12/13/2013] [Accepted: 12/27/2013] [Indexed: 01/06/2023]
Abstract
One of the major limitations to crop growth on acid soils is the prevalence of soluble aluminum ions (Al(3+)). Rice (Oryza sativa L.) has been reported to be highly Al tolerant; however, large-scale proteomic data of rice in response to Al(3+) are still very scanty. Here, we used an iTRAQ-based quantitative proteomics approach for comparative analysis of the expression profiles of proteins in rice roots in response to Al(3+) at an early phase. A total of 700 distinct proteins (homologous proteins grouped together) with >95% confidence were identified. Among them, 106 proteins were differentially expressed upon Al(3+) toxicity in sensitive and tolerant cultivars. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was the most significantly up-regulated biochemical process in response to excess Al(3+). The mRNA levels of eight proteins mapped in the glycolysis/gluconeogenesis were further analyzed by qPCR and the expression levels of all the eight genes were higher in tolerant cultivar than in sensitive cultivar, suggesting that these compounds may promote Al tolerance by modulating the production of available energy. Although the exact roles of these putative tolerance proteins remain to be examined, our data lead to a better understanding of the Al tolerance mechanisms in rice plants through the proteomics approach. BIOLOGICAL SIGNIFICANCE Aluminum (mainly Al(3+)) is one of the major limitations to the agricultural productivity on acid soils and causes heavy yield loss every year. Rice has been reported to be highly Al tolerant; however, the mechanisms of rice Al tolerance are still not fully understood. Here, a combined proteomics, bioinformatics and qPCR analysis revealed that Al(3+) invasion caused complex proteomic changes in rice roots involving energy, stress and defense, protein turnover, metabolism, signal transduction, transport and intracellular traffic, cell structure, cell growth/division, and transcription. Promotion of the glycolytic/gluconeogenetic pathway in roots appeared crucially important for Al tolerance. These results lead to a better understanding of the Al tolerance mechanisms in rice and help to improve plant performance on acid soils, eventually to increase the crop production.
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Affiliation(s)
- Zhan Qi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiao Yan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiao Qiao Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Chen Xie
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100101, China.
| | - Wei Fan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jian Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qi Shan Lin
- UAlbany Proteomics Facility, Center for Functional Genomics, University at Albany, Rensselaer, NY 12144, USA.
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Regier N, Baerlocher L, Münsterkötter M, Farinelli L, Cosio C. Analysis of the Elodea nuttallii transcriptome in response to mercury and cadmium pollution: development of sensitive tools for rapid ecotoxicological testing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:8825-8834. [PMID: 23802634 DOI: 10.1021/es401082h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Toxic metals polluting aquatic ecosystems are taken up by inhabitants and accumulate in the food web, affecting species at all trophic levels. It is therefore important to have good tools to assess the level of risk represented by toxic metals in the environment. Macrophytes are potential organisms for the identification of metal-responsive biomarkers but are still underrepresented in ecotoxicology. In the present study, we used next-generation sequencing to investigate the transcriptomic response of Elodea nuttallii exposed to enhanced concentrations of Hg and Cd. We de novo assembled more than 60 000 contigs, of which we found 170 to be regulated dose-dependently by Hg and 212 by Cd. Functional analysis showed that these genes were notably related to energy and metal homeostasis. Expression analysis using nCounter of a subset of genes showed that the gene expression pattern was able to assess toxic metal exposure in complex environmental samples and was more sensitive than other end points (e.g., bioaccumulation, photosynthesis, etc.). In conclusion, we demonstrate the feasibility of using gene expression signatures for the assessment of environmental contamination, using an organism without previous genetic information. This is of interest to ecotoxicology in a wider sense given the possibility to develop specific and sensitive bioassays.
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Affiliation(s)
- Nicole Regier
- Institut F.-A. Forel, University of Geneva , 10 route de Suisse, CP416, 1290 Versoix, Switzerland
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Brunner I, Sperisen C. Aluminum exclusion and aluminum tolerance in woody plants. FRONTIERS IN PLANT SCIENCE 2013; 4:172. [PMID: 23781222 PMCID: PMC3679494 DOI: 10.3389/fpls.2013.00172] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/14/2013] [Indexed: 05/18/2023]
Abstract
The aluminum (Al) cation Al(3) (+) is highly rhizotoxic and is a major stress factor to plants on acid soils, which cover large areas of tropical and boreal regions. Many woody plant species are native to acid soils and are well adapted to high Al(3) (+) conditions. In tropical regions, both woody Al accumulator and non-Al accumulator plants occur, whereas in boreal regions woody plants are non-Al accumulators. The mechanisms of these adaptations can be divided into those that facilitate the exclusion of Al(3) (+) from root cells (exclusion mechanisms) and those that enable plants to tolerate Al(3) (+) once it has entered the root and shoot symplast (internal tolerance mechanisms). The biochemical and molecular basis of these mechanisms have been intensively studied in several crop plants and the model plant Arabidopsis. In this review, we examine the current understanding of Al(3) (+) exclusion and tolerance mechanisms from woody plants. In addition, we discuss the ecology of woody non-Al accumulator and Al accumulator plants, and present examples of Al(3) (+) adaptations in woody plant populations. This paper complements previous reviews focusing on crop plants and provides insights into evolutionary processes operating in plant communities that are widespread on acid soils.
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Affiliation(s)
- Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape ResearchBirmensdorf, Switzerland
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Eckert AJ, Shahi H, Datwyler SL, Neale DB. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:1323-1334. [PMID: 22837407 DOI: 10.3732/ajb.1200055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Plant populations arrayed across sharp environmental gradients are ideal systems for identifying the genetic basis of ecologically relevant phenotypes. A series of five uplifted marine terraces along the northern coast of California represents one such system where morphologically distinct populations of lodgepole pine (Pinus contorta) are distributed across sharp soil gradients ranging from fertile soils near the coast to podzolic soils ca. 5 km inland. METHODS A total of 92 trees was sampled across four coastal marine terraces (N = 10-46 trees/terrace) located in Mendocino County, California and sequenced for a set of 24 candidate genes for growth and responses to various soil chemistry variables. Statistical analyses relying on patterns of nucleotide diversity were employed to identify genes whose diversity patterns were inconsistent with three null models. KEY RESULTS Most genes displayed patterns of nucleotide diversity that were consistent with null models (N = 19) or with the presence of paralogs (N = 3). Two genes, however, were exceptional: an aluminum responsive ABC-transporter with F(ST) = 0.664 and an inorganic phosphate transporter characterized by divergent haplotypes segregating at intermediate frequencies in most populations. CONCLUSIONS Spatially variable natural selection along gradients of aluminum and phosphate ion concentrations likely accounted for both outliers. These results shed light on some of the genetic components comprising the extended phenotype of this ecosystem, as well as highlight ecotones as fruitful study systems for the detection of adaptive genetic variants.
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, 23284, USA.
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Pagariya MC, Devarumath RM, Kawar PG. Biochemical characterization and identification of differentially expressed candidate genes in salt stressed sugarcane. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 184:1-13. [PMID: 22284704 DOI: 10.1016/j.plantsci.2011.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 12/01/2011] [Accepted: 12/02/2011] [Indexed: 05/23/2023]
Abstract
Sugarcane productivity is worldwide subjected to increasing environmental constraints, predominantly to drought and salinity owing to their high magnitude of impact and wide distribution. The present study provides insights into the knowledge of sugarcane responses at germination, tillering and respective recovery stages to high salinity at physio-biochemical and molecular level. Our results indicated that there was a negative relationship between catalase, and peroxidase activity with lipid peroxidation and SOD activity. Increase in MDA and SOD levels at the earlier stages of stress and later increase in CAT and POD levels on prolonged stress was evidenced. Thus they can be used as indicators of stress for sugarcane plants facing unfavourable environmental conditions. At molecular level, we have identified 137 salinity tolerant candidate cDNAs from sugarcane by cDNA-SSH, representing 20% of which are novel sugarcane genes. These unique sequences, never reported elsewhere to be stress related and might provide further understanding on perception, response and adaptations mechanisms of the non-model plant like sugarcane to salinity stress and will be potential candidates for manipulating salt tolerant trait.
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Affiliation(s)
- Madhuri Chandrakant Pagariya
- Molecular Biology & Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk), Tal. Haveli, Pune 412307, Maharashtra, India
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Hao S, Zhao T, Xia X, Yin W. Genome-wide comparison of two poplar genotypes with different growth rates. PLANT MOLECULAR BIOLOGY 2011; 76:575-91. [PMID: 21614644 DOI: 10.1007/s11103-011-9790-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/07/2011] [Indexed: 05/26/2023]
Abstract
The ecologically dominant and economically important genus Populus, with its available full genome sequence, has become an ideal woody species for genomic study. Rapid growth is one of the primary advantageous features of Populus, and extensive physiological research has been carried out on the growth of Populus throughout the growing period among different clones. However, the molecular information related to the mechanisms of rapid growth is rather limited. In this study, an Affymetrix poplar genome array was employed to analyze the transcriptomic changes from the pre-growth to the fast-growth phase in two poplar clones (P.deltoides × P.nigra, DN2, and P.nigra × (P.deltoides × P. nigra), NE19) with different growth rates. A total of 1,695 differently expressed genes were identified between two time points in NE19 and DN2 (two-way ANOVA, P < 0.01 and fold change ≥2). Except for genes changing in common for both clones, many transcripts were regulated specifically in one genotype. After functional analysis of the differentially expressed genes, distinct biological strategies seemed to be utilized by the two genotypes to accommodate their fast-growth phase. The faster-growing clone NE19, which has a higher photosynthetic rate and larger total leaf area, emphasized growth-related primary metabolism. However, the slower-growing DN2 tended to have more up-regulated genes involved in defense-related secondary metabolism and stress response. Emphasis of such divergent biological processes in two clones may explain their significant growth differences during the fast-growth phase.
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Affiliation(s)
- Shuang Hao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People's Republic of China
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Larsen PE, Sreedasyam A, Trivedi G, Podila GK, Cseke LJ, Collart FR. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC SYSTEMS BIOLOGY 2011. [PMID: 21569493 DOI: 10.1186/1752‐0509‐5‐70] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. RESULTS We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. CONCLUSIONS The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.
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Affiliation(s)
- Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60490, USA.
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Larsen PE, Sreedasyam A, Trivedi G, Podila GK, Cseke LJ, Collart FR. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC SYSTEMS BIOLOGY 2011; 5:70. [PMID: 21569493 PMCID: PMC3114729 DOI: 10.1186/1752-0509-5-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/13/2011] [Indexed: 11/29/2022]
Abstract
Background Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. Results We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. Conclusions The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.
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Affiliation(s)
- Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60490, USA.
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