1
|
Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane. Int J Mol Sci 2022; 23:ijms231911603. [PMID: 36232906 PMCID: PMC9569758 DOI: 10.3390/ijms231911603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022] Open
Abstract
Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.
Collapse
|
2
|
Chen ZJ, Qiao YX, Zhang N, Liu J, Yang H. Insight into metabolism pathways of pesticide fomesafen in rice: Reducing cropping and environmental risks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 283:117128. [PMID: 33862343 DOI: 10.1016/j.envpol.2021.117128] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/20/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Fomesafen (FSA) is widely used in soybean fields for weed control. However, the persisting characteristics of FSA in the agricultural soil or water may become a hidden danger causing environmental pollution and phytotoxicity to succession crops. In this study, the growth and physiological responses of rice to FSA were investigated. It was found that the growth of rice seedlings was obviously inhibited by FSA exposure especially at over 0.1 mg L-1. To gain an insight into the molecular mechanisms for the potential ecotoxicology, four libraries of rice roots and shoots exposed to FSA were created and subjected to the global RNA-sequencing (RNA-Seq) combined with HRLC-Q-TOF-MS/MS analytical technologies to comprehensively characterize the biochemical processes and catalytic reactions involved in FSA metabolism in rice. Compared with those without FSA, 499 and 450 up-regulated genes in roots and shoots with FSA were detected. Many of them were closely correlated with the tolerance to environmental stress, detoxification of xenobiotics and molecular metabolism process including cytochrome P450, glutathione S-transferases and acetyltransferase. A total of eight metabolites and fourteen conjugates in the reactive pathways of hydrolysis, substitution, reduction, methylation, glycosylation, acetylation, and malonylation were characterized by HRLC-Q-TOF-MS/MS. The relationship between the metabolized derivatives of FSA and enhanced expression the corresponding enzymatic regulators was established. This study will help understand the mechanisms and pathways of FSA metabolism and inspire the further research on FSA degradation in the paddy crops and environmental or health risks.
Collapse
Affiliation(s)
- Zhao Jie Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yu Xin Qiao
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
3
|
Mishra D, Kumar S, Mishra BN. An Overview of Morpho-Physiological, Biochemical, and Molecular Responses of Sorghum Towards Heavy Metal Stress. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 256:155-177. [PMID: 33866418 DOI: 10.1007/398_2020_61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Heavy metal (HM) contamination is a serious global environmental crisis. Over the past decade, industrial effluents, modern agricultural practices, and other anthropogenic activities have significantly depleted the soil environment. In plants, metal toxicity leads to compromised growth, development, productivity, and yield. Also, HMs negatively affect human health due to food chain contamination. Thus, it is imperative to reduce metal accumulation and toxicity. In nature, certain plant species exhibit an inherent capacity of amassing large amounts of HMs with remarkable tolerance. These plants with unique characteristics can be employed for the remediation of contaminated soil and water. Among different plant species, Sorghum bicolor has the potential of accumulating huge amounts of HMs, thus could be regarded as a hyperaccumulator. This means that it is a metal tolerant, high biomass producing energy crop, and thus can be utilized for phytoremediation. However, high concentrations of HMs hamper plant height, root hair density, shoot biomass, number of leaves, chlorophyll, carotenoid, and carbohydrate content. Thus, understanding the response of Sorghum towards different HMs holds considerable importance. Considering this, we have uncovered the basic information about the metal uptake, translocation, and accumulation in Sorghum. Plants respond to different HMs via sensing, signaling, and modulations in physico-chemical processes. Therefore, in this review, a glimpse of HM toxicity and the response of Sorghum at the morphological, physiological, biochemical, and molecular levels has been provided. The review highlights the future research needs and emphasizes the extensive molecular dissection of Sorghum to explore its genetic adaptability towards different abiotic stresses that can be exploited to develop resilient crop varieties.
Collapse
Affiliation(s)
- Dewanshi Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh, India
| | - Smita Kumar
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India.
| | - Bhartendu Nath Mishra
- Department of Biotechnology, Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
4
|
Yang L, Zhang Y, Wang F, Luo Z, Guo S, Strähle U. Toxicity of mercury: Molecular evidence. CHEMOSPHERE 2020; 245:125586. [PMID: 31881386 DOI: 10.1016/j.chemosphere.2019.125586] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/28/2019] [Accepted: 12/08/2019] [Indexed: 05/25/2023]
Abstract
Minamata disease in Japan and the large-scale poisoning by methylmercury (MeHg) in Iraq caused wide public concerns about the risk emanating from mercury for human health. Nowadays, it is widely known that all forms of mercury induce toxic effects in mammals, and increasing evidence supports the concern that environmentally relevant levels of MeHg could impact normal biological functions in wildlife. The information of mechanism involved in mercurial toxicity is growing but knowledge gaps still exist between the adverse effects and mechanisms of action, especially at the molecular level. A body of data obtained from experimental studies on mechanisms of mercurial toxicity in vivo and in vitro points to that disruption of the antioxidant system may play an important role in the mercurial toxic effects. Moreover, the accumulating evidence indicates that signaling transduction, protein or/and enzyme activity, and gene regulation are involving in mediating toxic and adaptive response to mercury exposure. We conducted here a comprehensive review of mercurial toxic effects on wildlife and human, in particular synthesized key findings of molecular pathways involved in mercurial toxicity from the cells to human. We discuss the molecular evidence related mercurial toxicity to the adverse effects, with particular emphasis on the gene regulation. The further studies relying on Omic analysis connected to adverse effects and modes of action of mercury will aid in the evaluation and validation of causative relationship between health outcomes and gene expression.
Collapse
Affiliation(s)
- Lixin Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China; Center for Global Health, School of Public Health, Nanjing Medical University, 211166, Nanjing, China.
| | - Yuanyuan Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Feifei Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Zidie Luo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Shaojuan Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | - Uwe Strähle
- Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
5
|
Zhang L, Ding H, Jiang H, Wang H, Chen K, Duan J, Feng S, Wu G. Regulation of cadmium tolerance and accumulation by miR156 in Arabidopsis. CHEMOSPHERE 2020; 242:125168. [PMID: 31678850 DOI: 10.1016/j.chemosphere.2019.125168] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/18/2019] [Accepted: 10/20/2019] [Indexed: 05/28/2023]
Abstract
Plants have evolved effective strategies to cope with heavy metals Cd toxicity, but the regulatory mechanism underlying Cd tolerance and accumulation are still poorly understood. miR156 has been shown to be the master regulator of development and stress response in plants. However, whether miR156 is also involved in plant Cd stress response remains unknown. Here, we show that plants overexpressing miR156 (miR156OE) accumulated significantly less Cd in the shoot, and conferred enhanced tolerance to Cd stress. Plants with a knocked-down level of miR156 (MIM156) were sensitive to Cd stress, and accumulated significantly higher Cd. Under Cd stress, miR156OE had significantly longer primary root length, higher biomass and chlorophyll content, increased activities of antioxidative enzymes and lower levels of endogenous reactive oxygen species (ROS), while MIM156 had the opposite phenotype. To investigate the underlying mechanism of miR156-mediated Cd stress response in Arabidopsis, we profiled the expression of several Cd transporter genes. The expression of Cd uptake transporter of AtZIP1、AtZIP2 and vacuole segregated transporter AtABCC1 was significantly elevated in miR156OE, whereas it was significantly reduced in MIM156. MIM156 also led to an elevated level of AtHMA4 responsible for transporting Cd from the root to the shoot. Our results indicate that miR156 acts as a positive regulator of plant tolerance to Cd stress by modulating ROS levels and Cd uptake/transport genes expression. Therefore, our study adds a new layer of regulatory mechanism for Cd transport and tolerance in plants, and provides a perspective to regulate Cd transport artificially by modulating plant vegetative growth and development using miR156.
Collapse
Affiliation(s)
- Lu Zhang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Han Ding
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Hailing Jiang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Huasen Wang
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Kexin Chen
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Jinju Duan
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China; Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
| | - Shengjun Feng
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| | - Gang Wu
- State Key Laboratory of Subtropical Silviculture, Laboratory of Plant Molecular and Developmental Biology, Zhejiang Provincial Key Laboratory of Bioremediation of Soil Contamination, Zhejiang Agriculture and Forestry University, Hangzhou, China.
| |
Collapse
|
6
|
Identification of genomic ATP binding cassette (ABC) transporter genes and Cd-responsive ABCs in Brassica napus. Gene 2018; 664:139-151. [PMID: 29709635 DOI: 10.1016/j.gene.2018.04.060] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/11/2018] [Accepted: 04/19/2018] [Indexed: 12/19/2022]
Abstract
The plant ATP binding cassette (ABC) transporters are one of the integral membrane proteins responsible for uptake and allocation of a wide range of metabolites and xenobiotics including heavy metals (e.g. zinc, manganese and cadmium). They play multiple roles in plant growth, development and environmental stress responses. Although the ABC transporters have been identified in model plants such as Arabidopsis and rice, they are have not been annotated and identified in rapeseed (Brassica napus) and also, little is known about functionality of these metal transporters. B. napus is an important oil crop ranking the third largest source of vegetable oil worldwide. Importantly, it is long considered as a desirable candidate for phytoremediation owning to its massive dry weight productivity and moderate Cd accumulation. In this study, we identified 314 ABC protein genes from B. napus using bioinformatics and high-throughput sequencing. Eight subfamilies including ABCA-G and ABCI have been categorized. The ABCG proteins constitute the largest subfamily with 116 members, and the ABCB and ABCC subfamilies ranks second and third with 69 and 47 members, respectively. Analyses of ABCs in B. napus genome reveal that their evolutional expansion was through localized allele duplications. Most of the ABC genes (74.2%, 233/314) were validated by RNA-sequencing rapeseed seedlings. Among the 233 profiled BnaABCs, 132 genes were differentially expressed (>1.5 fold change, p < 0.05) and 84 genes were significantly induced under Cd stress. Analyses of specific cis-elements in the upstream of eight representative genes show diverse motifs, which potentially respond to environmental stress, hormone responsiveness and other development signals.
Collapse
|
7
|
Beauvais-Flück R, Slaveykova VI, Cosio C. Effects of two-hour exposure to environmental and high concentrations of methylmercury on the transcriptome of the macrophyte Elodea nuttallii. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 194:103-111. [PMID: 29172129 DOI: 10.1016/j.aquatox.2017.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 06/07/2023]
Abstract
The effects of two methylmercury (CH3Hg+, MeHg) concentrations, representative of environmental level and extreme contamination, were investigated on the macrophyte Elodea nuttallii during a 2h-exposure combining transcriptomic (RNA-Seq), physiological endpoints (pigment contents, activity of anti-oxidative stress enzymes) and bioaccumulation. Exposure to MeHg induced the up- and down-regulation of numerous genes (4389 and 16853 for 10ngL-1 and 10μgL-1 MeHg exposure, respectively) involved in sugar, amino acid and secondary metabolism (e.g. cinnamic acid, flavonoids) at both concentrations. Genes coding for photosynthesis, membrane integrity, metal homeostasis, water transport and anti-oxidative enzymes were additionally up- and down-regulated at the higher concentration. At the physiological level, exposure to both MeHg concentrations resulted in a strong increase of anthocyanin content in shoots. Chlorophyll content and antioxidant enzyme activities were unchanged. The data suggest that the macrophyte was able to efficiently cope with the stress resulting from MeHg exposure, possibly by using anthocyanin as anti-oxidant and S-rich amino acids (such as cysteine and methionine) as chelators. Transcriptomics analysis enabled gaining novel insights on molecular effects of MeHg in primary producers, which are one of the main entry pathway of hazardous MeHg in aquatic food webs.
Collapse
Affiliation(s)
- Rebecca Beauvais-Flück
- Department F.-A. Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Vera I Slaveykova
- Department F.-A. Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Claudia Cosio
- Department F.-A. Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva, 66, Boulevard Carl-Vogt, 1211 Genève 4, Switzerland.
| |
Collapse
|
8
|
Chen Y, Zhi J, Zhang H, Li J, Zhao Q, Xu J. Transcriptome analysis of Phytolacca americana L. in response to cadmium stress. PLoS One 2017; 12:e0184681. [PMID: 28898278 PMCID: PMC5595333 DOI: 10.1371/journal.pone.0184681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/29/2017] [Indexed: 11/18/2022] Open
Abstract
Phytolacca americana L. (pokeweed) has metal phytoremediation potential, but little is known about its metal accumulation-related genes. In this study, the de novo sequencing of total RNA produced 53.15 million reads covering 10.63 gigabases of transcriptome raw data in cadmium (Cd)-treated and untreated pokeweed. Of the 97,502 assembled unigenes, 42,197 had significant matches in a public database and were annotated accordingly. An expression level comparison between the samples revealed 1515 differentially expressed genes (DEGs), 923 down- and 592 up-regulated under Cd treatment. A KEGG pathway enrichment analysis of DEGs revealed that they were involved in 72 metabolism pathways, with photosynthesis, phenylalanine metabolism, ribosome, phenylpropanoid biosynthesis, flavonoid biosynthesis and carbon fixation in photosynthetic organisms containing 24, 18, 72, 14, 7 and 15 genes, respectively. Genes related to heavy metal tolerance, absorption, transport and accumulation were also identified, including 11 expansins, 8 nicotianamine synthases, 6 aquaporins, 4 ZRT/IRT-like proteins, 3 ABC transporters and 3 metallothioneins. The gene expression results of 12 randomly selected DEGs were validated using quantitative real-time PCR, and showed different response patterns to Cd in their roots, stems and leaves. These results may be helpful in increasing our understanding of heavy metal hyperaccumulators and in future phytoremediation applications.
Collapse
Affiliation(s)
- Yongkun Chen
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Junkai Zhi
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Hao Zhang
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jian Li
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Qihong Zhao
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
| | - Jichen Xu
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
- * E-mail:
| |
Collapse
|
9
|
Song J, Mo X, Yang H, Yue L, Song J, Mo B. The U-box family genes in Medicago truncatula: Key elements in response to salt, cold, and drought stresses. PLoS One 2017; 12:e0182402. [PMID: 28771553 PMCID: PMC5542650 DOI: 10.1371/journal.pone.0182402] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 07/17/2017] [Indexed: 11/18/2022] Open
Abstract
The ubiquitination pathway regulates growth, development, and stress responses in plants, and the U-box protein family of ubiquitin ligases has important roles in this pathway. Here, 64 putative U-box proteins were identified in the Medicago truncatula genome. In addition to the conserved U-box motif, other functional domains, such as the ARM, kinase, KAP, and WD40 domains, were also detected. Phylogenetic analysis of the M. truncatula U-box proteins grouped them into six subfamilies, and chromosomal mapping and synteny analyses indicated that tandem and segmental duplications may have contributed to the expansion and evolution of the U-box gene family in this species. Using RNA-seq data from M. truncatula seedlings subjected to three different abiotic stresses, we identified 33 stress-inducible plant U-box genes (MtPUBs). Specifically, 25 salinity-, 15 drought-, and 16 cold-regulated MtPUBs were detected. Among them, MtPUB10, MtPUB17, MtPUB18, MtPUB35, MtPUB42, and MtPUB44 responded to all three stress conditions. Expression profiling by qRT-PCR was consistent with the RNA-seq data, and stress-related elements were identified in the promoter regions. The present findings strongly indicate that U-box proteins play critical roles in abiotic stress response in M. truncatula.
Collapse
Affiliation(s)
- Jianbo Song
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang, China
| | - Xiaowei Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Haiqi Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Luming Yue
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jun Song
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| |
Collapse
|
10
|
Chueh TC, Hsu LS, Kao CM, Hsu TW, Liao HY, Wang KY, Chen SC. Transcriptome analysis of zebrafish embryos exposed to deltamethrin. ENVIRONMENTAL TOXICOLOGY 2017; 32:1548-1557. [PMID: 27785895 DOI: 10.1002/tox.22376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Deltamethrin (DTM), a type II pyrethroid, is one of the most commonly used insecticides. The increased use of pyrethroid leads to potential adverse effects, particularly in sensitive populations such as children and pregnant women. None of the related studies was focused on the transcriptome responses in zebrafish embryos after treatment with DTM; therefore, RNA-seq, a high-throughput method, was performed to analyze the global expression of differential expressed genes (DEGs) in zebrafish embryos treated with DTM (40 and 80 μg/L) from fertilization to 48 h postfertilization (hpf) as compared with that in the control group (without DTM treatment). Two cDNA libraries were generated from treated embryos and one cDNA library from nontreated embryos, respectively. Over 92% of reads mapped to the reference in these three libraries. It was observed that many differential genes were expressed in comparison with embryos before and after DTM. The 20 most differentially expressed upregulated or downregulated genes were majorly involved in the signaling transduction. Validation of selected nine genes expression using qRT-PCR confirmed RNA-seq results. The transcriptome sequences were further subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, showing G-protein-coupled receptor signaling pathway and neuroactive ligand-receptor interaction, respectively, were most enriched. The data from this study contributed to a better understanding of the potential consequences of fish exposed to DTM, to an evaluation of the potential threat of DTM to fish populations in aquatic environments. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1548-1557, 2017.
Collapse
Affiliation(s)
| | - Li-Sung Hsu
- Institute of Biochemistry, Microbiology, and Immunology, Chung Shan Medical University, Taichung, Taiwan
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chin-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Tung-Wei Hsu
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| | - Hung-Yu Liao
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| | - Kuan-Yi Wang
- Institute of Biochemistry, Microbiology, and Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Ssu Ching Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| |
Collapse
|
11
|
Lu X, Xiang Y, Yang G, Zhang L, Wang H, Zhong S. Transcriptomic characterization of zebrafish larvae in response to mercury exposure. Comp Biochem Physiol C Toxicol Pharmacol 2017; 192:40-49. [PMID: 27939723 DOI: 10.1016/j.cbpc.2016.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/21/2016] [Accepted: 12/02/2016] [Indexed: 12/17/2022]
Abstract
Mercury is a widespread toxicant in aquatic environment that can cause deleterious effects on fish. Although a number of mercury-regulated genes have been investigated in adult fish, the transcriptional responses of fish larvae to acute mercury exposure are not well understood. In this study, RNA sequencing was used to examine the transcriptional changes in developing zebrafish larvae under a low concentration of mercuric chloride exposure from 24 to 120hpf. Our initial results showed that a total of 142.59 million raw reads were obtained from sequencing libraries and about 86% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 391 up- and 87 down-regulated genes. Gene ontology enrichment analysis revealed that most of the differential expressed genes are closely related to the regulation of cellular process, metabolic process, multicellular organismal process, biological regulation, pigmentation, and response to stimulus. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis demonstrated that antigen processing and presentation was the most significantly enriched pathway. Moreover, we characterized a novel and sensitive mercury-induced ABCB (ATP- binding cassette B subfamily) transporter gene - abcb5. This gene is localized on zebrafish chromosome 16 and contains a 4014bp open-reading frame. The deduced polypeptide is composed of 1337 amino acids and possesses most of functional domains and critical residues defined in human and mouse ABCB5/Abcb5. Functional analysis in vitro demonstrated that overexpression of zebrafish abcb5 gene can significantly decrease the cytotoxicity of mercury in LLC-PK1 cells, implying it is a potential efflux transporter of mercury. Thus, these findings provide useful insights to help further understand the transcriptional response and detoxification ability of zebrafish larvae following acute exposure to mercury.
Collapse
Affiliation(s)
- Xing Lu
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, Hubei, China.
| | - Ying Xiang
- School of Basic Medical Science, Wuhan University, Wuhan 430071, Hubei, China.
| | - Guohua Yang
- School of Basic Medical Science, Wuhan University, Wuhan 430071, Hubei, China.
| | - Lang Zhang
- School of Basic Medical Science, Wuhan University, Wuhan 430071, Hubei, China.
| | - Hui Wang
- School of Basic Medical Science, Wuhan University, Wuhan 430071, Hubei, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, Hubei, China.
| | - Shan Zhong
- School of Basic Medical Science, Wuhan University, Wuhan 430071, Hubei, China; Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, Hubei, China; Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, Hubei, China.
| |
Collapse
|
12
|
Hsu LS, Chiou BH, Hsu TW, Wang CC, Chen SC. The regulation of transcriptome responses in zebrafish embryo exposure to triadimefon. ENVIRONMENTAL TOXICOLOGY 2017; 32:217-226. [PMID: 26790661 DOI: 10.1002/tox.22227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 06/05/2023]
Abstract
The residue of triadimefon (TDF) (a pesticide) has become the pollutant in water due to its intensive use in agriculture and medicine, and its stability in water leaching from soil and vegetation. In this study, RNA-seq, a high-throughput method was performed, to analyze the global expression of differential expressed genes (DEGs) in zebrafish embryos treated with TDF (10 μg/mL) from fertilization to 72 h post-fertilization (hpf) as compared with that in the control group (without TDF treatment). Two cDNA libraries were generated from treated and non-treated embryos, respectively. With the 79.4% and 78.8% of reads mapped to the reference, it was observed that many differential genes were expressed between the two libraries. The most 20 differentially expressed up-regulated or down-regulated genes were involving in the signaling transduction, the activation of many genes related to cytochrome P450 enzymes, and molecular metabolism. Validation of seven genes expression confirmed RNA-seq results. The transcriptome sequences were further subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and showed diverse biological functions and metabolic pathways. The data from this study contributed to a better understanding of the potential consequences of fish exposed to TDF, and to evaluate the potential threat of TDF to fish population in the aquatic environment. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 217-226, 2017.
Collapse
Affiliation(s)
- Li-Sung Hsu
- Institute of Biochemistry, Microbiology, Immunology, Chung Shan Medical University, Taichung, Taiwan
- Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Bin-Hao Chiou
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| | - Tung-Wei Hsu
- Institute of Biochemistry, Microbiology, Immunology, Chung Shan Medical University, Taichung, Taiwan
| | - Chien-Chia Wang
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| | - Ssu Ching Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan
| |
Collapse
|
13
|
Feng SJ, Liu XS, Tao H, Tan SK, Chu SS, Oono Y, Zhang XD, Chen J, Yang ZM. Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium. PLANT, CELL & ENVIRONMENT 2016; 39:2629-2649. [PMID: 27412910 DOI: 10.1111/pce.12793] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 06/23/2016] [Accepted: 07/05/2016] [Indexed: 05/17/2023]
Abstract
We report genome-wide single-base resolution maps of methylated cytosines and transcriptome change in Cd-exposed rice. Widespread differences were identified in CG and non-CG methylation marks between Cd-exposed and Cd-free rice genomes. There are 2320 non-redundant differentially methylated regions detected in the genome. RNA sequencing revealed 2092 DNA methylation-modified genes differentially expressed under Cd exposure. More genes were found hypermethylated than those hypomethylated in CG, CHH and CHG (where H is A, C or T) contexts in upstream, gene body and downstream regions. Many of the genes were involved in stress response, metal transport and transcription factors. Most of the DNA methylation-modified genes were transcriptionally altered under Cd stress. A subset of loss of function mutants defective in DNA methylation and histone modification activities was used to identify transcript abundance of selected genes. Compared with wide type, mutation of MET1 and DRM2 resulted in general lower transcript levels of the genes under Cd stress. Transcripts of OsIRO2, OsPR1b and Os09g02214 in drm2 were significantly reduced. A commonly used DNA methylation inhibitor 5-azacytidine was employed to investigate whether DNA demethylation affected physiological consequences. 5-azacytidine provision decreased general DNA methylation levels of selected genes, but promoted growth of rice seedlings and Cd accumulation in rice plant.
Collapse
Affiliation(s)
- Sheng Jun Feng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Song Liu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Tao
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shang Kun Tan
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan Shan Chu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youko Oono
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Xian Duo Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Chen
- Institute of Food Safety and Quality, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
14
|
Hou J, Liu X, Cui B, Bai J, Wang X. Microarray analysis and real-time PCR assay developed to find biomarkers for mercury-contaminated soil. Toxicol Res (Camb) 2016; 5:1539-1547. [PMID: 30090455 PMCID: PMC6062303 DOI: 10.1039/c6tx00210b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/25/2016] [Indexed: 02/06/2023] Open
Abstract
The evaluation of mercury (Hg) toxicity in agricultural soil is of great concern because its bioavailability and bioaccumulation in organisms through the food chain can have adverse effects on human health. Therefore, the aim of this study was to develop sensitive biomarkers for Hg stress in agricultural soil. With the results obtained from a high-throughput cDNA microarray, 12 Hg-responsive genes were selected to examine their concentration-dependent responses to Hg stress at different Hg concentrations. The lowest observable adverse effect concentrations (LOAECs) of Hg were 0.8 mg kg-1 for seed germination, 1.6 mg kg-1 for root biomass, 0.8 mg kg-1 for root elongation, and 0.8 mg kg-1 for root morphology, respectively, whereas the lowest Hg treatments (0.1-0.4 mg kg-1) could generally induce differential expression of genes. These results indicated that the detection of Hg in soil at the molecular level is a highly sensitive method. Moreover, the Hg soil content exhibited a significant positive correlation with the relative expression of probable glutathione S-transferase parA (r = 0.637, p = 0.05), chlorophyll a-b binding protein 13, chloroplastic-like (r = 0.689, p = 0.05) and geranylgeranyl pyrophosphate synthase 1 (r = 0.682, p = 0.05), implying that the three genes are good candidates to detect Hg-contaminated soil.
Collapse
Affiliation(s)
- Jing Hou
- School of Environment and Chemical Engineering , North China Electric Power University , Beijing 102206 , China . ; ; Tel: +86-10-61772890
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation , School of Environment , Beijing Normal University , Beijing 100875 , China . ; ; Tel: +86-10-58802996
| | - Baoshan Cui
- State Key Laboratory of Water Environment Simulation , School of Environment , Beijing Normal University , Beijing 100875 , China . ; ; Tel: +86-10-58802996
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation , School of Environment , Beijing Normal University , Beijing 100875 , China . ; ; Tel: +86-10-58802996
| | - Xiangke Wang
- School of Environment and Chemical Engineering , North China Electric Power University , Beijing 102206 , China . ; ; Tel: +86-10-61772890
| |
Collapse
|
15
|
Xuan Y, Zhou ZS, Li HB, Yang ZM. Identification of a group of XTHs genes responding to heavy metal mercury, salinity and drought stresses in Medicago truncatula. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 132:153-63. [PMID: 27318197 DOI: 10.1016/j.ecoenv.2016.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 05/23/2023]
Abstract
Xyloglucan endotransglucosylase/hydrolases (XTH) are one of the key enzymes regulating cell wall construction, extension and metabolism. In the study, 44 XTH protein genes from Medicago truncatula genome were identified using bioinformatics, microarray and RT-PCR. Each XTH was showed to possess a highly conserved domain ((D/N)-E-(I/L/F/V)-D-(F/I/L)-E-(F/L)-L-G), and most of XTHs possess four Cys in the C terminal region, which suggests the potential for generating disulfide bonds. Based on the XTH protein sequences, these XTHscan be classified into three major families and each family can be subdivided into more groups. Examination of the genomic location of XTH genes on M. truncatula chromosomes showed that the evolutional expansion of the genes was possibly attributed to localized gene duplications. To investigate the possible involvement of the XTHs responding to heavy metals and other abiotic stresses, the XTH genes were exposed to heavy metal (Hg or Cu), salt and drought stresses. There were 28, 21 and 21 MtXTH genes found to respond to HgCl2, salt and drought stresses, respectively, but their expression were different under the stresses. Some of the XTH genes were well confirmed by quantitative RT-PCR (qRT-PCR). We further specified expression of a XTH gene Medtr4g128580 (MtXTH3) under different environmental stresses, and showed that MtXTH3 was induced by Hg exposure. These results indicated that a group of MtXTHs could be differentially expressed under the environmental stresses.
Collapse
Affiliation(s)
- Yun Xuan
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; Agricultural Engineering Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Zhao Sheng Zhou
- Jiangsu Province Key Laboratory of Marine Biology, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China.
| | - Hai Bo Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
16
|
Huang MT, Lu YC, Zhang S, Luo F, Yang H. Rice (Oryza sativa) Laccases Involved in Modification and Detoxification of Herbicides Atrazine and Isoproturon Residues in Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:6397-406. [PMID: 27499219 DOI: 10.1021/acs.jafc.6b02187] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Atrazine (ATR) and isoproturon (IPU) as herbicides have become serious environmental contaminants due to their overuse in crop production. Although ATR and IPU in soils are easily absorbed by many crops, the mechanisms for their degradation or detoxification in plants are poorly understood. This study identified a group of novel genes encoding laccases (EC 1.10.3.2) that are possibly involved in catabolism or detoxification of ATR and IPU residues in rice. Transcriptome profiling shows at least 22 differentially expressed laccase genes in ATR/IPU-exposed rice. Some of the laccase genes were validated by RT-PCR analysis. The biochemical properties of the laccases were analyzed, and their activities in rice were induced under ATR/IPU exposure. To investigate the roles of laccases in degrading or detoxifying ATR/IPU in rice, transgenic yeast cells (Pichia pastoris X-33) expressing two rice laccase genes (LOC_Os01g63180 and LOC_Os12g15680) were generated. Both transformants were found to accumulate less ATR/IPU compared to the control. The ATR/IPU-degraded products in the transformed yeast cells using UPLC-TOF-MS/MS were further characterized. Two metabolites, hydroxy-dehydrogenated atrazine (HDHA) and 2-OH-isopropyl-IPU, catalyzed by laccases were detected in the eukaryotic cells. These results indicate that the laccase-coding genes identified here could confer degradation or detoxification of the herbicides and suggest that the laccases could be one of the important enzymatic pathways responsible for ATR/IPU degradation/detoxification in rice.
Collapse
Affiliation(s)
- Meng Tian Huang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University , Nanjing 210095, China
| | - Yi Chen Lu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University , Nanjing 210095, China
- College of Food Science and Light Industry, Nanjing Tech University , Nanjing 211800, China
| | - Shuang Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University , Wuxi 214122, China
| | - Fang Luo
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University , Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University , Nanjing 210095, China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University , Nanjing 210095, China
| |
Collapse
|
17
|
Zhang JJ, Lu YC, Zhang SH, Lu FF, Yang H. Identification of transcriptome involved in atrazine detoxification and degradation in alfalfa (Medicago sativa) exposed to realistic environmental contamination. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:103-112. [PMID: 27092973 DOI: 10.1016/j.ecoenv.2016.04.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 06/05/2023]
Abstract
Plants are constantly exposed to a variety of toxic compounds (or xenobiotics) such as pesticides (or herbicides). Atrazine (ATZ) as herbicide has become one of the environmental contaminants due to its intensive use during crop production. Plants have evolved strategies to cope with the adverse impact of ATZ. However, the mechanism for ATZ degradation and detoxification in plants is largely unknown. Here we employed a global RNA-sequencing (RNA-Seq) strategy to dissect transcriptome variation in alfalfa (Medicago sativa) exposed to ATZ. Four libraries were constructed including Root-ATZ (root control, ATZ-free), Shoot-ATZ, Root+ATZ (root treated with ATZ) and Shoot+ATZ. Hierarchical clustering was performed to display the expression patterns for all differentially expressed genes (DEGs) under ATZ exposure. Transcripts involved in ATZ detoxification, stress responses (e.g. oxidation and reduction, conjugation and hydrolytic reactions), and regulations of cysteine biosynthesis were identified. Several genes encoding glycosyltransferases, glutathione S-transferases or ABC transporters were up-regulated notably. Also, many other genes involved in oxidation-reduction, conjugation, and hydrolysis for herbicide degradation were differentially expressed. These results suggest that ATZ in alfalfa can be detoxified or degraded through different pathways. The expression patterns of some DEGs by high-throughput sequencing were well confirmed by qRT-PCR. Our results not only highlight the transcriptional complexity in alfalfa exposed to ATZ but represent a major improvement for analyzing transcriptional changes on a large scale as well.
Collapse
Affiliation(s)
- Jing Jing Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Chen Lu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu Hao Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Fan Lu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
18
|
Beauvais-Flück R, Slaveykova VI, Cosio C. Transcriptomic and Physiological Responses of the Green Microalga Chlamydomonas reinhardtii during Short-Term Exposure to Subnanomolar Methylmercury Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:7126-7134. [PMID: 27254783 DOI: 10.1021/acs.est.6b00403] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The effects of short-term exposure to subnanomolar methyl-mercury (MeHg) concentrations, representative of contaminated environments, on the microalga Chlamydomonas reinhardtii were assessed using both physiological end points and gene expression analysis. MeHg bioaccumulated and induced significant increase of the photosynthesis efficiency, while the algal growth, oxidative stress, and chlorophyll fluorescence were unaffected. At the molecular level, MeHg significantly dysregulated the expression of genes involved in motility, energy metabolism, lipid metabolism, metal transport, and antioxidant enzymes. Data suggest that the cells were able to cope with subnanomolar MeHg exposure, but this tolerance resulted in a significant cost to the cell energy and reserve metabolism as well as ample changes in the nutrition and motility of C. reinhardtii. The present results allowed gaining new insights on the effects and uptake mechanisms of MeHg at subnanomolar concentrations in aquatic primary producers.
Collapse
Affiliation(s)
- Rebecca Beauvais-Flück
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva , 66, boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Vera I Slaveykova
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva , 66, boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| | - Claudia Cosio
- Institute F.-A. Forel, Earth and Environmental Sciences, Faculty of Sciences, University of Geneva , 66, boulevard Carl-Vogt, 1211 Genève 4, Switzerland
| |
Collapse
|
19
|
Keunen E, Schellingen K, Vangronsveld J, Cuypers A. Ethylene and Metal Stress: Small Molecule, Big Impact. FRONTIERS IN PLANT SCIENCE 2016; 7:23. [PMID: 26870052 PMCID: PMC4735362 DOI: 10.3389/fpls.2016.00023] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/08/2016] [Indexed: 05/18/2023]
Abstract
The phytohormone ethylene is known to mediate a diverse array of signaling processes during abiotic stress in plants. Whereas many reports have demonstrated enhanced ethylene production in metal-exposed plants, the underlying molecular mechanisms are only recently investigated. Increasing evidence supports a role for ethylene in the regulation of plant metal stress responses. Moreover, crosstalk appears to exist between ethylene and the cellular redox balance, nutrients and other phytohormones. This review highlights our current understanding of the key role ethylene plays during responses to metal exposure. Moreover, particular attention is paid to the integration of ethylene within the broad network of plant responses to metal stress.
Collapse
|
20
|
Feng SJ, Zhang XD, Liu XS, Tan SK, Chu SS, Meng JG, Zhao KX, Zheng JF, Yang ZM. Characterization of long non-coding RNAs involved in cadmium toxic response in Brassica napus. RSC Adv 2016. [DOI: 10.1039/c6ra05459e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
There is increasing evidence of long non-coding RNA (lncRNA) involvement in a variety of biological responses to environmental stresses.
Collapse
Affiliation(s)
- Sheng Jun Feng
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Xian Duo Zhang
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Xue Song Liu
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Shang Kun Tan
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Shan Shan Chu
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Jin Guo Meng
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Kai Xuan Zhao
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Jian Feng Zheng
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology
- College of Life Science
- Nanjing Agricultural University
- Nanjing 210095
- China
| |
Collapse
|
21
|
Gul A, Ahad A, Akhtar S, Ahmad Z, Rashid B, Husnain T. Microarray: gateway to unravel the mystery of abiotic stresses in plants. Biotechnol Lett 2015; 38:527-43. [PMID: 26667130 DOI: 10.1007/s10529-015-2010-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/02/2015] [Indexed: 10/22/2022]
Abstract
Environmental factors, such as drought, salinity, extreme temperature, ozone poisoning, metal toxicity etc., significantly affect crops. To study these factors and to design a possible remedy, biological experimental data concerning these crops requires the quantification of gene expression and comparative analyses at high throughput level. Development of microarrays is the platform to study the differential expression profiling of the targeted genes. This technology can be applied to gene expression studies, ranging from individual genes to whole genome level. It is now possible to perform the quantification of the differential expression of genes on a glass slide in a single experiment. This review documents recently published reports on the use of microarrays for the identification of genes in different plant species playing their role in different cellular networks under abiotic stresses. The regulation pattern of differentially-expressed genes, individually or in group form, may help us to study different pathways and functions at the cellular and molecular level. These studies can provide us with a lot of useful information to unravel the mystery of abiotic stresses in important crop plants.
Collapse
Affiliation(s)
- Ambreen Gul
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Ammara Ahad
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Sidra Akhtar
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Zarnab Ahmad
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan
| | - Bushra Rashid
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan.
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab Lahore, 87 W Canal Bank Road, Thokar Niaz Baig, Lahore, 53700, Pakistan
| |
Collapse
|
22
|
Wang Y, Cheng ZZ, Chen X, Zheng Q, Yang ZM. CrGNAT gene regulates excess copper accumulation and tolerance in Chlamydomonas reinhardtii. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:120-129. [PMID: 26475193 DOI: 10.1016/j.plantsci.2015.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
Excess copper (Cu) in environment affects the growth and metabolism of plants and green algae. However, the molecular mechanism for regulating plant tolerance to excess Cu is not fully understood. Here, we report a gene CrGNAT enconding an acetyltransferase in Chlamydomonas reinhardtii and identified its role in regulating tolerance to Cu toxicity. Expression of CrGNAT was significantly induced by 75-400μM Cu. The top induction occurred at 100μM. Transgenic algae overexpressing CrGNAT (35S::CrGNAT) in C. reinhardtii showed high tolerance to excess Cu, with improved cell population, chlorophyll accumulation and photosynthesis efficiency, but with low degree of oxidation with regard to reduced hydrogen peroxide, lipid peroxides and non-protein thiol compounds. In contrast, CrGNAT knock-down lines with antisense led to sensitivity to Cu stress. 35S::CrGNAT algae accumulated more Cu and other metals (Zn, Fe, Cu, Mn and Mg) than wild-type, whereas the CrGNAT down-regulated algae (35S::AntiCrGNAT) had moderate levels of Cu and Mn, but no effects on Zn, Fe and Mg accumulation as compared to wild-type. The elevated metal absorption in CrGNAT overexpression algae implies that the metals can be removed from water media. Quantitative RT-PCR analysis revealed that expression of two genes encoding N-lysine histone methyltransferases was repressed in 35S::CrGNAT algae, suggesting that CrGNAT-regulated algal tolerance to Cu toxicity is likely associated with histone methylation and chromatin remodeling. The present work provided an example a basis to develop techniques for environmental restoration of metal-contaminated aquatic ecosystems.
Collapse
Affiliation(s)
- Ye Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhen Zhen Cheng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xi Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Qi Zheng
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
23
|
Rong Tan L, Chen Lu Y, Jing Zhang J, Luo F, Yang H. A collection of cytochrome P450 monooxygenase genes involved in modification and detoxification of herbicide atrazine in rice (Oryza sativa) plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 119:25-34. [PMID: 25968601 DOI: 10.1016/j.ecoenv.2015.04.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/25/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Plant cytochrome P450 monooxygenases constitute one of the largest families of protein genes involved in plant growth, development and acclimation to biotic and abiotic stresses. However, whether these genes respond to organic toxic compounds and their biological functions for detoxifying toxic compounds such as herbicides in rice are poorly understood. The present study identified 201 genes encoding cytochrome P450s from an atrazine-exposed rice transcriptome through high-throughput sequencing. Of these, 69 cytochrome P450 genes were validated by microarray and some of them were confirmed by real time PCR. Activities of NADPH-cytochrome P450 reductase (CPR) and p-nitroanisole O-demethylase (PNOD) related to toxicity were determined and significantly induced by atrazine exposure. To dissect the mechanism underlying atrazine modification and detoxification by P450, metabolites (or derivatives) of atrazine in plants were analyzed by ultra performance liquid chromatography mass spectrometry (UPLC/MS). Major metabolites comprised desmethylatrazine (DMA), desethylatrazine (DEA), desisopropylatrazine (DIA), hydroxyatrazine (HA), hydroxyethylatrazine (HEA) and hydroxyisopropylatrazine (HIA). All of them were chemically modified by P450s. Furthermore, two specific inhibitors of piperonyl butoxide (PBO) and malathion (MAL) were used to assess the correlation between the P450s activity and rice responses including accumulation of atrazine in tissues, shoot and root growth and detoxification.
Collapse
Affiliation(s)
- Li Rong Tan
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen Lu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jing Jing Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Fang Luo
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
24
|
Xu L, Wang Y, Liu W, Wang J, Zhu X, Zhang K, Yu R, Wang R, Xie Y, Zhang W, Gong Y, Liu L. De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:313-23. [PMID: 26025544 DOI: 10.1016/j.plantsci.2015.04.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/04/2015] [Accepted: 04/20/2015] [Indexed: 05/04/2023]
Abstract
Cadmium (Cd) is a nonessential metallic trace element that poses potential chronic toxicity to living organisms. To date, little is known about the Cd-responsive regulatory network in root vegetable crops including radish. In this study, 31,015 unigenes representing 66,552 assembled unique transcripts were isolated from radish root under Cd stress based on de novo transcriptome assembly. In all, 1496 differentially expressed genes (DEGs) consisted of 3579 transcripts were identified from Cd-free (CK) and Cd-treated (Cd200) libraries. Gene Ontology and pathway enrichment analysis indicated that the up- and down-regulated DEGs were predominately involved in glucosinolate biosynthesis as well as cysteine and methionine-related pathways, respectively. RT-qPCR showed that the expression profiles of DEGs were in consistent with results from RNA-Seq analysis. Several candidate genes encoding phytochelatin synthase (PCS), metallothioneins (MTs), glutathione (GSH), zinc iron permease (ZIPs) and ABC transporter were responsible for Cd uptake, accumulation, translocation and detoxification in radish. The schematic model of DEGs and microRNAs-involved in Cd-responsive regulatory network was proposed. This study represents a first comprehensive transcriptome-based characterization of Cd-responsive DEGs in radish. These results could provide fundamental insight into complex Cd-responsive regulatory networks and facilitate further genetic manipulation of Cd accumulation in root vegetable crops.
Collapse
Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jin Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
| | - Keyun Zhang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rugang Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ronghua Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yiqin Gong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.
| |
Collapse
|
25
|
Wang ZQ, Li GZ, Gong QQ, Li GX, Zheng SJ. OsTCTP, encoding a translationally controlled tumor protein, plays an important role in mercury tolerance in rice. BMC PLANT BIOLOGY 2015; 15:123. [PMID: 25990386 PMCID: PMC4438481 DOI: 10.1186/s12870-015-0500-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/21/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Mercury (Hg) is not only a threat to public health but also a growth risk factor to plants, as it is readily accumulated by higher plants. Accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development; however, the detoxification and tolerance mechanisms of plants to Hg stress are still not fully understood. Exposure to toxic Hg also occurs in some crops cultivated under anoxic conditions, such as rice (Oryza sativa L.), a model organism and one of the most important cultivated plants worldwide. In this study, we functionally characterized a rice translationally controlled tumor protein gene (Os11g43900, OsTCTP) involved in Hg stress tolerance. RESULTS OsTCTP was ubiquitously expressed in all examined plant tissues, especially in actively dividing and differentiating tissues, such as roots and nodes. OsTCTP was found to localize both the cytosol and the nucleus. OsTCTP was induced by mercuric chloride, cupric sulfate, abscisic acid, and hydrogen peroxide at the protein level in a time-dependent manner. Overexpression of OsTCTP potentiated the activities of several antioxidant enzymes, reduced the Hg-induced H2O2 levels, and promoted Hg tolerance in rice, whereas knockdown of OsTCTP produced opposite effects. And overexpression of OsTCTP did not prevent Hg absorption and accumulation in rice. We also demonstrated that Asn 48 and Asn 97 of OsTCTP amino acids were not the potential N-glycosylation sites. CONCLUSIONS Our results suggest that OsTCTP is capable of decreasing the Hg-induced reactive oxygen species (ROS), therefore, reducing the damage of ROS and enhancing the tolerance of rice plants to Hg stress. Thus, OsTCTP is a valuable gene for genetic engineering to improve rice performance under Hg contaminated paddy soils.
Collapse
Affiliation(s)
- Zhan Qi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Ge Zi Li
- 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.
| | - Gui Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
26
|
The F-box family genes as key elements in response to salt, heavy mental, and drought stresses in Medicago truncatula. Funct Integr Genomics 2015; 15:495-507. [PMID: 25877816 DOI: 10.1007/s10142-015-0438-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 12/12/2022]
Abstract
F-box protein is a subunit of Skp1-Rbx1-Cul1-F-box protein (SCF) complex with typically conserved F-box motifs of approximately 40 amino acids and is one of the largest protein families in eukaryotes. F-box proteins play critical roles in selective and specific protein degradation through the 26S proteasome. In this study, we bioinformatically identified 972 putative F-box proteins from Medicago truncatula genome. Our analysis showed that in addition to the conserved motif, the F-box proteins have several other functional domains in their C-terminal regions (e.g., LRRs, Kelch, FBA, and PP2), some of which were found to be M. truncatula species-specific. By phylogenetic analysis of the F-box motifs, these proteins can be classified into three major families, and each family can be further grouped into more subgroups. Analysis of the genomic distribution of F-box genes on M. truncatula chromosomes revealed that the evolutional expansion of F-box genes in M. truncatula was probably due to localized gene duplications. To investigate the possible response of the F-box genes to abiotic stresses, both publicly available and customer-prepared microarrays were analyzed. Most of the F-box protein genes can be responding to salt and heavy metal stresses. Real-time PCR analysis confirmed that some of the F-box protein genes containing heat, drought, salicylic acid, and abscisic acid responsive cis-elements were able to respond to the abiotic stresses.
Collapse
|
27
|
Zhao D, Li T, shen M, Wang J, Zhao Z. Diverse strategies conferring extreme cadmium (Cd) tolerance in the dark septate endophyte (DSE), Exophiala pisciphila: Evidence from RNA-seq data. Microbiol Res 2015; 170:27-35. [DOI: 10.1016/j.micres.2014.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/10/2014] [Accepted: 09/17/2014] [Indexed: 12/17/2022]
|
28
|
Ding H, Gao J, Qin C, Ma H, Huang H, Song P, Luo X, Lin H, Shen Y, Pan G, Zhang Z. The dynamics of DNA methylation in maize roots under Pb stress. Int J Mol Sci 2014; 15:23537-54. [PMID: 25526567 PMCID: PMC4284779 DOI: 10.3390/ijms151223537] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/15/2023] Open
Abstract
Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb) stress. Therefore, in this study, we aimed to compare DNA methylation profiles during the dynamic development of maize roots following Pb treatment to identify candidate genes involved in the response to Pb stress. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation patterns in maize roots under normal condition (A1) and 3 mM Pb(NO3)2 stress for 12 h (K2), 24 h (K3) and 48 h (K4). The results showed that the average methylation density was the highest in CpG islands (CGIs), followed by the intergenic regions. Within the gene body, the methylation density of the introns was higher than those of the UTRs and exons. In total, 3857 methylated genes were found in 4 tested samples, including 1805 differentially methylated genes for K2 versus A1, 1508 for K3 versus A1, and 1660 for K4 versus A1. Further analysis showed that 140 genes exhibited altered DNA methylation in all three comparisons, including some well-known stress-responsive transcription factors and proteins, such as MYB, AP2/ERF, bZIP, serine-threonine/tyrosine-proteins, pentatricopeptide repeat proteins, RING zinc finger proteins, F-box proteins, leucine-rich repeat proteins and tetratricopeptide repeat proteins. This study revealed the genome-scale DNA methylation patterns of maize roots in response to Pb exposure and identified candidate genes that potentially regulate root dynamic development under Pb stress at the methylation level.
Collapse
Affiliation(s)
- Haiping Ding
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Jian Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Cheng Qin
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
| | - Haixia Ma
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Hong Huang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Pan Song
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Xirong Luo
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China.
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Ya'ou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China.
| |
Collapse
|
29
|
Kang G, Li G, Wang L, Wei L, Yang Y, Wang P, Yang Y, Wang Y, Feng W, Wang C, Guo T. Hg-Responsive Proteins Identified in Wheat Seedlings Using iTRAQ Analysis and the Role of ABA in Hg Stress. J Proteome Res 2014; 14:249-67. [DOI: 10.1021/pr5006873] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guozhang Kang
- The
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- The
National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Gezi Li
- The
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lina Wang
- The
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liting Wei
- The
National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yang Yang
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pengfei Wang
- The
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingying Yang
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yonghua Wang
- The
National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Feng
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chenyang Wang
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tiancai Guo
- The
Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
- The
National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou, 450002, China
| |
Collapse
|
30
|
Kapoor D, Kaur S, Bhardwaj R. Physiological and biochemical changes in Brassica juncea plants under Cd-induced stress. BIOMED RESEARCH INTERNATIONAL 2014; 2014:726070. [PMID: 25133178 PMCID: PMC4123575 DOI: 10.1155/2014/726070] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 12/03/2022]
Abstract
Plants of Brassica juncea L. var. RLC-1 were exposed for 30 days to different concentrations (0, 0.2, 0.4, and 0.6 mM) of cadmium (Cd) to analyze the Cd uptake, H2O2 content, hormonal profiling, level of photosynthetic pigments (chlorophyll, carotenoid, and flavonoid), gaseous exchange parameters (photosynthetic rate, vapour pressure deficit, intercellular CO2 concentration, and intrinsic mesophyll rate), antioxidative enzymes (superoxide dismutase, polyphenol oxidase, glutathione-S transferase, and glutathione peroxidase), antioxidant assays (DPPH, ABTS, and total phenolic content), and polyphenols. Results of the present study revealed the increased H2O2 content and Cd uptake with increasing metal doses. UPLC analysis of plants showed the presence of various polyphenols. Gaseous exchange measurements were done by infrared gas analyzer (IRGA), which was negatively affected by metal treatment. In addition, LC/MS study showed the variation in the expression of plant hormones. Level of photosynthetic pigments and activities of antioxidative enzymes were altered significantly in response to metal treatment. In conclusion, the antioxidative defence system of plants got activated due to heavy metal stress, which protects the plants by scavenging free radicals.
Collapse
Affiliation(s)
- Dhriti Kapoor
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Satwinderjeet Kaur
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab 143005, India
| |
Collapse
|
31
|
Montero-Palmero MB, Martín-Barranco A, Escobar C, Hernández LE. Early transcriptional responses to mercury: a role for ethylene in mercury-induced stress. THE NEW PHYTOLOGIST 2014; 201:116-130. [PMID: 24033367 DOI: 10.1111/nph.12486] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/01/2013] [Indexed: 05/21/2023]
Abstract
Understanding the cellular mechanisms of plant tolerance to mercury (Hg) is important for developing phytoremediation strategies of Hg-contaminated soils. The early responses of alfalfa (Medicago sativa) seedlings to Hg were studied using transcriptomics analysis. A Medicago truncatula microarray was hybridized with high-quality root RNA from M. sativa treated with 3 μM Hg for 3, 6 and 24 h. The transcriptional pattern data were complementary to the measurements of root growth inhibition, lipid peroxidation, hydrogen peroxide (H2 O2 ) accumulation and NADPH-oxidase activity as stress indexes. Of 559 differentially expressed genes (DEGs), 91% were up-regulated. The majority of DEGs were shared between the 3 and 6 h (60%) time points, including the 'stress', 'secondary metabolism' and 'hormone metabolism' functional categories. Genes from ethylene metabolism and signalling were highly represented, suggesting that this phytohormone may be relevant for metal perception and homeostasis. Ethylene-insensitive alfalfa seedlings preincubated with the ethylene signalling inhibitor 1-methylcyclopronene and Arabidopsis thaliana ein2-5 mutants confirmed that ethylene participates in the early perception of Hg stress. It modulates root growth inhibition, NADPH-oxidase activity and Hg-induced apoplastic H2 O2 accumulation. Therefore, ethylene signalling attenuation could be useful in future phytotechnological applications to ameliorate stress symptoms in Hg-polluted plants.
Collapse
Affiliation(s)
- M Belén Montero-Palmero
- Laboratorio de Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Laboratorio de Fisiología Vegetal, Departamento de Ciencias Ambientales, Universidad de Castilla-La Mancha, Campus Fábrica de Armas, 45070, Toledo, Spain
| | - Amanda Martín-Barranco
- Laboratorio de Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Carolina Escobar
- Laboratorio de Fisiología Vegetal, Departamento de Ciencias Ambientales, Universidad de Castilla-La Mancha, Campus Fábrica de Armas, 45070, Toledo, Spain
| | - Luis E Hernández
- Laboratorio de Fisiología Vegetal, Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| |
Collapse
|