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Dai H, Wei S, Grzebelus D, Skuza L, Jia J, Hou N. Mechanism exploration of Solanum nigrum L. hyperaccumulating Cd compared to Zn from the perspective of metabolic pathways based on differentially expressed proteins using iTRAQ. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129717. [PMID: 35961076 DOI: 10.1016/j.jhazmat.2022.129717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
It is challenging to determine the mechanism involved in only Cd hyperaccumulation by Solanum nigrum L. owing to the uniqueness of the process. Isobaric tags for relative and absolute quantitation (iTRAQ) were used to explore the mechanism by which S. nigrum hyperaccumulates Cd by comparing the differentially expressed proteins (DEPs) for Cd and Zn accumulation (non-Zn hyperaccumulator). Based on the comparison between the DEPs associated with Cd and Zn accumulation, the relative metabolic pathways reflected by 17 co-intersecting specific proteins associated with Cd and Zn accumulation included phagosome, aminoacyl-tRNA biosynthesis, and carbon metabolism. Apart from the 17 co-intersecting specific proteins, the conjoint metabolic pathways reported by 21 co-intersecting specific proteins associated with Cd accumulation and 30 co-intersecting specific proteins associated with Zn accumulation, the most differentially expressed metabolic pathways might cause Cd TF (Translocation factor)> 1 and Zn TF< 1, including protein export, ribosome, amino sugar, and nucleotide sugar metabolism. The determined DEPs were verified using qRT-PCR with the four key proteins M1CW30, A0A3Q7H652, A0A0V0IFB9, and A0A0V0IAC4. The plasma membrane H+-ATPase protein was identified using western blotting. Some physiological indices for protein-related differences indirectly confirmed the above results. These results are crucial to further explore the mechanisms involved in Cd hyperaccumulation.
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Affiliation(s)
- Huiping Dai
- College of Biological Science & Engineering, Shaanxi Province Key Laboratory of Bio-resources, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C, State Key Laboratory of Biological Resources And Ecological Environment Jointly Built By Qinba Province and Ministry, Shaanxi University of Technology, Hanzhong 723001, China
| | - Shuhe Wei
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow 31-120, Poland
| | - Lidia Skuza
- Institute of Biology, Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin 71-415, Poland
| | - Jibao Jia
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Nan Hou
- College of Biological Science & Engineering, Shaanxi Province Key Laboratory of Bio-resources, Qinling-Bashan Mountains Bioresources Comprehensive Development C.I.C, State Key Laboratory of Biological Resources And Ecological Environment Jointly Built By Qinba Province and Ministry, Shaanxi University of Technology, Hanzhong 723001, China
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Wang Y, Salt DE, Koornneef M, Aarts MGM. Construction and analysis of a Noccaea caerulescens TILLING population. BMC PLANT BIOLOGY 2022; 22:360. [PMID: 35869423 PMCID: PMC9308233 DOI: 10.1186/s12870-022-03739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.
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Affiliation(s)
- Yanli Wang
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- College of Horticulture Science & Technology, Hebei Normal University of Science & Technology, No 360, West of HeBei street, Qinhuang Dao, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Liang G, Ma Z, Lu S, Ma W, Feng L, Mao J, Chen B. Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation. PLANT CELL REPORTS 2022; 41:1357-1373. [PMID: 35316376 DOI: 10.1007/s00299-022-02862-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.
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Affiliation(s)
- Guoping Liang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Weifeng Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lidan Feng
- College of Food Science and Engineering, Gansu Agriculture University, Lanzhou, 730070, China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, China.
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
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Wang X, Gong F, Duan H, He C, Yang Z. Pieces of evidence of enhanced cellulose biosynthesis in the low-Cd cultivar and high expression level of transportation genes in the high-Cd cultivar of Lactuca sativa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:42913-42928. [PMID: 35092588 DOI: 10.1007/s11356-022-18882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
To investigate the molecular mechanism of Cd-accumulating difference between Lactuca sativa cultivars, full-length transcriptome comparison, as well as biochemical validation, have been conducted between Cd pollution-safe cultivar (Cd-PSC, cv. LYDL) and high-Cd-accumulating cultivar (cv. HXDWQ). The full-length transcriptome of L. sativa cultivars was achieved for the first time. The results showed high Cd compartmentalization in the cell wall of cv. LYDL was ascribed to the enhanced cell wall biosynthesis under Cd stress, which was consistent with the high cellular debris Cd level (32.10-43.58%). The expression levels of transporter genes in cv. HXDWQ were about 1.19 to 1.21-fold higher than those in cv. LYDL, which was in accordance with the high ratio of easy migrative Cd chemical forms (68.59-81.98%), indicating the high Cd accumulation in the shoot of cv. HXDWQ was ascribed to the higher transportation capacity in cv. HXDWQ. Moreover, the Cd-induced endoplasmic reticulum (ER) stress was associated with the higher Cd detoxification and tolerance in cv. HXDWQ rather than in cv. LYDL. The study provides new insights into the Cd-induced transcriptomic difference between L. sativa cultivars and further contributes to the molecular breeding of L. sativa Cd-PSC.
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Affiliation(s)
- Xuesong Wang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), 510070, Guangzhou, China
| | - Feiyue Gong
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Huixia Duan
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Chuntao He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China.
- School of Agriculture, Sun Yat-Sen University, 510275, Guangzhou, China.
| | - Zhongyi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China.
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Hanikenne M, Esteves SM, Fanara S, Rouached H. Coordinated homeostasis of essential mineral nutrients: a focus on iron. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2136-2153. [PMID: 33175167 DOI: 10.1093/jxb/eraa483] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/13/2020] [Indexed: 05/22/2023]
Abstract
In plants, iron (Fe) transport and homeostasis are highly regulated processes. Fe deficiency or excess dramatically limits plant and algal productivity. Interestingly, complex and unexpected interconnections between Fe and various macro- and micronutrient homeostatic networks, supposedly maintaining general ionic equilibrium and balanced nutrition, are currently being uncovered. Although these interactions have profound consequences for our understanding of Fe homeostasis and its regulation, their molecular bases and biological significance remain poorly understood. Here, we review recent knowledge gained on how Fe interacts with micronutrient (e.g. zinc, manganese) and macronutrient (e.g. sulfur, phosphate) homeostasis, and on how these interactions affect Fe uptake and trafficking. Finally, we highlight the importance of developing an improved model of how Fe signaling pathways are integrated into functional networks to control plant growth and development in response to fluctuating environments.
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Affiliation(s)
- Marc Hanikenne
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Sara M Esteves
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Steven Fanara
- InBioS - PhytoSystems, Functional Genomics and Plant Molecular Imaging, University of Liège, 4000 Liège, Belgium
| | - Hatem Rouached
- BPMP, Univ. Montpellier, CNRS, INRA, Montpellier SupAgro, Montpellier, France
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
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Rosatto S, Mariotti M, Romeo S, Roccotiello E. Root and Shoot Response to Nickel in Hyperaccumulator and Non-Hyperaccumulator Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10030508. [PMID: 33803420 PMCID: PMC7998499 DOI: 10.3390/plants10030508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/06/2021] [Indexed: 05/04/2023]
Abstract
The soil-root interface is the micro-ecosystem where roots uptake metals. However, less than 10% of hyperaccumulators' rhizosphere has been examined. The present study evaluated the root and shoot response to nickel in hyperaccumulator and non-hyperaccumulator species, through the analysis of root surface and biomass and the ecophysiological response of the related aboveground biomass. Ni-hyperaccumulators Alyssoides utriculata (L.) Medik. and Noccaea caerulescens (J. Presl and C. Presl) F.K. Mey. and non-hyperaccumulators Alyssum montanum L. and Thlaspi arvense L. were grown in pot on Ni-spiked soil (0-1000 mg Ni kg-1, total). Development of root surfaces was analysed with ImageJ; fresh and dry root biomass was determined. Photosynthetic efficiency was performed by analysing the fluorescence of chlorophyll a to estimate the plants' physiological conditions at the end of the treatment. Hyperaccumulators did not show a Ni-dependent decrease in root surfaces and biomass (except Ni 1000 mg kg-1 for N. caerulescens). The non-hyperaccumulator A. montanum suffers metal stress which threatens plant development, while the excluder T. arvense exhibits a positive ecophysiological response to Ni. The analysis of the root system, as a component of the rhizosphere, help to clarify the response to soil nickel and plant development under metal stress for bioremediation purposes.
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Grosjean N, Blaby-Haas CE. Leveraging computational genomics to understand the molecular basis of metal homeostasis. THE NEW PHYTOLOGIST 2020; 228:1472-1489. [PMID: 32696981 DOI: 10.1111/nph.16820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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Mahmud K, Burslem DFRP. Contrasting growth responses to aluminium addition among populations of the aluminium accumulator Melastoma malabathricum. AOB PLANTS 2020; 12:plaa049. [PMID: 33376588 PMCID: PMC7750992 DOI: 10.1093/aobpla/plaa049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/08/2020] [Indexed: 06/12/2023]
Abstract
Aluminium (Al) hyper-accumulation is a common trait expressed by tropical woody plants growing on acidic soils. Studies on Al accumulators have suggested that Al addition may enhance plant growth rates, but the functional significance of this trait and the mechanistic basis of the growth response are uncertain. This study aimed to test the hypothesis that differential growth responses to Al among populations of an Al accumulator species are associated with variation in biomass allocation and nutrient uptake. We conducted two experiments to test differential responses to the presence of Al in the growth medium for seedlings of the Al accumulator shrub Melastoma malabathricum collected from 18 populations across Peninsular Malaysia. Total dry mass and relative growth rate of dry mass were significantly greater for seedlings that had received Al in the growth medium than for control plants that did not receive Al, but growth declined in response to 5.0 mM Al addition. The increase in growth rate in response to Al addition was greater for a fast-growing than a slow-growing population. The increase in growth rate in response to Al addition occurred despite a reduction in dry mass allocation to leaves, at the expense of higher allocation to roots and stems, for plants grown with Al. Foliar concentrations of P, K, Mg and Ca increased in response to Al addition and the first axis of a PCA summarizing foliar nutrient concentrations among populations was correlated positively with seedling relative growth rates. Some populations of the Al hyper-accumulator M. malabathricum express a physiological response to Al addition which leads to a stimulation of growth up to an optimum value of Al in the growth medium, beyond which growth declines. This was associated with enhanced nutrient concentrations in leaves, which suggests that Al accumulation functions to optimize elemental stoichiometry and growth rate.
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Affiliation(s)
- Khairil Mahmud
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Seri Kembangan, Selangor, Malaysia
- School of Biological Sciences, University of Aberdeen, AB242UU Aberdeen, Scotland, UK
- School of Agricultural Science, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut Campus, Besut, Terengganu, Malaysia
| | - David F R P Burslem
- School of Biological Sciences, University of Aberdeen, AB242UU Aberdeen, Scotland, UK
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Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
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Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Fan SK, Ye JY, Zhang LL, Chen HS, Zhang HH, Zhu YX, Liu XX, Jin CW. Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition. PLANT, CELL & ENVIRONMENT 2020; 43:275-291. [PMID: 31703150 DOI: 10.1111/pce.13670] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 10/08/2019] [Accepted: 10/27/2019] [Indexed: 05/03/2023]
Abstract
Although the alteration of DNA methylation due to abiotic stresses, such as exposure to the toxic metal cadmium (Cd), has been often observed in plants, little is known about whether such epigenetic changes are linked to the ability of plants to adapt to stress. Herein, we report a close linkage between DNA methylation and the adaptational responses in Arabidopsis plants under Cd stress. Exposure to Cd significantly inhibited the expression of three DNA demethylase genes ROS1/DML2/DML3 (RDD) and elevated DNA methylation at the genome-wide level in Col-0 roots. Furthermore, the profile of DNA methylation in Cd-exposed Col-0 roots was similar to that in the roots of rdd triple mutants, which lack RDD, indicating that Cd-induced DNA methylation is associated with the inhibition of RDD. Interestingly, the elevation in DNA methylation in rdd conferred a higher tolerance against Cd stress and improved cellular Fe nutrition in the root tissues. In addition, lowering the Fe supply abolished improved Cd tolerance due to the lack of RDD in rdd. Together, these data suggest that the inhibition of RDD-mediated DNA demethylation in the roots by Cd would in turn enhance plant tolerance to Cd stress by improving Fe nutrition through a feedback mechanism.
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Affiliation(s)
- Shi Kai Fan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Jia Yuan Ye
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Lin Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Hong Shan Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Hai Hua Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Ya Xin Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Xing Xing Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Chong Wei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Natural Resources and Environmental Science, Zhejiang University, Hangzhou, China
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Wang W, Singh SK, Li X, Sun H, Yang Y, Jiang M, Zi H, Liu R, Zhang H, Chu Z. Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots. PeerJ 2019; 7:e7102. [PMID: 31223535 PMCID: PMC6571136 DOI: 10.7717/peerj.7102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023] Open
Abstract
Background There have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon. Results Our Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice. Conclusions This study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation.
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Affiliation(s)
- Wei Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Sunil Kumar Singh
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiwen Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China.,College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hui Sun
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Yang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hailing Zi
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Renyi Liu
- Center for Agroforestry Mega Data Science and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhaoqing Chu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.,Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
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12
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Chai WW, Wang WY, Ma Q, Yin HJ, Hepworth SR, Wang SM. Comparative transcriptome analysis reveals unique genetic adaptations conferring salt tolerance in a xerohalophyte. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:670-683. [PMID: 31064640 DOI: 10.1071/fp18295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Most studies on salt tolerance in plants have been conducted using glycophytes like Arabidopsis thaliana (L.) Heynh., with limited resistance to salinity. The xerohalophyte Zygophyllum xanthoxylum (Bunge) Engl. is a salt-accumulating desert plant that efficiently transports Na+ into vacuoles to manage salt and exhibits increased growth under salinity conditions, suggesting a unique transcriptional response compared with glycophytes. We used transcriptome profiling by RNA-seq to compare gene expression in roots of Z. xanthoxylum and A. thaliana under 50 mM NaCl treatments. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis suggested that 50 mM NaCl was perceived as a stimulus for Z. xanthoxylum whereas a stress for A. thaliana. Exposure to 50 mM NaCl caused metabolic shifts towards gluconeogenesis to stimulate growth of Z. xanthoxylum, but triggered defensive systems in A. thaliana. Compared with A. thaliana, a vast array of ion transporter genes was induced in Z. xanthoxylum, revealing an active strategy to uptake Na+ and nutrients from the environment. An ascorbate-glutathione scavenging system for reactive oxygen species was also crucial in Z. xanthoxylum, based on high expression of key enzyme genes. Finally, key regulatory genes for the biosynthesis pathways of abscisic acid and gibberellin showed distinct expression patterns between the two species and auxin response genes were more active in Z. xanthoxylum compared with A. thaliana. Our results provide an important framework for understanding unique patterns of gene expression conferring salt resistance in Z. xanthoxylum.
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Affiliation(s)
- Wei-Wei Chai
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Wen-Ying Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Qing Ma
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Hong-Ju Yin
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China
| | - Shelley R Hepworth
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Suo-Min Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, PR China; and Corresponding author.
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13
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Shu H, Zhang J, Liu F, Bian C, Liang J, Liang J, Liang W, Lin Z, Shu W, Li J, Shi Q, Liao B. Comparative Transcriptomic Studies on a Cadmium Hyperaccumulator Viola baoshanensis and Its Non-Tolerant Counterpart V. inconspicua. Int J Mol Sci 2019; 20:E1906. [PMID: 30999673 PMCID: PMC6515270 DOI: 10.3390/ijms20081906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/14/2019] [Accepted: 04/16/2019] [Indexed: 12/29/2022] Open
Abstract
Many Viola plants growing in mining areas exhibit high levels of cadmium (Cd) tolerance and accumulation, and thus are ideal organisms for comparative studies on molecular mechanisms of Cd hyperaccumulation. However, transcriptomic studies of hyperaccumulative plants in Violaceae are rare. Viola baoshanensis is an amazing Cd hyperaccumulator in metalliferous areas of China, whereas its relative V. inconspicua is a non-tolerant accumulator that resides at non-metalliferous sites. Here, comparative studies by transcriptome sequencing were performed to investigate the key pathways that are potentially responsible for the differential levels of Cd tolerance between these two Viola species. A cascade of genes involved in the ubiquitin proteosome system (UPS) pathway were observed to have constitutively higher transcription levels and more activation in response to Cd exposure in V. baoshanensis, implying that the enhanced degradation of misfolded proteins may lead to high resistance against Cd in this hyperaccumulator. Many genes related to sucrose metabolism, especially those involved in callose and trehalose biosynthesis, are among the most differentially expressed genes between the two Viola species, suggesting a crucial role of sucrose metabolism not only in cell wall modification through carbon supply but also in the antioxidant system as signaling molecules or antioxidants. A comparison among transcriptional patterns of some known transporters revealed that several tonoplast transporters are up-regulated in V. baoshanensis under Cd stress, suggesting more efficient compartmentalization of Cd in the vacuoles. Taken together, our findings provide valuable insight into Cd hypertolerance in V. baoshanensis, and the corresponding molecular mechanisms will be useful for future genetic engineering in phytoremediation.
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Affiliation(s)
- Haoyue Shu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Jun Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Fuye Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Jieliang Liang
- School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Jiaqi Liang
- School of Biosciences and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Weihe Liang
- School of Biosciences and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Zhiliang Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Jintian Li
- School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Bin Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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14
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Meier SK, Adams N, Wolf M, Balkwill K, Muasya AM, Gehring CA, Bishop JM, Ingle RA. Comparative RNA-seq analysis of nickel hyperaccumulating and non-accumulating populations of Senecio coronatus (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1023-1038. [PMID: 29952120 DOI: 10.1111/tpj.14008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 06/20/2018] [Indexed: 06/08/2023]
Abstract
Most metal hyperaccumulating plants accumulate nickel, yet the molecular basis of Ni hyperaccumulation is not well understood. We chose Senecio coronatus to investigate this phenomenon as this species displays marked variation in shoot Ni content across ultramafic outcrops in the Barberton Greenstone Belt (South Africa), thus allowing an intraspecific comparative approach to be employed. No correlation between soil and shoot Ni contents was observed, suggesting that this variation has a genetic rather than environmental basis. This was confirmed by our observation that the accumulation phenotype of plants from two hyperaccumulator and two non-accumulator populations was maintained when the plants were grown on a soil mix from these four sites for 12 months. We analysed the genetic variation among 12 serpentine populations of S. coronatus, and used RNA-seq for de novo transcriptome assembly and analysis of gene expression in hyperaccumulator versus non-accumulator populations. Genetic analysis revealed the presence of hyperaccumulators in two well supported evolutionary lineages, indicating that Ni hyperaccumulation may have evolved more than once in this species. RNA-Seq analysis indicated that putative homologues of transporters associated with root iron uptake in plants are expressed at elevated levels in roots and shoots of hyperaccumulating populations of S. coronatus from both evolutionary lineages. We hypothesise that Ni hyperaccumulation in S. coronatus may have evolved through recruitment of these transporters, which play a role in the iron-deficiency response in other plant species.
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Affiliation(s)
- Stuart K Meier
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Nicolette Adams
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Michael Wolf
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
| | - Kevin Balkwill
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa
| | - Abraham Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Christoph A Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jacqueline M Bishop
- Department of Biological Sciences, University of Cape Town, Rondebosch, 7700, South Africa
| | - Robert A Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7700, South Africa
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15
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Gullì M, Marchi L, Fragni R, Buschini A, Visioli G. Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:464-475. [PMID: 29656392 DOI: 10.1002/em.22191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/09/2018] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Laura Marchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Rosaria Fragni
- SSICA, Experimental Station for the Food Preserving Industry, via Tanara 31, Parma, 43100, Italy
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
| | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma, 43124, Italy
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16
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Merlot S, Sanchez Garcia de la Torre V, Hanikenne M. Physiology and Molecular Biology of Trace Element Hyperaccumulation. AGROMINING: FARMING FOR METALS 2018. [DOI: 10.1007/978-3-319-61899-9_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Bothe H, Słomka A. Divergent biology of facultative heavy metal plants. JOURNAL OF PLANT PHYSIOLOGY 2017; 219:45-61. [PMID: 29028613 DOI: 10.1016/j.jplph.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 05/04/2023]
Abstract
Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current literature favours the idea that hyperaccumulation of heavy metals serves plants as deterrent against attack by feeding animals (termed elemental defense hypothesis). The capability to hyperaccumulate heavy metals in A. halleri and N. caerulescens is achieved by duplications and alterations of the cis-regulatory properties of genes coding for heavy metal transporting/excreting proteins. Several metallophytes have developed ecotypes with a varying content of such heavy metal transporters as an adaption to the specific toxicity of a heavy metal site.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany.
| | - Aneta Słomka
- Department of Plant Cytology and Embryology, Jagiellonian University, Gronostajowa 9 Str., 30-387 Cracow, Poland.
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18
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Goyal E, Amit SK, Singh RS, Mahato AK, Chand S, Kanika K. Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local. Sci Rep 2016; 6:27752. [PMID: 27293111 PMCID: PMC4904219 DOI: 10.1038/srep27752] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/24/2016] [Indexed: 11/23/2022] Open
Abstract
Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using Roche 454-GS FLX Titanium sequencing technology. From these reads 22,241 ESTs were generated out of which, 17,911 unigenes were obtained. A total of 14,898 unigenes were annotated against nr protein database. Seventy seven transcription factors families in 826 unigenes and 11,002 SSRs in 6,939 unigenes were identified. Kyoto Encyclopedia of Genes and Genomes database identified 310 metabolic pathways. The expression pattern of few selected genes was compared during the time course of salt stress treatment between salt-tolerant (Kharchia Local) and susceptible (HD2687). The transcriptome data is the first report, which offers an insight into the mechanisms and genes involved in salt tolerance. This information can be used to improve salt tolerance in elite wheat cultivars and to develop tolerant germplasm for other cereal crops.
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Affiliation(s)
- Etika Goyal
- Banasthali University, Banasthali, Rajasthan, India.,Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Singh K Amit
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Ravi S Singh
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Ajay K Mahato
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
| | - Suresh Chand
- Banasthali University, Banasthali, Rajasthan, India.,Devi Ahilya University, Indore, India
| | - Kumar Kanika
- Biotechnology and Climate Change Laboratory, ICAR-NRC on Plant Biotechnology, New Delhi, India
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19
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Theriault G, Michael P, Nkongolo K. Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera). PLoS One 2016; 11:e0153762. [PMID: 27082755 PMCID: PMC4833294 DOI: 10.1371/journal.pone.0153762] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/04/2016] [Indexed: 11/18/2022] Open
Abstract
White birch (Betula papyrifera) is a dominant tree species of the Boreal Forest. Recent studies have shown that it is fairly resistant to heavy metal contamination, specifically to nickel. Knowledge of regulation of genes associated with metal resistance in higher plants is very sketchy. Availability and annotation of the dwarf birch (B. nana) enables the use of high throughout sequencing approaches to understanding responses to environmental challenges in other Betula species such as B. papyrifera. The main objectives of this study are to 1) develop and characterize the B. papyrifera transcriptome, 2) assess gene expression dynamics of B. papyrifera in response to nickel stress, and 3) describe gene function based on ontology. Nickel resistant and susceptible genotypes were selected and used for transcriptome analysis. A total of 208,058 trinity genes were identified and were assembled to 275,545 total trinity transcripts. The transcripts were mapped to protein sequences and based on best match; we annotated the B. papyrifera genes and assigned gene ontology. In total, 215,700 transcripts were annotated and were compared to the published B. nana genome. Overall, a genomic match for 61% transcripts with the reference genome was found. Expression profiles were generated and 62,587 genes were found to be significantly differentially expressed among the nickel resistant, susceptible, and untreated libraries. The main nickel resistance mechanism in B. papyrifera is a downregulation of genes associated with translation (in ribosome), binding, and transporter activities. Five candidate genes associated to nickel resistance were identified. They include Glutathione S-transferase, thioredoxin family protein, putative transmembrane protein and two Nramp transporters. These genes could be useful for genetic engineering of birch trees.
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Affiliation(s)
- Gabriel Theriault
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Paul Michael
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
- Department of Biology, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
- * E-mail:
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20
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Martos S, Gallego B, Sáez L, López-Alvarado J, Cabot C, Poschenrieder C. Characterization of Zinc and Cadmium Hyperaccumulation in Three Noccaea (Brassicaceae) Populations from Non-metalliferous Sites in the Eastern Pyrenees. FRONTIERS IN PLANT SCIENCE 2016; 7:128. [PMID: 26904085 PMCID: PMC4746256 DOI: 10.3389/fpls.2016.00128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/23/2016] [Indexed: 05/08/2023]
Abstract
The Southern slope of the Pyrenees is the meridional limit for the distribution of several Noccaea populations. However, the systematic description of these populations and their hyperaccumulation mechanisms are not well established. Morphological and genetic analysis (ITS and 3 chloroplast regions) were used to identify Noccaea populations localized on non-metallicolous soils during a survey in the Catalonian Pyrenees. Cd and Zn concentrations were analyzed in soils and plants both sampled in the field and grown hydroponically. The expression of selected metal transporter genes was assessed by quantitative PCR. The populations were identified as Noccaea brachypetala (Jord.) F.K. Mey by conspicuous morphological traits. Principal component analysis provided a clear separation among N. brachypetala, Noccaea caerulescens J. Presl & C. Presl and Noccaea occitanica (Jord.) F.K. Mey., three Noccaea species reported in the Pyrenees. Contrastingly, ITS and cpDNA analyses were unable to clearly differentiate these taxa. Differences in the expression of the metal transporter genes HMA3, HMA4, and MTP1 between N. caerulescens and N. brachypetala, and those amongst the N. brachypetala populations suggest differences in the strategies for handling enhanced Cd and Zn availability. This is the first report demonstrating Cd and Zn hyperaccumulation by N. brachypetala both in the field and in hydroponics. This comprehensive study based on taxonomic, molecular, and physiological data allows both the correct identification of this species and the characterization of population differences in hyperaccumulation and tolerance of Zn and Cd.
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Affiliation(s)
- Soledad Martos
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Berta Gallego
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Llorenç Sáez
- Botany Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Javier López-Alvarado
- Botany Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Catalina Cabot
- Biology Department, Universitat de les Illes BalearsPalma de Mallorca, Spain
| | - Charlotte Poschenrieder
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de BarcelonaBarcelona, Spain
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21
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Huang CH, Sun R, Hu Y, Zeng L, Zhang N, Cai L, Zhang Q, Koch MA, Al-Shehbaz I, Edger PP, Pires JC, Tan DY, Zhong Y, Ma H. Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution. Mol Biol Evol 2015; 33:394-412. [PMID: 26516094 PMCID: PMC4866547 DOI: 10.1093/molbev/msv226] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.
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Affiliation(s)
- Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Renran Sun
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, The Huck Institute of the Life Sciences, Pennsylvania State University
| | - Liping Zeng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Zhang
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC
| | - Liming Cai
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia
| | - Dun-Yan Tan
- Xinjiang Key Laboratory of Grassland Resources and Ecology, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Yang Zhong
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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22
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Ricachenevsky FK, Menguer PK, Sperotto RA, Fett JP. Got to hide your Zn away: Molecular control of Zn accumulation and biotechnological applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 236:1-17. [PMID: 26025516 DOI: 10.1016/j.plantsci.2015.03.009] [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: 11/14/2014] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 05/20/2023]
Abstract
Zinc (Zn) is an essential micronutrient for all organisms, with key catalytic and structural functions. Zn deficiency in plants, common in alkaline soils, results in growth arrest and sterility. On the other hand, Zn can become toxic at elevated concentrations. Several studies revealed molecules involved with metal acquisition in roots, distribution within the plant and translocation to seeds. Transmembrane Zn transport proteins and Zn chelators are involved in avoiding its toxic effects. Plant species with the capacity to hyperaccumulate and hypertolerate Zn have been characterized. Plants that accumulate and tolerate high amounts of Zn and produce abundant biomass may be useful for phytoremediation, allowing cleaning of metal-contaminated soils. The study of Zn hyperaccumulators may provide indications of genes and processes useful for biofortification, for developing crops with high amounts of nutrients in edible tissues. Future research needs to focus on functional characterization of Zn transporters in planta, elucidation of Zn uptake and sensing mechanisms, and on understanding the cross-talk between Zn homeostasis and other physiological processes. For this, new research should use multidisciplinary approaches, combining traditional and emerging techniques, such as genome-encoded metal sensors and multi-element imaging, quantification and speciation using synchrotron-based methods.
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Affiliation(s)
- Felipe Klein Ricachenevsky
- Centro de Biotecnologia & Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Paloma Koprovski Menguer
- Centro de Biotecnologia & Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; John Innes Centre, Norwich, United Kingdom.
| | - Raul Antonio Sperotto
- Centro de Ciências Biológicas e da Saúde & Programa de Pós-Graduação em Biotecnologia, Centro Universitário UNIVATES, Lajeado, RS, Brazil.
| | - Janette Palma Fett
- Centro de Biotecnologia & Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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23
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Yamamoto N, Takano T, Tanaka K, Ishige T, Terashima S, Endo C, Kurusu T, Yajima S, Yano K, Tada Y. Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. FRONTIERS IN PLANT SCIENCE 2015; 6:241. [PMID: 25954282 PMCID: PMC4404951 DOI: 10.3389/fpls.2015.00241] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/26/2015] [Indexed: 05/06/2023]
Abstract
The turf grass Sporobolus virginicus is halophyte and has high salinity tolerance. To investigate the molecular basis of its remarkable tolerance, we performed Illumina high-throughput RNA sequencing on roots and shoots of a S. virginicus genotype under normal and saline conditions. The 130 million short reads were assembled into 444,242 unigenes. A comparative analysis of the transcriptome with rice and Arabidopsis transcriptome revealed six turf grass-specific unigenes encoding transcription factors. Interestingly, all of them showed root specific expression and five of them encode bZIP type transcription factors. Another remarkable transcriptional feature of S. virginicus was activation of specific pathways under salinity stress. Pathway enrichment analysis suggested transcriptional activation of amino acid, pyruvate, and phospholipid metabolism. Up-regulation of several unigenes, previously shown to respond to salt stress in other halophytes was also observed. Gene Ontology enrichment analysis revealed that unigenes assigned as proteins in response to water stress, such as dehydrin and aquaporin, and transporters such as cation, amino acid, and citrate transporters, and H(+)-ATPase, were up-regulated in both shoots and roots under salinity. A correspondence analysis of the enriched pathways in turf grass cells, but not in rice cells, revealed two groups of unigenes similarly up-regulated in the turf grass in response to salt stress; one of the groups, showing excessive up-regulation under salinity, included unigenes homologos to salinity responsive genes in other halophytes. Thus, the present study identified candidate genes involved in salt tolerance of S. virginicus. This genetic resource should be valuable for understanding the mechanisms underlying high salt tolerance in S. virginicus. This information can also provide insight into salt tolerance in other halophytes.
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Affiliation(s)
- Naoki Yamamoto
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Tomoyuki Takano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Taichiro Ishige
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Shin Terashima
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
| | - Chisato Endo
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
| | - Takamitsu Kurusu
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
| | - Shunsuke Yajima
- NODAI Genome Research Center, Tokyo University of AgricultureSetagaya-ku, Japan
- Department of Bioscience, Tokyo University of AgricultureSetagaya-ku, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji UniversityTama-ku, Kawasaki, Japan
- *Correspondence: Kentaro Yano, Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan
| | - Yuichi Tada
- School of Bioscience and Biotechnology, Tokyo University of TechnologyHachioji, Japan
- Yuichi Tada, School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan
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24
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Visioli G, D'Egidio S, Sanangelantoni AM. The bacterial rhizobiome of hyperaccumulators: future perspectives based on omics analysis and advanced microscopy. FRONTIERS IN PLANT SCIENCE 2014; 5:752. [PMID: 25709609 PMCID: PMC4285865 DOI: 10.3389/fpls.2014.00752] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/08/2014] [Indexed: 05/20/2023]
Abstract
Hyperaccumulators are plants that can extract heavy metal ions from the soil and translocate those ions to the shoots, where they are sequestered and detoxified. Hyperaccumulation depends not only on the availability of mobilized metal ions in the soil, but also on the enhanced activity of metal transporters and metal chelators which may be provided by the plant or its associated microbes. The rhizobiome is captured by plant root exudates from the complex microbial community in the soil, and may colonize the root surface or infiltrate the root cortex. This community can increase the root surface area by inducing hairy root proliferation. It may also increase the solubility of metals in the rhizosphere and promote the uptake of soluble metals by the plant. The bacterial rhizobiome, a subset of specialized microorganisms that colonize the plant rhizosphere and endosphere, makes an important contribution to the hyperaccumulator phenotype. In this review, we discuss classic and more recent tools that are used to study the interactions between hyperaccumulators and the bacterial rhizobiome, and consider future perspectives based on the use of omics analysis and microscopy to study plant metabolism in the context of metal accumulation. Recent data suggest that metal-resistant bacteria isolated from the hyperaccumulator rhizosphere and endosphere could be useful in applications such as phytoextraction and phytoremediation, although more research is required to determine whether such properties can be transferred successfully to non-accumulator species.
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Affiliation(s)
- Giovanna Visioli
- *Correspondence: Giovanna Visioli, Department of Life Sciences, University of Parma, Parco Area delle Scienze 33/A, 43124 Parma, Italy e-mail:
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