1
|
Šutković J, Van Wieren A, Peljto E, Yildirim A. Phytoremediation potential of Brassica oleracea varieties through cadmium tolerance gene expression analysis. J Genet Eng Biotechnol 2024; 22:100381. [PMID: 38797549 PMCID: PMC11103569 DOI: 10.1016/j.jgeb.2024.100381] [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: 12/07/2023] [Revised: 04/20/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Brassica oleracea var. acephala, commonly referred to as kale, is a well-documented plant species, a food crop but well recognized for its capacity to endure and manage the accumulation of heavy metals. In this research, the phytoremediation potential of kale was evaluated based on cadmium intake, utilizing three distinct kale varieties originating from Bosnia and Herzegovina. All kales were grown in controlled conditions, with different concentrations of cadmium (Cd), a known strong pollutant found in small concentrations in soil under normal environmental conditions. After the root length analysis and cadmium atomic spectrometry, we utilized quantitative PCR (qPCR) and cycle threshold (Ct) values to calculate the expression levels of five genes associated with Cd heavy metal response: Mitogen-activated protein kinase 2 (MAPK2), Farnesylated protein 26 and 27 (HIPP26, HIPP27), Natural resistance-associated macrophage protein 6 (RAMP6), and Heavy metal accumulator 2 (HMA2). RESULTS The atomic reader's analysis of rising cadmium concentrations revealed a proportional decline in the length of kale roots. The gene expression levels corresponded to cadmium stress differently among varieties, but mostly showing notable up-regulations under Cd stress, indicating the strong Cd presence within the plant. CONCLUSIONS This study demonstrated differences in gene expression behavior among three B. oleracea varieties from Bosnia and Herzegovina, indicating and filtering the Cd-resistant kale, and kale varieties suitable for phytoremediation. For the first time, such a study was conducted on kale varieties from Bosnia and Herzegovina, analyzing the impact of cadmium on the growth and resilience of these species.
Collapse
Affiliation(s)
- Jasmin Šutković
- International University of Sarajevo, Faculty of Engineering and Natural Sciences, Bosnia and Herzegovina.
| | - Annissa Van Wieren
- International University of Sarajevo, Faculty of Engineering and Natural Sciences, Bosnia and Herzegovina
| | - Ensar Peljto
- International University of Sarajevo, Faculty of Engineering and Natural Sciences, Bosnia and Herzegovina
| | - Ahmet Yildirim
- International University of Sarajevo, Faculty of Engineering and Natural Sciences, Bosnia and Herzegovina
| |
Collapse
|
2
|
Wang P, Zhu L, Li Z, Cheng M, Chen X, Wang A, Wang C, Zhang X. Genome-Wide Identification of the U-Box E3 Ubiquitin Ligase Gene Family in Cabbage ( Brassica oleracea var. capitata) and Its Expression Analysis in Response to Cold Stress and Pathogen Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1437. [PMID: 37050063 PMCID: PMC10097260 DOI: 10.3390/plants12071437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/19/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Plant U-box E3 ubiquitin ligases (PUBs) play an important role in growth, development, and stress responses in many species. However, the characteristics of U-box E3 ubiquitin ligase genes in cabbage (Brassica oleracea var. capitata) are still unclear. Here, we carry out the genome-wide analysis of U-box E3 ubiquitin ligase genes in cabbage and identify 65 Brassica oleracea var. capitata U-box E3 ubiquitin ligase (BoPUB) genes in the cabbage genome. Phylogenetic analysis indicates that all 65 BoPUB genes are grouped into six subfamilies, whose members are relatively conserved in the protein domain and exon-intron structure. Chromosomal localization and synteny analyses show that segmental and tandem duplication events contribute to the expansion of the U-box E3 ubiquitin ligase gene family in cabbage. Protein interaction prediction presents that heterodimerization may occur in BoPUB proteins. In silico promoter analysis and spatio-temporal expression profiling of BoPUB genes reveal their involvement in light response, phytohormone response, and growth and development. Furthermore, we find that BoPUB genes participate in the biosynthesis of cuticular wax and in response to cold stress and pathogenic attack. Our findings provide a deep insight into the U-box E3 ubiquitin ligase gene family in cabbage and lay a foundation for the further functional analysis of BoPUB genes in different biological processes.
Collapse
Affiliation(s)
- Peiwen Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Lin Zhu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Ziheng Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Mozhen Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Xiuling Chen
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Chao Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoxuan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (P.W.); (L.Z.); (Z.L.); (M.C.); (X.C.); (A.W.); (C.W.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin 150030, China
| |
Collapse
|
3
|
Jaskulak M, Rostami S, Zorena K, Vandenbulcke F. Transcriptome sequencing of Brassica napus highlights the complex issues with soil supplementation with sewage sludge. CHEMOSPHERE 2022; 298:134321. [PMID: 35306057 DOI: 10.1016/j.chemosphere.2022.134321] [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: 12/29/2021] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
The soil supplementation with sewage sludge (SS) has become a widespread method to improve soil quality, but its long-term possible consequences are still relatively unknown. SS may contain several groups of contaminants to which the biological responses of the organisms are still poorly understood mainly due to the mixture toxicity. In this context, RNA-seq has been used to assess the impact of the exposure to sewage sludge supplemented soil at the whole-transcriptome level in the Brassica napus (B. napus). Although the municipal sewage sludge passed all safety regulations set by the EU commission (86/278/EEC), soil supplementation with SS caused a significant (p < 0.05) increase in the content of lead (by 68.8%, 71.4% in plant shoots and roots, respectively), zinc (by 22.4% and 31.2%), nickel (by 67.0% and 30.2%), and copper (by 33.1% and 39.2%). The de-novo assembled transcriptome of B. napus identified 555 differently expressed genes (DEGs) in a response to sewage sludge supplementation at the false detection rate below 0.001 (FDR <0.001). Among them, 313 genes were up-regulated and 242 genes were down-regulated. The gene ontology analysis (GO) had shown, that significantly enriched GO groups included genes involved in photosynthesis, carbohydrate metabolism and photosystems repair (41 genes), response to oxidative stress (50 genes), response to pathogens (36 genes), response to xenobiotics (15 genes), and heavy metals (41 genes), cell death (8 genes), cell wall structure (15 genes). These results suggest a significant impact of contaminants in sewage sludge on plants transcriptome. The transcriptomic approach facilitated a better understanding of the molecular level of the potential toxicity of sewage sludge in B. napus. RNA-seq allowed for the identification of potential novel early-warning molecular markers of environmental contamination. This work highlights the crucial necessity for rapid legislation change concerning the allowable levels of contaminants in sewage sludge applied on land, to mitigate the possible adverse outcomes in the ecosystem after its use as a fertilizer.
Collapse
Affiliation(s)
- Marta Jaskulak
- University of Lille, IMT Lille Douai, University of Artois, Yncrea Hauts-de-France, ULR4515, LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000, Lille, France; Department of Immunobiology and Environmental Microbiology, Medical University of Gdańsk, Poland; Institute of Environmental Engineering, Czestochowa University of Technology, Czestochowa, Poland.
| | - Saeid Rostami
- Department of Environmental Health, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Katarzyna Zorena
- Department of Immunobiology and Environmental Microbiology, Medical University of Gdańsk, Poland
| | - Franck Vandenbulcke
- University of Lille, IMT Lille Douai, University of Artois, Yncrea Hauts-de-France, ULR4515, LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000, Lille, France
| |
Collapse
|
4
|
Chaâbene Z, Rorat A, Kriaa W, Rekik I, Mejdoub H, Vandenbulcke F, Elleuch A. In-site and Ex-site Date Palm Exposure to Heavy Metals Involved Infra-Individual Biomarkers Upregulation. PLANTS 2021; 10:plants10010137. [PMID: 33445405 PMCID: PMC7826821 DOI: 10.3390/plants10010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
As a tree of considerable importance in arid regions-date palm, Phoenix dactylifera L. survival in contaminated areas of Sfax city has drawn our attention. Leaf samples of the plants grown in the study area showed high levels of cadmium (Cd), copper (Cu), and chromium (Cr). On the basis of this finding, the cellular mechanisms that explain these metal accumulations were investigated in controlled conditions. After four months of exposure to Cd, Cr, or Cu, high bioconcentration and translocation factor (TF>1) have been shown for date palm plantlets exposed to Cd and low TF values were obtained for plantlets treated with Cr and Cu. Moreover, accumulation of oxidants and antioxidant enzyme activities occurred in exposed roots to Cu and Cd. Secondary metabolites, such as polyphenols and flavonoids, were enhanced in plants exposed at low metal concentrations and declined thereafter. Accumulation of flavonoids in cells may be correlated with the expression of the gene encoding Pdmate5, responsible for the transport of secondary metabolites, especially flavonoids. Other transporter genes responded positively to metal incorporation, especially Pdhma2, but also Pdabcc and Pdnramp6. The latter would be a new candidate gene sensitive to metallic stress in plants. Expressions of gene coding metal chelators were also investigated. Pdpcs1 and Pdmt3 exhibited a strong induction in plants exposed to Cr. These modifications of the expression of some biochemical and molecular based-markers in date palm helped to better understand the ability of the plant to tolerate metals. They could be useful in assessing heavy metal contaminations in polluted soils and may improve accumulation capacity of other plants.
Collapse
Affiliation(s)
- Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
- Correspondence:
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Walid Kriaa
- Environmental Science Center, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Imen Rekik
- High Institute of Applied Biology of Medenine, Medenine 4119, Tunisia;
| | - Hafedh Mejdoub
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement–Université de Lille 1, F-59655 Villeneuve d’Ascq, France; (A.R.); (F.V.)
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Sfax 3000, Tunisia; (H.M.); (A.E.)
| |
Collapse
|
5
|
Jaskulak M, Grobelak A, Vandenbulcke F. Effects of sewage sludge supplementation on heavy metal accumulation and the expression of ABC transporters in Sinapis alba L. during assisted phytoremediation of contaminated sites. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 197:110606. [PMID: 32304921 DOI: 10.1016/j.ecoenv.2020.110606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
ATP binding cassette (ABC) transporters, types C, G, and B were monitored via qPCR in order to investigate the influence of heavy metal (HM) contamination of post-industrial and post-agricultural soils and the effects of its supplementation with sewage sludge, on Sinapis alba plants. Five house-keeping genes were selected and validated to ensure the best reference points. The relative expression of ABC types C and G genes was profoundly affected by experimental conditions and included their upregulation after plants exposure to heavy metals and downregulation after supplementation with sewage sludge. However, ABC type C was more responsive then type G. The experimental conditions altered the expression of ABC type C gene faster than ABC type G and thus, the expression of ABC type C can therefore potentially be used as a bioindicator during assisted phytoremediation of degraded sites. In clean soil, supplementation with sewage sludge with a slight content of heavy metals still caused an upregulation in the expression of ABC types C and G, which showed that proper toxicity assessments are necessary to ensure safe application of sewage sludge into soils. Results showed that the analysed genes take a significant part in plants metal detoxification and that their expression is regulated at transcriptional level after exposure to soil contaminated with heavy metals by both, industrial activities and by sewage sludge supplementation. Thus, their expression can potentially be used as an early-warning biomarker when soil supplementation with sewage sludge is incorporated into the soil-management process.
Collapse
Affiliation(s)
- Marta Jaskulak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland; University of Lille, Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, F-59650, Villeneuve d'Ascq, France.
| | - Anna Grobelak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland
| | - Franck Vandenbulcke
- University of Lille, Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, F-59650, Villeneuve d'Ascq, France
| |
Collapse
|
6
|
Rekik I, Chaâbene Z, Kriaa W, Rorat A, Franck V, Hafedh M, Elleuch A. Transcriptome assembly and abiotic related gene expression analysis of date palm reveal candidate genes involved in response to cadmium stress. Comp Biochem Physiol C Toxicol Pharmacol 2019; 225:108569. [PMID: 31302231 DOI: 10.1016/j.cbpc.2019.108569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/03/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Date palm in Tunisia is of major economic importance but are also factors of social, environmental and economic stability. An annotated assembly of the transcriptome of cultivar Deglet Nour was reported. RNA was isolated from plant Cd-contaminated leaves, and 37,049 unique Illumina RNA-seq reads were used in a transcriptome assembly. The draft transcriptome assembly consists of 6789 contigs and 17.285 singletons with a means length of 858 bp and 1.042 bp, respectively. The final assembly was functionally annotated using Blast2GO software, allowing the identification of putative genes controlling important agronomic traits. The annotated transcriptome data sets were used to query all known Kyoto Encyclopedia of Genes and Genomes pathways. The most represented molecular functions and biological processes were nucleotide binding and transcription, transport and response to stress and abiotic and biotic stimuli. A prediction of the genes interaction network was proposed by selecting corresponding functionally similar genes from Arabidopsis datasets, downloaded by GeneMANIA version 2.1. Several Cd-responsive genes expression was monitored in in vitro isolated explant of Cd stressed Deglet Nour. Some chelators encoding genes were upregulated confirming in silico findings. Genes encoding HMs transporters in date palm showed expression enhancement more pronounced after 20 days of exposure. P. dactylifera transcriptome provides a valuable resource for future functional analysis of candidate genes involved in metal stress response.
Collapse
Affiliation(s)
- Imen Rekik
- High Institute of Applied Biology of Medenine, Tunisia; Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia; Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Walid Kriaa
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia; Environmental Science Center, Qatar University, PO. Box 2713, Doha, Qatar
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Vandenbulcke Franck
- Laboratoire de Génie Civil et géo-Environnement - Université de Lille 1, F-59655 Villeneuve d'Ascq, France.
| | - Mejdoub Hafedh
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Amine Elleuch
- Laboratory of Plant Biotechnology, Faculty of Sciences of Sfax, University of Sfax, Tunisia
| |
Collapse
|
7
|
Jaskulak M, Grobelak A, Grosser A, Vandenbulcke F. Gene expression, DNA damage and other stress markers in Sinapis alba L. exposed to heavy metals with special reference to sewage sludge application on contaminated sites. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 181:508-517. [PMID: 31234065 DOI: 10.1016/j.ecoenv.2019.06.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 06/09/2023]
Abstract
Bioindicators are promising tools used to detect the long-term effects of selected biosolids on plants development and should be implemented before large-scale supplementation of sewage sludge into the soil. The presented study shows the impact of sewage sludge application on metal-sensitive toxicity biological parameters (biomarkers) in Sinapis alba including: germination, root length, the activity of guaiacol peroxidase, the chlorophyll content, the level of DNA damage and the expression level of Ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and metallothionein (mt). We evaluated data from selected biomarkers in order to broaden our understanding of plants defense mechanisms against heavy metal contamination and the application of sewage sludge into soils. Overall, in contaminated soil after supplementation with both municipal sewage sludges, an increase in toxicity was noticed in DNA damage, mt and rbcl expression and total chlorophyll content. The supplementation of both soils with municipal sewage sludge caused a two-time induction in the mt expression. Moreover, clean soil supplemented with sewage sludge caused an increase in DNA damage shown as the tail moment from approximately 12 μm on control to 40 μm after supplementation. Even if those biosolids increased the initial germination, roots length, and biomass in comparison to the unamended soil, the toxicity was evidenced with other stress markers. Results showed, that in order to accurately assess the influence of sewage sludge application on plants the use of several specific biomarkers is required for safe land restoration. The conducted study also confirmed, both under biochemical and genotoxic tests, that iron enrichment for biosolids or contaminated soil can significantly reduce the bioavailability and toxicity of other metals.
Collapse
Affiliation(s)
- Marta Jaskulak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland; University of Lille, Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, F-59650 Villeneuve d'Ascq, France.
| | - Anna Grobelak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland
| | - Anna Grosser
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland
| | - Franck Vandenbulcke
- University of Lille, Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, F-59650 Villeneuve d'Ascq, France
| |
Collapse
|
8
|
Dappe V, Dumez S, Bernard F, Hanoune B, Cuny D, Dumat C, Sobanska S. The role of epicuticular waxes on foliar metal transfer and phytotoxicity in edible vegetables: case of Brassica oleracea species exposed to manufactured particles. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:20092-20106. [PMID: 30264340 DOI: 10.1007/s11356-018-3210-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The rapid industrialization and urbanization of intra- and peri-urban areas at the world scale are responsible for the degradation of the quality of edible crops, because of their contamination with airborne pollutants. Their consumption could lead to serious health risks. In this work, we aim to investigate the phytotoxicity induced by foliar transfer of atmospheric particles of industrial/urban origin. Leaves of cabbage plants (Brassica oleracea var. Prover) were contaminated with metal-rich particles (PbSO4 CuO and CdO) of micrometer size. A trichloroacetic acid (TCA) treatment was used to inhibit the synthesis of the epicuticular waxes in order to investigate their protective role against metallic particles toxicity. Besides the location of the particles on/in the leaves by microscopic techniques, photosynthetic activity measurements, genotoxicity assessment, and quantification of the gene expression have been studied for several durations of exposure (5, 10, and 15 days). The results show that the depletion of epicuticular waxes has a limited effect on the particle penetration in the leaf tissues. The stomatal openings appear to be the main pathway of particles entry inside the leaf tissues, as demonstrated by the overexpression of the BolC.CHLI1 gene. The effects of particles on the photosynthetic activity are limited, considering only the photosynthetic Fv/Fm parameter. The genotoxic effects were significant for the contaminated TCA-treated plants, especially after 10 days of exposure. Still, the cabbage plants are able to implement repair mechanisms quickly, and to thwart the physiological effects induced by the particles. Finally, the foliar contamination by metallic particles induces no serious damage to DNA, as observed by monitoring the BolC.OGG1 gene.
Collapse
Affiliation(s)
- Vincent Dappe
- Laboratoire de Spectrochimie Infrarouge et Raman, CNRS UMR 8516, Université de Lille, 59655, Villeneuve d'Ascq, France.
| | - Sylvain Dumez
- Laboratoire des Sciences Végétales et Fongiques EA4483, Université de Lille, 3 rue du Professeur Laguesse, B.P. 83, Lille, France
| | - Fabien Bernard
- Laboratoire des Sciences Végétales et Fongiques EA4483, Université de Lille, 3 rue du Professeur Laguesse, B.P. 83, Lille, France
| | - Benjamin Hanoune
- Laboratoire de Physico-Chimie des Processus de Combustion et de l'Atmosphère, UMR 8522 CNRS, Université de Lille, 59655, Villeneuve d'Ascq, France
| | - Damien Cuny
- Laboratoire des Sciences Végétales et Fongiques EA4483, Université de Lille, 3 rue du Professeur Laguesse, B.P. 83, Lille, France
| | - Camille Dumat
- Université de Toulouse INP-ENSAT, Avenue de l'Agrobiopole, 31326, Castanet-Tolosan, France
- Université Toulouse - Le Mirail UTM-CERTOP CNRS UMR, 5044, Toulouse, France
| | - Sophie Sobanska
- Laboratoire de Spectrochimie Infrarouge et Raman, CNRS UMR 8516, Université de Lille, 59655, Villeneuve d'Ascq, France.
- Institut des Sciences Moléculaires UMR CNRS 5255, Université de Bordeaux, 351, Cours de la Libération, 33405, Talence, France.
| |
Collapse
|
9
|
Jaskulak M, Rorat A, Grobelak A, Chaabene Z, Kacprzak M, Vandenbulcke F. Bioaccumulation, antioxidative response, and metallothionein expression in Lupinus luteus L. exposed to heavy metals and silver nanoparticles. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:16040-16052. [PMID: 30968299 DOI: 10.1007/s11356-019-04972-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Yellow-lupin (Lupinus luteus L.) was grown on soils contaminated with heavy metals during two parallel studies. In the first one, the soil was contaminated by industrial activities whereas, in the second one, the soil was artificially contaminated with a single metal including Cd, Pb, Zn, Ni (in nitrate form), and Ag (in nitrate and nanoparticles form). The study was performed to assess a plant's response to contamination including its antioxidative response and molecular mechanisms involved in metal detoxification through the expression level of metallothioneins (MTs). Overall, the study provided insights into identification and validation of housekeeping genes (HKG) in L. luteus under exposure to metal stress and showed the effects of selected heavy metals and silver nanoparticles on the expression of metallothioneins, the activity of guaiacol peroxidase (GPX) and bioaccumulation of metals in leaves of L. luteus. As such, HKG validation using BestKeeper, NormFinder, and geNorm software allowed for the selection of four most stable reference genes in a context metal contamination for the selected plant. Moreover, a significant increase in the expression levels of MT was observed in plants grown under heavy metal stress and none on plants grown on 25 mg kg-1 of silver nanoparticles. Also, the GPX activity and MT expression showed statistically significant changes between different conditions and doses which means that they can be used as highly sensitive stress markers for planning the phytoremediation process on a large scale.
Collapse
Affiliation(s)
- Marta Jaskulak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland.
- Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, University of Lille, F-59650, Villeneuve d'Ascq, France.
| | - Agnieszka Rorat
- Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, University of Lille, F-59650, Villeneuve d'Ascq, France
| | - Anna Grobelak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland
| | - Zayneb Chaabene
- Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, University of Lille, F-59650, Villeneuve d'Ascq, France
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, Université de Sfax, Sfax, Tunisie
| | - Małgorzata Kacprzak
- Institute of Environmental Engineering, Faculty of Infrastructure and Environment, Czestochowa University of Technology, Czestochowa, Poland
| | - Franck Vandenbulcke
- Laboratory of Civil Engineering and Environment (LGCgE), Environmental Axis, University of Lille, F-59650, Villeneuve d'Ascq, France
| |
Collapse
|
10
|
Witzel K, Abu Risha M, Albers P, Börnke F, Hanschen FS. Identification and Characterization of Three Epithiospecifier Protein Isoforms in Brassica oleracea. FRONTIERS IN PLANT SCIENCE 2019; 10:1552. [PMID: 31921230 PMCID: PMC6930892 DOI: 10.3389/fpls.2019.01552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/06/2019] [Indexed: 05/03/2023]
Abstract
Glucosinolates present in Brassicaceae play a major role in herbivory defense. Upon tissue disruption, glucosinolates come into contact with myrosinase, which initiates their breakdown to biologically active compounds. Among these, the formation of epithionitriles is triggered by the presence of epithiospecifier protein (ESP) and a terminal double bond in the glucosinolate side chain. One ESP gene is characterized in the model plant Arabidopsis thaliana (AtESP; At1g54040.2). However, Brassica species underwent genome triplication since their divergence from the Arabidopsis lineage. This indicates the presence of multiple ESP isoforms in Brassica crops that are currently poorly characterized. We identified three B. oleracea ESPs, specifically BoESP1 (LOC106296341), BoESP2 (LOC106306810), and BoESP3 (LOC106325105) based on in silico genome analysis. Transcript and protein abundance were assessed in shoots and roots of four B. oleracea vegetables, namely broccoli, kohlrabi, white, and red cabbage, because these genotypes showed a differential pattern for the formation of glucosinolate hydrolysis products as well for their ESP activity. BoESP1 and BoESP2 were expressed mainly in shoots, while BoESP3 was abundant in roots. Biochemical characterization of heterologous expressed BoESP isoforms revealed different substrate specificities towards seven glucosinolates: all isoforms showed epithiospecifier activity on alkenyl glucosinolates, but not on non-alkenyl glucosinolates. The pH-value differently affected BoESP activity: while BoESP1 and BoESP2 activities were optimal at pH 6-7, BoESP3 activity remained relatively stable from pH 4 to 7. In order test their potential for the in vivo modification of glucosinolate breakdown, the three isoforms were expressed in A. thaliana Hi-0, which lacks AtESP expression, and analyzed for the effect on their respective hydrolysis products. The BoESPs altered the hydrolysis of allyl glucosinolate in the A. thaliana transformants to release 1-cyano-2,3-epithiopropane and reduced formation of the corresponding 3-butenenitrile and allyl isothiocyanate. Plants expressing BoESP2 showed the highest percentage of released epithionitriles. Given these results, we propose a model for isoform-specific roles of B. oleracea ESPs in glucosinolate breakdown.
Collapse
Affiliation(s)
- Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Marua Abu Risha
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Philip Albers
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Frederik Börnke
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Franziska S. Hanschen
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
- *Correspondence: Franziska S. Hanschen,
| |
Collapse
|
11
|
Identification of reference genes for RT-qPCR data normalization in Gammarus fossarum (Crustacea Amphipoda). Sci Rep 2018; 8:15225. [PMID: 30323236 PMCID: PMC6189083 DOI: 10.1038/s41598-018-33561-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 09/07/2018] [Indexed: 11/08/2022] Open
Abstract
Gene expression profiling via RT-qPCR is a robust technique increasingly used in ecotoxicology. Determination and validation of optimal reference genes is a requirement for initiating RT-qPCR experiments. To our best knowledge, this study is the first attempt of identifying a set of reference genes for the freshwater crustacean Gammarus fossarum. Six candidate genes (Actin, TUB, UB, SDH, Clathrin and GAPDH) were tested in order to determine the most stable ones in different stress conditions and to increase the robustness of RT-qPCR data. SDH and Clathrin appeared as the most stable ones. A validation was performed using G. fossarum samples exposed for 15 days to AgNO3, silver nanoparticles (AgNPs) 40 nm and gold nanoparticles (AuNPs) 40 nm. Effects on HSP90 were evaluated and data normalized using Clathrin and SDH. A down-regulation of HSP90 was observed when G. fossarum were exposed to AuNPs 40 nm whereas no effects were observed when G. fossarum were exposed to AgNPs 40 nm. This study highlights the importance of the preliminary determination of suitable reference genes for RT-qPCR experiments. Additionally, this study allowed, for the first time, the determination of a set of valuable genes that can be used in other RT-qPCR studies using G. fossarum as model organism.
Collapse
|
12
|
Lukaszewicz G, Amé MV, Menone ML. Selection of reference genes for reverse transcription-qPCR analysis in the biomonitor macrophyte Bidens laevis L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:781-792. [PMID: 30150854 PMCID: PMC6103946 DOI: 10.1007/s12298-018-0534-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/27/2018] [Accepted: 04/09/2018] [Indexed: 05/25/2023]
Abstract
The RT-qPCR has been the method used to analyze gene expression in plants but its benefits have not been completely exploited in the field of plants ecotoxicology when used as molecular biomarkers. The correct use of RT-qPCR demands to establish a certain number of reference genes (RG) which are expected to be invariable in their expression although it does not always happen. The main goals of this work were to: (1) analyze the stability of six potential RG, (2) establish the optimum number of RG, (3) select the most suitable RG to be applied in Bidens laevis under different test conditions and tissues and (4) confirm its convenience by normalizing the expression of one gene of interest under three different challenges. When all data were pooled together, the geNorm algorithm pointed out beta-actin and beta-tubulin (TUB) as the optimal RG pair while NormFinder algorithm selected nicotinamide adenine dinucleotide dehydrogenase (NADHD) and histone 3 (H3) as possessing the most invariable levels of expression. On the other hand, when data were grouped by tissues, ANOVA test selected H3 and TUB, while data grouped by conditions indicated that H3 and NADHD were the most stable RG under this analysis. Therefore, for a general-purpose set of RG, the overall analysis showed that a set of three RG would be optimum, and H3, TUB and NADHD were the selected ones. On the other hand, as RG can vary depending on the tissues or conditions, results achieved with ANOVA would be more reliable. Thus, appropriate normalization process would clearly need more than one RG.
Collapse
Affiliation(s)
- Germán Lukaszewicz
- Instituto de Investigaciones Marinas y Costeras (IIMyC) UNMDP, CONICET, Mar del Plata, Argentina
- Dto. Bioquímica Clínica—CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba - CONICET, Haya de la Torre esq. Medina Allende, 5000 Córdoba, Argentina
| | - María Valeria Amé
- Dto. Bioquímica Clínica—CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba - CONICET, Haya de la Torre esq. Medina Allende, 5000 Córdoba, Argentina
| | - Mirta Luján Menone
- Instituto de Investigaciones Marinas y Costeras (IIMyC) UNMDP, CONICET, Mar del Plata, Argentina
- Dto. Bioquímica Clínica—CIBICI, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba - CONICET, Haya de la Torre esq. Medina Allende, 5000 Córdoba, Argentina
| |
Collapse
|
13
|
Meesapyodsuk D, Ye S, Chen Y, Chen Y, Chapman RG, Qiu X. An engineered oilseed crop produces oil enriched in two very long chain polyunsaturated fatty acids with potential health-promoting properties. Metab Eng 2018; 49:192-200. [PMID: 30149205 DOI: 10.1016/j.ymben.2018.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
Abstract
Very long chain polyunsaturated fatty acids (VLCPUFAs) are well recognized for their health benefits in humans and animals. Here we report that identification and characterization of a gene (EhELO1) encoding the first functional ELO type elongase (3-ketoacyl-CoA synthase) in higher plants that is involved in the biosynthesis of two VLCPUFAs docosadienoic acid (DDA, 22:2n-6) and docosatrienoic acid (DTA, 22:3n-3) that possess potential health-promoting properties. Functional analysis of the gene in yeast indicated that this novel enzyme could elongate a wide range of polyunsaturated fatty acids with 18-22 carbons and effectively catalyze the biosynthesis of DDA and DTA by the sequential elongations of linoleic acid and alpha-linolenic acid, respectively. Seed-specific expression of this gene in oilseed crop Brassica carinata showed that the transgenic plants produced the level of DDA and DTA at approximately 30% of the total fatty acids in seeds, and the amount of the two fatty acids remained stable over four generations. The oilseed crop producing a high and sustained level of DDA and DTA provides an opportunity for high value agricultural products for nutritional and medical uses.
Collapse
Affiliation(s)
| | - Shengjian Ye
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yan Chen
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yi Chen
- Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Xiao Qiu
- National Research Council of Canada, Saskatoon, Saskatchewan, Canada; Department of Food & Bioproduct Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
| |
Collapse
|
14
|
Chaâbene Z, Hakim IR, Rorat A, Elleuch A, Mejdoub H, Vandenbulcke F. Copper toxicity and date palm (Phoenix dactylifera) seedling tolerance: Monitoring of related biomarkers. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2018; 37:797-806. [PMID: 29023967 DOI: 10.1002/etc.4007] [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: 03/29/2017] [Revised: 04/24/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Date palm (Phoenix dactylifera) seeds were exposed to different copper (Cu) solutions to examine plant stress responses. Low Cu concentrations (0.02 and 0.2 mM) caused an increase of seed germination, whereas higher Cu amounts (2 mM) significantly inhibited seed germination, delayed hypocotyl elongation, increased seedling mortality, and reduced the germination index by more than 90%. Metal-related toxicity symptoms appeared after 15 d of 2 mM of Cu exposure. Biochemical activities such as amylase activity and redox balance elements were examined to study the relationship between external Cu amount and internal plant response. The present study showed that amylolytic activity was dose- and time-dependent. Likewise, H2 O2 production increased after exposure to Cu, which was correlated with thiobarbituric acid reactive substance (TBARS) accumulation. Furthermore at low Cu concentrations, superoxide dismutase (SOD) and catalase (CAT) activities increased, suggesting that date palm seed stimulated its metal homeostasis networks. However, the highest cupric ion amounts increased cell oxidant accumulation and reduced enzyme production. Gene expression level measures of P. dactylifera phytochelatin synthase (Pdpcs) and P. dactylifera metallothionein (Pdmt) encoding genes have been carried out to investigate the implication of PdPCS and PdMT proteins in Cu homeostasis and/or its sequestration. Phoenix dactylifera metallothionein induction reached a peak after 30 d of exposure to 0.2 mM of Cu. However, it was down-regulated in plants exposed to higher Cu concentrations. In the same conditions, Pdpcs was overexpressed during 1 mo of exposure before it decreased thereafter. These observations provide a new insight into date palm cell response to Cu, a metal that can be toxic but that is also an essential element. Environ Toxicol Chem 2018;37:797-806. © 2017 SETAC.
Collapse
Affiliation(s)
- Zayneb Chaâbene
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, Sfax, Tunisia
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille, Villeneuve d'Ascq, Lille, France
| | - Imen Rekik Hakim
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Agnieszka Rorat
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille, Villeneuve d'Ascq, Lille, France
| | - Amine Elleuch
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille, Villeneuve d'Ascq, Lille, France
| | - Hafedh Mejdoub
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille, Villeneuve d'Ascq, Lille, France
| | - Franck Vandenbulcke
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille, Villeneuve d'Ascq, Lille, France
| |
Collapse
|
15
|
Rorat A, Vandenbulcke F, Gałuszka A, Klimek B, Plytycz B. Protective role of metallothionein during regeneration in Eisenia andrei exposed to cadmium. Comp Biochem Physiol C Toxicol Pharmacol 2017; 203:39-50. [PMID: 29038073 DOI: 10.1016/j.cbpc.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 02/08/2023]
Abstract
Lumbricid earthworms are often exposed to simultaneous action of various environmental stressors like soil contamination, temperature fluctuation or predators' attacks, which may induce extrusion of coelomocyte-containing coelomic fluid or loss of tail segments. If the injuries are not lethal, renewal of the immune-competent cells and soluble components of coelomic fluid and/or the regeneration of tail segments occurs. The aim of our investigations was to test the hypothesis that exposure of adult earthworms Eisenia andrei to cadmium-polluted soil at room temperature (RT) and/or low temperature (6°C) have adverse effects on restoration of experimentally depleted coelomocytes or on regeneration of amputated posterior segments. Intact control earthworms and their experimental counterparts subjected to electrostimulation-induced coelomocyte depletion or surgical amputation of posterior segments were maintained either in control soil or in soil spiked with cadmium chloride (500mg/kg air-dried soil) at RT or 6°C. Four weeks after the beginning of experiments, cadmium accumulation in earthworm bodies was significantly lower at 6°C than at room temperature. The numbers of restored cells and fluorophore contents were hardly affected by temperature or cadmium. However, cocoon production was reduced by cadmium and completely abolished at 6°C and regeneration of amputated posterior segments was inhibited in cold but was enhanced by cadmium exposure at RT. Independently on the temperature, the 4-week cadmium exposure of adult earthworms was connected with significantly upregulated expression of Cd-metallothionein (but not of catalase, lysenin and phytochelatin) in coelomocytes.
Collapse
Affiliation(s)
- Agnieszka Rorat
- Institute of Environmental Engineering, Czestochowa University of Technology, Czestochowa, Poland; Université de Lille, Sciences et Technologies, Laboratoire de Génie Civil et géo-Environnement, SN3 59655 Villeneuve d'Ascq, France.
| | - Franck Vandenbulcke
- Université de Lille, Sciences et Technologies, Laboratoire de Génie Civil et géo-Environnement, SN3 59655 Villeneuve d'Ascq, France
| | - Adrianna Gałuszka
- Department of Evolutionary Immunology, Institute of Zoology, Jagiellonian University, Krakow, Poland
| | - Beata Klimek
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Barbara Plytycz
- Department of Evolutionary Immunology, Institute of Zoology, Jagiellonian University, Krakow, Poland
| |
Collapse
|
16
|
Poli M, Salvi S, Li M, Varotto C. Selection of reference genes suitable for normalization of qPCR data under abiotic stresses in bioenergy crop Arundo donax L. Sci Rep 2017; 7:10719. [PMID: 28878356 PMCID: PMC5587670 DOI: 10.1038/s41598-017-11019-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/16/2017] [Indexed: 02/08/2023] Open
Abstract
Suitable reference gene selection in qRT-PCR is a key pre-requisite to produce reliable data in gene expression analyses. In this study, novel primers for six commonly used reference genes (AC1, TLF, Act2, TUB α, EF-1α and GAPDH) plus two new candidates (pDUF221 and RPN6) were designed and comparatively tested for expression stability under abiotic stresses (osmotic, heavy metal and heat shock) in shoot, root and their combination of Arundo donax L., a raising non-food energy crop. Expression stability rankings from the most to the least stable gene in each condition and in two tissues (young shoots and roots) were generated with geNorm, NormFinder and BestKeeper programs. All programs provided similar rankings and, strikingly, in most cases identified one of the new candidates, RPN6, as the most suitable reference gene. This novel set of reliable references allows to choose either the best combination of reference genes across multiple stress/organ conditions or to select condition-specific genes that can improve the quality of qRT-PCR analysis. This work provides a solid basis for the functional characterization of A. donax, by enabling accurate quantification of the transcriptional responsiveness under a series of common stress conditions of any gene of interest in this promising biomass/bioenergy species.
Collapse
Affiliation(s)
- Michele Poli
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.,Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, S. Michele all'Adige (TN), Italy.
| |
Collapse
|
17
|
Zayneb C, Imen RH, Walid K, Grubb CD, Bassem K, Franck V, Hafedh M, Amine E. The phytochelatin synthase gene in date palm (Phoenix dactylifera L.): Phylogeny, evolution and expression. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 140:7-17. [PMID: 28231507 DOI: 10.1016/j.ecoenv.2017.02.020] [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: 09/22/2016] [Revised: 02/11/2017] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
We studied date palm phytochelatin synthase type I (PdPCS1), which catalyzes the cytosolic synthesis of phytochelatins (PCs), a heavy metal binding protein, in plant cells. The gene encoding PdPCS1 (Pdpcs) consists of 8 exons and 7 introns and encodes a protein of 528 amino acids. PCs gene history was studied using Notung phylogeny. During evolution, gene loss from several lineages was predicted including Proteobacteria, Bilateria and Brassicaceae. In addition, eleven gene duplication events appeared toward interior nodes of the reconciled tree and four gene duplication events appeared toward the external nodes. These latter sequences belong to species with a second copy of PCs suggesting that this gene evolved through subfunctionalization. Pdpcs1 gene expression was measured in seedling hypocotyls exposed to Cd, Cu and Cr using quantitative real-time polymerase chain reaction (qPCR). A Pdpcs1 overexpression was evidenced in P. dactylifera seedlings exposed to metals suggesting that 1-the Pdpcs1 gene is functional, 2-there is an implication of the enzyme in metal detoxification mechanisms. Additionally, the structure of PdPCS1 was predicted using its homologue from Nostoc (cyanobacterium, NsPCS) as a template in Discovery studio and PyMol software. These analyses allowed us to identify the phytochelatin synthase type I enzyme in date palm (PdPCS1) via recognition of key consensus amino acids involved in the catalytic mechanism, and to propose a hypothetical binding and catalytic site for an additional substrate binding cavity.
Collapse
Affiliation(s)
- Chaâbene Zayneb
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia; Laboratoire de Génie Civil et géo-Environnement, Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Rekik Hakim Imen
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Kriaa Walid
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia
| | - C Douglas Grubb
- Biorecycling Operations Research Laboratory, Des Moines, IA, USA
| | - Khemakhem Bassem
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Vandenbulcke Franck
- Laboratoire de Génie Civil et géo-Environnement, Université de Lille 1, F-59655 Villeneuve d'Ascq, France
| | - Mejdoub Hafedh
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Elleuch Amine
- Laboratory of Plant Biotechnology, Faculty of Sciences, University of Sfax, BP 1171, 3000 Sfax, Tunisia.
| |
Collapse
|
18
|
Kaur P, Bali S, Sharma A, Vig AP, Bhardwaj R. Effect of earthworms on growth, photosynthetic efficiency and metal uptake in Brassica juncea L. plants grown in cadmium-polluted soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13452-13465. [PMID: 28386902 DOI: 10.1007/s11356-017-8947-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
The present study has been carried out to examine the role of earthworms in phytoremediation of Cd and its effect on growth, pigment content, expression of genes coding key enzymes of pigments, photosynthetic efficiency and osmoprotectants in Brassica juncea L. plants grown under cadmium (Cd) metal stress. The effect of different Cd concentrations (0.50, 0.75, 1.0, 1.25 mM) was studied in 30 and 60-day-old plants grown in soils containing earthworms. It was observed that earthworm inoculation showed stimulatory effect on phytoremediation capacity and Cd uptake has increased by 49% (in 30-day-old plants) and 35% (in 60-day-old plants) in shoots and 13.3% (in 30-day-old plants) and 10% (in 60-day-old plants) in roots in 30 and 60-day-old plants in Cd (1.25 mM) treatments. Plant growth parameters such as root and shoot length, relative water content and tolerance index were found to increase in the presence of earthworms. Recovery in photosynthetic pigments (chlorophyll and carotenoid) and gas exchange parameters, i.e. net photosynthetic rate (P n ), stomatal conductance (G s ), intercellular CO2 concentration (C i ) and transpiration rate (E t ), was observed after earthworm's supplementation. Modulation in expression of key enzymes for pigment synthesis, i.e. chlorophyllase, phytoene synthase, chalcone synthase and phenylalanine ammonia lyase, was also observed. The results of our study revealed that earthworms help to mitigate the toxic effects produced by Cd on plant growth and photosynthetic efficiency along with enhanced phytoremediation capacity when co-inoculated with Cd in soil.
Collapse
Affiliation(s)
- Parminder Kaur
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Shagun Bali
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Anket Sharma
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Adarsh Pal Vig
- 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
|
19
|
Beaumelle L, Hedde M, Vandenbulcke F, Lamy I. Relationships between metal compartmentalization and biomarkers in earthworms exposed to field-contaminated soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 224:185-194. [PMID: 28284548 DOI: 10.1016/j.envpol.2017.01.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 06/06/2023]
Abstract
Partitioning tissue metal concentration into subcellular compartments reflecting toxicologically available pools may provide good descriptors of the toxicological effects of metals on organisms. Here we investigated the relationships between internal compartmentalization of Cd, Pb and Zn and biomarker responses in a model soil organism: the earthworm. The aim of this study was to identify metal fractions reflecting the toxic pressure in an endogeic, naturally occurring earthworm species (Aporrectodea caliginosa) exposed to realistic field-contaminated soils. After a 21 days exposure experiment to 31 field-contaminated soils, Cd, Pb and Zn concentrations in earthworms and in three subcellular fractions (cytosol, debris and granules) were quantified. Different biomarkers were measured: the expression of a metallothionein gene (mt), the activity of catalase (CAT) and of glutathione-s-transferase (GST), and the protein, lipid and glycogen reserves. Biomarkers were further combined into an integrated biomarker index (IBR). The subcellular fractionation provided better predictors of biomarkers than the total internal contents hence supporting its use when assessing toxicological bioavailability of metals to earthworms. The most soluble internal pools of metals were not always the best predictors of biomarker responses. metallothionein expression responded to increasing concentrations of Cd in the insoluble fraction (debris + granules). Protein and glycogen contents were also mainly related to Cd and Pb in the insoluble fraction. On the other hand, GST activity was better explained by Pb in the cytosolic fraction. CAT activity and lipid contents variations were not related to metal subcellular distribution. The IBR was best explained by both soluble and insoluble fractions of Pb and Cd. This study further extends the scope of mt expression as a robust and specific biomarker in an ecologically representative earthworm species exposed to field-contaminated soils. The genetic lineage of the individuals, assessed by DNA barcoding with cytochrome c oxidase subunit I, did not influence mt expression.
Collapse
Affiliation(s)
- Léa Beaumelle
- UMR ECOSYS, INRA, AgroParisTech, Université Paris Saclay, 78026, Versailles, France
| | - Mickaël Hedde
- UMR ECOSYS, INRA, AgroParisTech, Université Paris Saclay, 78026, Versailles, France
| | - Franck Vandenbulcke
- LGCgE-Lille 1, Ecologie Numérique et Ecotoxicologie, Université de Lille, 59650 Villeneuve d'Ascq, France
| | - Isabelle Lamy
- UMR ECOSYS, INRA, AgroParisTech, Université Paris Saclay, 78026, Versailles, France.
| |
Collapse
|
20
|
Becker TM, Jeffery EH, Juvik JA. Proposed Method for Estimating Health-Promoting Glucosinolates and Hydrolysis Products in Broccoli (Brassica oleracea var. italica) Using Relative Transcript Abundance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:301-308. [PMID: 27992213 DOI: 10.1021/acs.jafc.6b04668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Due to the importance of glucosinolates and their hydrolysis products in human nutrition and plant defense, optimizing the content of these compounds is a frequent breeding objective for Brassica crops. Toward this goal, we investigated the feasibility of using models built from relative transcript abundance data for the prediction of glucosinolate and hydrolysis product concentrations in broccoli. We report that predictive models explaining at least 50% of the variation for a number of glucosinolates and their hydrolysis products can be built for prediction within the same season, but prediction accuracy decreased when using models built from one season's data for prediction of an opposing season. This method of phytochemical profile prediction could potentially allow for lower phytochemical phenotyping costs and larger breeding populations. This, in turn, could improve selection efficiency for phase II induction potential, a type of chemopreventive bioactivity, by allowing for the quick and relatively cheap content estimation of phytochemicals known to influence the trait.
Collapse
Affiliation(s)
- Talon M Becker
- Department of Crop Sciences and ‡Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-3838, United States
| | - Elizabeth H Jeffery
- Department of Crop Sciences and ‡Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-3838, United States
| | - John A Juvik
- Department of Crop Sciences and ‡Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801-3838, United States
| |
Collapse
|
21
|
Bernard F, Dumez S, Brulle F, Lemière S, Platel A, Nesslany F, Cuny D, Deram A, Vandenbulcke F. Antioxidant defense gene analysis in Brassica oleracea and Trifolium repens exposed to Cd and/or Pb. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:3136-51. [PMID: 26514569 DOI: 10.1007/s11356-015-5636-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/18/2015] [Indexed: 05/04/2023]
Abstract
This study focused on the expression analysis of antioxidant defense genes in Brassica oleracea and in Trifolium repens. Plants were exposed for 3, 10, and 56 days in microcosms to a field-collected suburban soil spiked by low concentrations of cadmium and/or lead. In both species, metal accumulations and expression levels of genes encoding proteins involved and/or related to antioxidant defense systems (glutathione transferases, peroxidases, catalases, metallothioneins) were quantified in leaves in order to better understand the detoxification processes involved following exposure to metals. It appeared that strongest gene expression variations in T. repens were observed when plants are exposed to Cd (metallothionein and ascorbate peroxidase upregulations) whereas strongest variations in B. oleracea were observed in case of Cd/Pb co-exposures (metallothionein, glutathione transferase, and peroxidase upregulations). Results also suggest that there is a benefit to use complementary species in order to better apprehend the biological effects in ecotoxicology.
Collapse
Affiliation(s)
- F Bernard
- Université de Lille, F-59000, Lille, France
- Laboratoire de Génie Civil et géo-Environnement EA4515, Université Lille Nord de France-Lille 1, F-59655, Villeneuve d'Ascq, France
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Lille, EA4483, 59006, Lille Cedex, France
| | - S Dumez
- Université de Lille, F-59000, Lille, France
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Lille, EA4483, 59006, Lille Cedex, France
| | - F Brulle
- Université de Lille, F-59000, Lille, France
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Lille, EA4483, 59006, Lille Cedex, France
| | - S Lemière
- Université de Lille, F-59000, Lille, France
- Laboratoire de Génie Civil et géo-Environnement EA4515, Université Lille Nord de France-Lille 1, F-59655, Villeneuve d'Ascq, France
| | - A Platel
- Université de Lille, F-59000, Lille, France
- Laboratoire de Toxicologie Génétique, Institut Pasteur de Lille, EA 4483, 59800, Lille, France
| | - F Nesslany
- Université de Lille, F-59000, Lille, France
- Laboratoire de Toxicologie Génétique, Institut Pasteur de Lille, EA 4483, 59800, Lille, France
| | - D Cuny
- Université de Lille, F-59000, Lille, France
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Lille, EA4483, 59006, Lille Cedex, France
| | - A Deram
- Université de Lille, F-59000, Lille, France
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Lille, EA4483, 59006, Lille Cedex, France
- Faculté de Management de la Santé (ILIS), Université de Lille, EA4483, F-59120, Loos, France
| | - F Vandenbulcke
- Université de Lille, F-59000, Lille, France.
- Laboratoire de Génie Civil et géo-Environnement EA4515, Université Lille Nord de France-Lille 1, F-59655, Villeneuve d'Ascq, France.
| |
Collapse
|
22
|
Lee MA, Guo R, Ebenezer V, Ki JS. Evaluation and selection of reference genes for ecotoxicogenomic study of the green alga Closterium ehrenbergii using quantitative real-time PCR. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:863-872. [PMID: 25724346 DOI: 10.1007/s10646-015-1430-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2015] [Indexed: 06/04/2023]
Abstract
The green alga Closterium ehrenbergii occurs in fresh water environments and has been suggested as a model for ecotoxicological assessment. Quantitative real-time PCR (qRT-PCR), with its high sensitivity and specificity, is a preferred method for reliable quantification of gene expression levels. qRT-PCR requires reference genes to normalize the transcription level of the target gene, and selection of appropriate references is crucial. Here, we evaluated nine housekeeping genes, that is, 18S rRNA, ACT, TUA, TUB, eIF, H4, UBQ, rps4, and GAPDH, using 34 RNA samples of C. ehrenbergii cultured in various environments (e.g. exposure to heat shock, UV, metals, and non-metallic chemicals). Each housekeeping gene tested displayed different ranges of C T values for each experimental condition. The gene stability was determined using the descriptive statistic software geNorm, which showed that ACT, H4, and TUA were the most suitable reference genes for all the conditions tested. In addition, at least three genes were required for proper normalization. With these references, we assessed the expression level of the heat shock protein 70 (HSP70) gene in C. ehrenbergii cells exposed to thermal and toxic contaminant stress and found that it was significantly up-regulated by these stressors. This study provides potential reference genes for gene expression studies on C. ehrenbergii with qRT-PCR.
Collapse
Affiliation(s)
- Min-Ah Lee
- Department of Life Science, Sangmyung University, Seoul, 110-743, South Korea
| | | | | | | |
Collapse
|
23
|
Niu J, Zhu B, Cai J, Li P, Wang L, Dai H, Qiu L, Yu H, Ha D, Zhao H, Zhang Z, Lin S. Selection of reference genes for gene expression studies in Siberian Apricot (Prunus sibirica L.) Germplasm using quantitative real-time PCR. PLoS One 2014; 9:e103900. [PMID: 25105495 PMCID: PMC4126684 DOI: 10.1371/journal.pone.0103900] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 07/03/2014] [Indexed: 01/09/2023] Open
Abstract
Quantitative real time reverse transcription polymerase chain reaction has been applied in a vast range of studies of gene expression analysis. However, real-time PCR data must be normalized with one or more reference genes. In this study, eleven putative consistently expressed genes (ACT, TUA, TUB, CYP, DNAj, ELFA, F-box27, RPL12, GAPDH, UBC and UBQ) in nine Siberian Apricot Germplasms (including much variability) were evaluated for their potential as references for the normalization of gene expression by NormFinder and geNorm programs. From our studies, ACT, UBC, CYP, UBQ and RPL12 as suitable for normalization were identified by geNorm, while UBC and CYP as the best pair by NormFinder. Moreover, UBC was selected as the most stably expressed gene by both algorithms in different Siberian Apricot seed samples. We also detected that a set of three genes (ACT, CYP and UBC) by geNorm as control for normalization could lead to accurate results. Furthermore, the expression levels of oleosin gene were analyzed to validate the suitability of the selected reference genes. These obtained experimental results could make an important contribution to normalize real-time PCR data for gene expression analysis in Siberian Apricot Germplasm.
Collapse
Affiliation(s)
- Jun Niu
- College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Baoqing Zhu
- College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Jian Cai
- College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Peixue Li
- Jigongshan National Nature Reserve, Xingyang, China
| | - Libing Wang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Huitang Dai
- Jigongshan National Nature Reserve, Xingyang, China
| | - Lin Qiu
- Jigongshan National Nature Reserve, Xingyang, China
| | - Haiyan Yu
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Denglong Ha
- Jigongshan National Nature Reserve, Xingyang, China
| | - Haiyan Zhao
- Jigongshan National Nature Reserve, Xingyang, China
| | - Zhixiang Zhang
- College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Shanzhi Lin
- College of Biological Sciences and Biotechnology, College of Nature Conservation, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Beijing Forestry University, Beijing, China
- * E-mail:
| |
Collapse
|