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Wang M, Song B, Song T, Sun K, He J, Deng J, Fang L, Luan T, Lin L. Efflux transport proteins of Tetrahymena thermophila play important roles in resistance to perfluorooctane sulfonate exposure. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132287. [PMID: 37591171 DOI: 10.1016/j.jhazmat.2023.132287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Abstract
The biotoxicity of perfluorooctane sulfonate (PFOS) has been a concern. However, the effects of PFOS on Tetrahymena thermophila, a unicellular model organism, remain unclear. This study aimed to investigate the toxicity and detoxification mechanism of PFOS in this protozoan. PFOS did not show prominent toxic effects on T. thermophila. Cell viability of T. thermophila can be concentration-dependently increased by PFOS. PFOS also increased the stability of cell membranes and the activity of lysosomes. However, PFOS inhibited efflux transporter activities. Most of the PFOS amount remained in the culture medium during the culture periods. Only a low amount of PFOS was absorbed by cells, where PFOS molecules were mainly combined with membrane proteins. The expressions of four membrane protein genes involved in transporting xenobiotics were analyzed by real time-PCR. The gene abcg25 was significantly up-regulated. The growth of abcg25 gene knockout protozoans under PFOS treatment was slightly inhibited. However, the amount of PFOS adsorbed by the knockout protozoans showed no significant difference from the Wild-type protozoans. We concluded that the ABCG25 protein might play a key role in preventing PFOS from entering the cell or being exported from the cells to protect T. thermophila against PFOS. However, ABCG25 was not the only membrane protein able to bind with PFOS.
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Affiliation(s)
- Mengmeng Wang
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bingyu Song
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tianyu Song
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kailun Sun
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jin He
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiewei Deng
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ling Fang
- Instrumental Analysis and Research Center, Sun Yat-sen University, Guangzhou 510275, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Li Lin
- State Key Laboratory of Biocontrol/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Zhang X, Zhao Y, Zheng W, Nan B, Fu J, Qiao Y, Zufall RA, Gao F, Yan Y. Genome-wide identification of ATP-binding cassette transporter B subfamily, focusing on its structure, evolution and rearrangement in ciliates. Open Biol 2023; 13:230111. [PMID: 37788709 PMCID: PMC10547551 DOI: 10.1098/rsob.230111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
ATP-binding cassette subfamily B (ABCB) has been implicated in various essential functions such as multidrug resistance, auxin transport and heavy metal tolerance in animals and plants. However, the functions, the genomic distribution and the evolutionary history have not been characterized systematically in lower eukaryotes. As a lineage of highly specialized unicellular eukaryotes, ciliates have extremely diverse genomic features including nuclear dimorphism. To further understand the genomic structure and evolutionary history of this gene family, we investigated the ABCB gene subfamily in 11 ciliates. The results demonstrate that there is evidence of substantial gene duplication, which has occurred by different mechanisms in different species. These gene duplicates show consistent purifying selection, suggesting functional constraint, in all but one species, where positive selection may be acting to generate novel function. We also compare the gene structures in the micronuclear and macronuclear genomes and find no gene scrambling during genome rearrangement, despite the abundance of such scrambling in two of our focal species. These results lay the foundation for future analyses of the function of these genes and the mechanisms responsible for their evolution across diverse eukaryotic lineages.
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Affiliation(s)
- Xue Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China
| | - Weibo Zheng
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, People's Republic of China
| | - Bei Nan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Jinyu Fu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Yu Qiao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
| | - Rebecca A. Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, People's Republic of China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China
- Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China
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Su H, Xu J, Li J, Yi Z. Four ciliate-specific expansion events occurred during actin gene family evolution of eukaryotes. Mol Phylogenet Evol 2023; 184:107789. [PMID: 37105243 DOI: 10.1016/j.ympev.2023.107789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Actin gene family is a divergent and ancient eukaryotic cellular cytoskeletal gene family, and participates in many essential cellular processes. Ciliated protists offer us an excellent opportunity to investigate gene family evolution, since their gene families evolved faster in ciliates than in other eukaryotes. Nonetheless, actin gene family is well studied in few model ciliate species but little is known about its evolutionary patterns in ciliates. Here, we analyzed the evolutionary pattern of eukaryotic actin gene family based on genomes/transcriptomes of 36 species covering ten ciliate classes, as well as those of nine non-ciliate eukaryotic species. Results showed: (1) Except for conventional actins and actin-related proteins (Arps) shared by various eukaryotes, at least four ciliate-specific subfamilies occurred during evolution of actin gene family. Expansions of Act2 and ArpC were supposed to have happen in the ciliate common ancestor, while expansions of ActI and ActII may have occurred in the ancestor of Armophorea, Muranotrichea, and Spirotrichea. (2) The number of actin isoforms varied greatly among ciliate species. Environmental adaptability, whole genome duplication (WGD) or segmental duplication events, distinct spatial and temporal patterns of expression might play driving forces for the increasement of isoform numbers. (3) The 'birth and death' model of evolution could explain the evolution of actin gene family in ciliates. And actin genes have been generally under strong negative selection to maintain protein structures and physiological functions. Collectively, we provided meaningful information for understanding the evolution of eukaryotic actin gene family.
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Affiliation(s)
- Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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Pan H, Deng M, Zhang B, Fang T, Liu Y. Transcriptome analysis of Tetrahymena thermophila response to exposure with dihydroartemisinin. Heliyon 2023; 9:e14069. [PMID: 36923843 PMCID: PMC10008979 DOI: 10.1016/j.heliyon.2023.e14069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Dihydroartemisinin (DHA) is a derivative of artemisinin and is toxic to parasites. We used the Tetrahymena thermophila (T. thermophila) as a model to explore DHA toxicity. Results showed that low concentration of DHA (20 μmol/L) promoted cell proliferation, whereas high concentrations of DHA (40-1280 μmol/L) inhibited that. Appearance of nucleus was pycnosis by laser scanning confocal microscope. DHA significantly elevated activities of SOD and GSH-Px (P < 0.01) and MDA was markedly increased at high level but decreased at low level (P < 0.01). Further results of transcriptome in T. thermophila treated with different concentration DHA group (0, 20, 160 μmol/L) showed that differentially expressed genes (DEGs) were involved in oxidation-reduction and metabolism of exogenous substances indicated oxidative stress stimulation. Kyoto Encyclopedia of Genes and Genomes showed that DEGs were involved in the cytochrome P450-mediated metabolism of exogenous substances, glutathione metabolism and ABC transport. Remarkably, DNA replication was significantly enriched in low concentration DHA, energy metabolism related pathways and necrotic process were considerably enriched in high concentration DHA. The results of RT-qPCR of 13 DEGs were the same as that of transcriptome, in which the expression of GST and GPx family genes were significantly altered after exposed to high-DHA group. DHA induced oxidative stress damage through disturbing with energy. However, detoxification pathways in T. thermophila to resist oxidative damage and cell alleviated low concentration DHA stress by regulating antioxidant enzyme. This study provides good practice on pharmacological mechanism of artemisinin-based drugs in antiparasitic.
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Affiliation(s)
- Houjun Pan
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou, 510380, China
| | - Meiling Deng
- School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Bin Zhang
- School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Tiantian Fang
- School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Yuguo Liu
- School of Public Health, Guangdong Medical University, Dongguan, 523808, China
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Kapkaç HA, Arslanyolu M. Identification of glutathione-S-transferase m19 and m34 among responsive GST genes against 1-chloro-2,4-dinitrobenzene treatment of Tetrahymena thermophila. Eur J Protistol 2021; 81:125838. [PMID: 34481325 DOI: 10.1016/j.ejop.2021.125838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Industrial xenobiotic pollutants have toxic effects on diverse organisms in their natural environments. This study aims to identify the Glutathione-S-transferases (GST) from Tetrahymena thermophila that are highly responsive to the treatment of synthetic substrate 1-chloro-2,4-dinitrobenzene (CDNB). The LD50 value of CDNB was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test as 0.079 mM at 9 h exposure. The glutathione affinity-purified 22 kDa and 23 kDa GSTs from CDNB-treated cells were identified as GSTm19 and GSTm34 with 2D-gel electrophoresis coupled MALDI-Tof MS/MS analysis. The specific activitiy of the affinity-purified GSTs was upregulated upon the treatment of 0.072 mM CDNB with the decreased cell survival. GSTm19 and GSTm34 had also upregulated the mRNA expression under the highest dose treatment. The high cell survival and elevated total GST enzyme activity at 9 h under CDNB doses could be the result of both transcriptional upregulations as well as post-translational modifications. As a result, the cell survival of Tetrahymena thermophila was significantly affected by CDNB exposure in a concentration-dependent manner with the effect of low-dose stimulation and high-dose inhibition.
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Affiliation(s)
- Handan Açelya Kapkaç
- Eskisehir Technical University, Faculty of Sciences, Department of Biology, Yunusemre Campus, Eskisehir 26470, Turkey
| | - Muhittin Arslanyolu
- Eskisehir Technical University, Faculty of Sciences, Department of Biology, Yunusemre Campus, Eskisehir 26470, Turkey.
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Wu C, Guo WB, Liu YY, Yang L, Miao AJ. Perturbation of calcium homeostasis and multixenobiotic resistance by nanoplastics in the ciliate Tetrahymena thermophila. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123923. [PMID: 33264974 DOI: 10.1016/j.jhazmat.2020.123923] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/23/2020] [Accepted: 09/07/2020] [Indexed: 06/12/2023]
Abstract
Microplastics (MPs) are an environmental hazard of growing concern, including their potential toxic effects on the biota of different trophic levels. Nevertheless, the molecular mechanisms underlying MP-induced toxicity remain largely unknown. In the present study, Tetrahymena thermophila was exposed to polystyrene nanoplastics (PS-NPs) and the responses of this relatively sensitive ciliate were then followed using transcriptome analysis together with several other verification methods. The results showed that PS-NPs perturbed calcium (Ca) homeostasis, by inducing the inositol-1,4,5-trisphosphate-dependent liberation of Ca from the endoplasmic reticulum into the cytosol. The high cytosolic concentration of Ca induced Ca accumulation in mitochondria, which increased mitochondrial permeability and the generation of reactive oxygen species, finally leading to growth inhibition. Such toxicity is the so-called direct effects of PS-NPs. By contrast, PS-NPs also inhibited the activity of multixenobiotic resistance transporter, by down-regulating the ATP-binding cassette transporter genes Abcb15 and Abcc52. This additional effect may alter cellular responses to other pollutants and implicates PS-NPs in the risks to the organism posed by subsequent toxic exposures, which was named as the indirect effects of PS-NPs. Our study highlights the importance of considering both direct and indirect biological effects of MPs in evaluations of their environmental and health risks.
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Affiliation(s)
- Chao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province, 210046, PR China
| | - Wen-Bo Guo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province, 210046, PR China
| | - Yue-Yue Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province, 210046, PR China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province, 210046, PR China
| | - Ai-Jun Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province, 210046, PR China.
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Lv H, Xu J, Bo T, Wang W. Comparative transcriptome analysis uncovers roles of hydrogen sulfide for alleviating cadmium toxicity in Tetrahymena thermophila. BMC Genomics 2021; 22:21. [PMID: 33407108 PMCID: PMC7788932 DOI: 10.1186/s12864-020-07337-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
Background Cadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfide (H2S) effectively alleviates heavy metal toxicity in plants and reduces oxidative stress in mammals. However, the function of H2S for alleviating heavy metal toxicity in aquatic organisms remains less clear. Tetrahymena thermophila is an important model organism to evaluate toxic contaminants in an aquatic environment. In this study, the molecular roles of exogenously H2S application were explored by RNA sequencing under Cd stress in T. thermophila. Results The exposure of 30 μM Cd resulted in T. thermophila growth inhibition, cell nigrescence, and malondialdehyde (MDA) content considerably increase. However, exogenous NaHS (donor of H2S, 70 μM) significantly alleviated the Cd-induced toxicity by inhibiting Cd absorbtion, promoting CdS nanoparticles formation and improving antioxidant system. Comparative transcriptome analysis showed that the expression levels of 9152 genes changed under Cd stress (4658 upregulated and 4494 downregulated). However, only 1359 genes were differentially expressed with NaHS treatment under Cd stress (1087 upregulated and 272 downregulated). The functional categories of the differentially expressed genes (DEGs) by gene ontology (GO) revealed that the transcripts involved in the oxidation–reduction process, oxidoreductase activity, glutathione peroxidase activity, and cell redox homeostasis were the considerable enrichments between Cd stress and NaHS treatment under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the carbon metabolism, glutathione metabolism, metabolism of xenobiotics by cytochrome P450, and ABC transporters were significantly differentially expressed components between Cd stress and NaHS treatment under Cd stress in T. thermophila. The relative expression levels of six DEGs were further confirmed through quantitative real-time polymerase chain reaction (qRT-PCR). Conclusion NaHS alleviated Cd stress mainly through inhibiting Cd absorbtion, promoting CdS nanoparticles formation, increasing oxidation resistance, and regulation of transport in free-living unicellular T. thermophila. These findings will expand our understanding for H2S functions in the freshwater protozoa. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07337-9.
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Affiliation(s)
- Hongrui Lv
- School of Life Science, Shanxi University, Taiyuan, 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Jing Xu
- School of Life Science, Shanxi University, Taiyuan, 030006, China.,Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China.
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Feng T, He X, Zhuo R, Qiao G, Han X, Qiu W, Chi L, Zhang D, Liu M. Identification and functional characterization of ABCC transporters for Cd tolerance and accumulation in Sedum alfredii Hance. Sci Rep 2020; 10:20928. [PMID: 33262396 PMCID: PMC7708633 DOI: 10.1038/s41598-020-78018-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Cd is one of the potential toxic elements (PTEs) exerting great threats on the environment and living organisms and arising extensive attentions worldwide. Sedum alfredii Hance, a Cd hyperaccumulator, is of great importance in studying the mechanisms of Cd hyperaccumulation and has potentials for phytoremediation. ATP-binding cassette sub-family C (ABCC) belongs to the ABC transporter family, which is deemed to closely associate with multiple physiological processes including cellular homeostasis, metal detoxification, and transport of metabolites. In the present work, ten ABCC proteins were identified in S. alfredii Hance, exhibiting uniform domain structure and divergently clustering with those from Arabidopsis. Tissue-specific expression analysis indicated that some SaABCC genes had significantly higher expression in roots (Sa23221 and Sa88F144), stems (Sa13F200 and Sa14F98) and leaves (Sa13F200). Co-expression network analysis using these five SaABCC genes as hub genes produced two clades harboring different edge genes. Transcriptional expression profiles responsive to Cd illustrated a dramatic elevation of Sa14F190 and Sa18F186 genes. Heterologous expression in a Cd-sensitive yeast cell line, we confirmed the functions of Sa14F190 gene encoding ABCC in Cd accumulation. Our study performed a comprehensive analysis of ABCCs in S. alfredii Hance, firstly mapped their tissue-specific expression patterns responsive to Cd stress, and characterized the roles of Sa14F190 genes in Cd accumulation.
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Affiliation(s)
- Tongyu Feng
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Xuelian He
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Renying Zhuo
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Guirong Qiao
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Xiaojiao Han
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Wenmin Qiu
- Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou, 311400, People's Republic of China
| | - Linfeng Chi
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, People's Republic of China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Mingying Liu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, People's Republic of China.
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Srikant S. Evolutionary history of ATP-binding cassette proteins. FEBS Lett 2020; 594:3882-3897. [PMID: 33145769 DOI: 10.1002/1873-3468.13985] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
ATP-binding cassette (ABC) proteins are found in every sequenced genome and evolved deep in the phylogenetic tree of life. ABC proteins form one of the largest homologous protein families, with most being involved in substrate transport across biological membranes, and a few cytoplasmic members regulating in essential processes like translation. The predominant ABC protein classification scheme is derived from human members, but the increasing number of fully sequenced genomes permits to reevaluate this paradigm in the light of the evolutionary history the ABC-protein superfamily. As we study the diversity of substrates, mechanisms, and physiological roles of ABC proteins, knowledge of the evolutionary relationships highlights similarities and differences that can be attributed to specific branches in protein divergence. While alignments and trees built on natural sequence variation account for the evolutionary divergence of ABC proteins, high-throughput experiments and next-generation sequencing creating experimental sequence variation are instrumental in identifying functional constraints. The combination of natural and experimentally produced sequence variation allows a broader and more rational study of the function and physiological roles of ABC proteins.
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Affiliation(s)
- Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology
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Valle A, Leiro JM, Pereiro P, Figueras A, Novoa B, Dirks RPH, Lamas J. Interactions between the Parasite Philasterides dicentrarchi and the Immune System of the Turbot Scophthalmus maximus. A Transcriptomic Analysis. BIOLOGY 2020; 9:biology9100337. [PMID: 33076342 PMCID: PMC7602577 DOI: 10.3390/biology9100337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
Abstract
The present study analyses the interactions between Philasterides dicentrarchi (a ciliate parasite that causes high mortalities in cultured flatfish) and the peritoneal cells of the turbot Scophthalmus maximus during an experimental infection. The transcriptomic response was evaluated in the parasites and in the fish peritoneal cells, at 1, 2 and 4 h post-infection (hpi) in turbot injected intraperitoneally (ip) with 107 ciliates and at 12 and 48 hpi in turbot injected ip with 105 ciliates. Numerous genes were differentially expressed (DE) in P. dicentrarchi, relative to their expression in control ciliates (0 hpi): 407 (369 were up-regulated) at 1 hpi, 769 (415 were up-regulated) at 2 hpi and 507 (119 were up-regulated) at 4 hpi. Gene ontology (GO) analysis of the DE genes showed that the most representative categories of biological processes affected at 1, 2 and 4 hpi were biosynthetic processes, catabolic processes, biogenesis, proteolysis and transmembrane transport. Twelve genes of the ABC transporter family and eight genes of the leishmanolysin family were DE at 1, 2 and 4 hpi. Most of these genes were strongly up-regulated (UR), suggesting that they are involved in P. dicentrarchi infection. A third group of UR genes included several genes related to ribosome biogenesis, DNA transcription and RNA translation. However, expression of tubulins and tubulin associated proteins, such as kinesins or dyneins, which play key roles in ciliate division and movement, was down-regulated (DR). Similarly, genes that coded for lysosomal proteins or that participate in the cell cycle mitotic control, glycolysis, the Krebs cycle and/or in the electron transport chain were also DR. The transcriptomic analysis also revealed that in contrast to many parasites, which passively evade the host immune system, P. dicentrarchi strongly stimulated turbot peritoneal cells. Many genes related to inflammation were DE in peritoneal cells at 1, 2 and 4 hpi. However, the response was much lower at 12 hpi and almost disappeared completely at 48 hpi in fish that were able to kill P. dicentrarchi during the first few hpi. The genes that were DE at 1, 2 and 4 hpi were mainly related to the apoptotic process, the immune response, the Fc-epsilon receptor signalling pathway, the innate immune response, cell adhesion, cell surface receptors, the NF-kappaB signalling pathway and the MAPK cascade. Expression of toll-like receptors 2, 5 and 13 and of several components of NF-κB, MAPK and JAK/STAT signalling pathways was UR in the turbot peritoneal cells. Genes expressing chemokines and chemokine receptors, genes involved in prostaglandin and leukotriene synthesis, prostaglandins, leukotriene receptors, proinflammatory cytokines and genes involved in apoptosis were strongly UR during the first four hours of infection. However, expression of anti-inflammatory cytokines such as Il-10 and lipoxygenases with anti-inflammatory activity (i.e., arachidonate 15-lipoxygenase) were only UR at 12 and/or 48 hpi, indicating an anti-inflammatory state in these groups of fish. In conclusion, the present study shows the regulation of several genes in P. dicentrarchi during the early stages of infection, some of which probably play important roles in this process. The infection induced a potent acute inflammatory response, and many inflammatory genes were regulated in peritoneal cells, showing that the turbot uses all the protective mechanisms it has available to prevent the entry of the parasite.
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Affiliation(s)
- Alejandra Valle
- Department of Fundamental Biology, Institute of Aquaculture, Campus Vida, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - José Manuel Leiro
- Department of Microbiology and Parasitology, Laboratory of Parasitology, Institute of Research on Chemical and Biological Analysis, Campus Vida, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Patricia Pereiro
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas-CSIC, 36208 Vigo, Spain; (P.P.); (A.F.); (B.N.)
| | - Antonio Figueras
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas-CSIC, 36208 Vigo, Spain; (P.P.); (A.F.); (B.N.)
| | - Beatriz Novoa
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas-CSIC, 36208 Vigo, Spain; (P.P.); (A.F.); (B.N.)
| | - Ron P. H. Dirks
- Future Genomics Technologies, Leiden BioScience Park, 2333 BE Leiden, The Netherlands;
| | - Jesús Lamas
- Department of Fundamental Biology, Institute of Aquaculture, Campus Vida, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Correspondence: ; Tel.: +34-88-181-6951; Fax: +34-88-159-6904
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Najle SR, Hernández J, Ocaña-Pallarès E, García Siburu N, Nusblat AD, Nudel CB, Slamovits CH, Uttaro AD. Genome-wide Transcriptional Analysis of Tetrahymena thermophila Response to Exogenous Cholesterol. J Eukaryot Microbiol 2019; 67:209-222. [PMID: 31705733 DOI: 10.1111/jeu.12774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
The ciliate Tetrahymena thermophila does not require sterols for growth and synthesizes pentacyclic triterpenoid alcohols, mainly tetrahymanol, as sterol surrogates. However, when sterols are present in the environment, T. thermophila efficiently incorporates and modifies them. These modifications consist of desaturation reactions at positions C5(6), C7(8), and C22(23), and de-ethylation at C24 of 29-carbon sterols (i.e. phytosterols). Three out of four of the enzymes involved in the sterol modification pathway have been previously identified. However, identification of the sterol C22 desaturase remained elusive, as did other basic aspects of this metabolism. To get more insights into this peculiar metabolism, we here perform a whole transcriptome analysis of T. thermophila in response to exogenous cholesterol. We found 356 T. thermophila genes to be differentially expressed after supplementation with cholesterol for 2 h. Among those that were upregulated, we found two genes belonging to the long spacing family of desaturases that we tentatively identified by RNAi analysis as sterol C22 desaturases. Additionally, we determined that the inhibition of tetrahymanol synthesis after supplementation with cholesterol occurs by a transcriptional downregulation of genes involved in squalene synthesis and cyclization. Finally, we identified several uncharacterized genes that are likely involved in sterols transport and signaling.
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Affiliation(s)
- Sebastián R Najle
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario, CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina.,Institut de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain
| | - Josefina Hernández
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario, CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina
| | - Eduard Ocaña-Pallarès
- Institut de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Pg. Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain
| | - Nicolás García Siburu
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario, CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina
| | - Alejandro D Nusblat
- Facultad de Farmacia y Bioquímica, Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Clara B Nudel
- Facultad de Farmacia y Bioquímica, Instituto de Nanobiotecnología (NANOBIOTEC), CONICET, Universidad de Buenos Aires, Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, B3H 4R2, Nova Scotia, Canada
| | - Antonio D Uttaro
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Instituto de Biología Molecular y Celular de Rosario, CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda s/n, S2000FHQ, Rosario, Argentina
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12
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Functional characterization of two ABC transporters in Sinonovacula constricta gills and their barrier action in response to pathogen infection. Int J Biol Macromol 2019; 121:443-453. [DOI: 10.1016/j.ijbiomac.2018.10.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 11/21/2022]
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13
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Genome-wide analysis of the Tetrahymena thermophila glutathione S-transferase gene superfamily. Genomics 2018; 111:534-548. [PMID: 30572113 DOI: 10.1016/j.ygeno.2018.11.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/21/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022]
Abstract
The ciliate Tetrahymena thermophila has a rapid response to detoxify xenobiotics, which presents opportunity to study the diversification of Glutathione S-Transferase superfamily. In-silico identification of putative GST genes were resulted with 70 GST genes; 49 TtGSTmu, 7 TtGSTomega, 5 TtGSTtheta, 2 TtGSTzeta, 4 TtMAPEG and 3 TtEF1G. TtGST superfamily has short intron carrying or intronless genes. The most expressed mRNAs of TtGST are limited to 4 members at all life stages. TtGST genes are widely distributed to all five micronuclear chromosomes with the highest diversified members from different classes in chromosome 4. The clustering and the orientation of some TtGSTs in the T. thermophila genome give clues about the recent gene duplication. Analysis of GSH affinity-purified GST proteins with Western blot and activity assay showed GST activity carrying purified TtGST populations. In conclusion, the enhanced genome capacity of TtGST superfamily may have evolved through improved GST enzymatic activity.
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Kim H, Yim B, Kim J, Kim H, Lee YM. Molecular characterization of ABC transporters in marine ciliate, Euplotes crassus: Identification and response to cadmium and benzo[a]pyrene. MARINE POLLUTION BULLETIN 2017; 124:725-735. [PMID: 28139231 DOI: 10.1016/j.marpolbul.2017.01.046] [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: 07/27/2016] [Revised: 01/12/2017] [Accepted: 01/24/2017] [Indexed: 06/06/2023]
Abstract
ATP-binding cassette (ABC) transporters participate in transporting various substances, including xenobiotics, in or out of cells. However, their genetic information and function in ciliates remain still unclear. In this study, we sequenced and characterized two ABC transporter genes (EcABCB and EcABCC), and investigated the effect of cadmium (Cd) and benzo[a]pyrene (B[a]P) on their function and gene expression, using efflux assay and real-time reverse transcription-polymerase chain reaction (qRT-PCR), respectively, in the marine ciliate, Euplotes crassus. Sequencing analysis and efflux assay showed that EcABCB and EcABCC are typical ABC transporters, possessing conserved function. Exposure to Cd (≥5mg/L) and B[a]P (≥50.5μg/L) enhanced accumulation of a substrate. A significant increase in the expression of EcABCB and EcABC mRNA was observed at lower concentration in response to Cd and B[a]P. Our findings indicate that Cd and B[a]P could inhibit the efflux function of ABC transporters, leading to cellular toxicity in the ciliate.
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Affiliation(s)
- Hokyun Kim
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 03016, South Korea
| | - Bora Yim
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 03016, South Korea
| | - Jisoo Kim
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 03016, South Korea
| | - Haeyeon Kim
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 03016, South Korea
| | - Young-Mi Lee
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 03016, South Korea.
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15
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Gao L, Yuan T, Cheng P, Zhou C, Ao J, Wang W, Zhang H. Organic UV filters inhibit multixenobiotic resistance (MXR) activity in Tetrahymena thermophila: investigations by the Rhodamine 123 accumulation assay and molecular docking. ECOTOXICOLOGY (LONDON, ENGLAND) 2016; 25:1318-1326. [PMID: 27315091 DOI: 10.1007/s10646-016-1684-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 06/06/2023]
Abstract
Multixenobiotic resistance (MXR) transporters, which belong to ATP-binding cassette (ABC) family proteins, are present in living organisms as a first line of defense system against xenobiotics and environmental contaminants. The effects of six organic UV filters (4-methyl -benzylidene camphor, 4-MBC; benzophenone-3, BP-3; butyl methoxydibenzoyl-methane, BM-DBM; ethylhexyl methoxy cinnamate, EHMC; octocrylene, OC and homosalate, HMS) on multixenobiotic resistance (MXR) in Tetrahymena thermophila were investigated in this study. It was found that 4-MBC, BP-3 and BM-DBM could significantly inhibit activity of the MXR system, causing concentration dependent accumulation of rhodamine 123; while EHMC, OC and HMS had weak MXR inhibition. The IC50 (50 % inhibition concentration) values of 4-MBC, BP-3 and BM-DBM were 23.54, 40.59 and 26.37 μM, respectively, with inhibitory potentials of 23.1, 13.4 and 20.6 % relative to verapamil (VER, a model inhibitor of P-glycoprotein). Our results firstly provide the evidence for UV filters inhibition effect on MXR in aquatic organisms. In addition, it was revealed by molecular docking analysis that the selected six UV filters can occupy the same binding site on T. thermophila P-gp as VER does; and form H-bonds with residues Ser 328 and/or Asn 281. This study raises the awareness of aquatic ecological risk from the organic UV filters exposure, as they would be involved in potentiating toxic effects by chemosensitizing.
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Affiliation(s)
- Li Gao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- School of Resource and Environment, Ningxia University, Yinchuan, 750021, China
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Peng Cheng
- School of Life Science, Hubei University, Wuhan, 430062, China
| | - Chuanqi Zhou
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Junjie Ao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Wenhua Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, No.800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Haimou Zhang
- School of Life Science, Hubei University, Wuhan, 430062, China
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Tracing the structural evolution of eukaryotic ATP binding cassette transporter superfamily. Sci Rep 2015; 5:16724. [PMID: 26577702 PMCID: PMC4649718 DOI: 10.1038/srep16724] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/19/2015] [Indexed: 01/12/2023] Open
Abstract
The ATP binding cassette (ABC) transporters superfamily is one of the largest classes of membrane proteins. The core of the ABC transporter protein is composed of transmembrane domains (TMDs) and nucleotide binding domains (NBD). Eukaryotes ABC transporters are classified into seven main families (ABCA to ABCG) based on sequence similarity and domain organizations. With different domain number and domain organizations, eukaryote ABC transporters show diverse structures: the single structure (NBD or TMD), the ABC2 structure (NBD-NBD), the half structure (TMD-NBD or NBD-TMD) and the full structure (TMD-NBD-TMD-NBD or NBD-TMD-NBD-TMD). However, studies on how various ABC transporter gene structures evolved is still absent. Therefore, in this study, we comprehensively investigated the structural evolution of eukaryotic ABC transporters. The seven eukaryote ABC transporter families (A to G) fell into three groups: A&G group, B,C&D group and E&F group. There were at least four times the number of NBD and TMD fusion events in the origin of the half structure transporter. Two fusion modes were found in the full and ABC2 structure origination. Based on these findings, we present a putative structural evolutionary path of eukaryote ABC transporters that will increase our understanding on their origin, divergence and function.
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17
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Gao L, Yuan T, Cheng P, Bai Q, Zhou C, Ao J, Wang W, Zhang H. Effects of triclosan and triclocarban on the growth inhibition, cell viability, genotoxicity and multixenobiotic resistance responses of Tetrahymena thermophila. CHEMOSPHERE 2015; 139:434-440. [PMID: 26246462 DOI: 10.1016/j.chemosphere.2015.07.059] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
The information about adverse effects of emerging contaminants on aquatic protozoa is very scarce. The growth inhibition effect, cell viability, genotoxicity and multixenobiotic resistance (MXR) responses of two commonly used antimicrobial agents, triclosan (TCS) and triclocarban (TCC) to protozoan Tetrahymena thermophila were investigated in this study. The results revealed that TCS and TCC can inhibit the growth of T. thermophila with 24h EC50 values of 1063 and 295μgL(-1), respectively. The impairment of plasma membrane was observed after 2h exposure of TCS or TCC at the level of mg/L. Furthermore, it is noticeable that at environmentally relevant concentration (1.0μgL(-1)), both TCS and TCC can lead to statistically significant DNA damage in T. thermophila, while the inhibition of growth and change of cell viability cannot be observed. Our results firstly provide the evidence for genotoxic effects of TCS and TCC on the freshwater protozoan. Additionally, both TCS and TCC were found to inhibit the efflux transporter activities, with the inhibitory potencies of 39% and 40% (using verapamil as a model inhibitor), respectively. Particularly, TCC could significantly down-regulate the expression of MXR related gene Abcb15, which encodes the membrane efflux protein that acting as P-gp in T. thermophila. The results raise the awareness of potential aquatic ecological and human health risks from the exposure of TCS and TCC, as they might potentiate the toxic effects by chemosensitizing with co-existing toxicants.
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Affiliation(s)
- Li Gao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; School of Resource and Environment, Ningxia University, Yinchuan 750021, China
| | - Tao Yuan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Peng Cheng
- School of Life Science, Hubei University, Wuhan 430062, China
| | - Qifeng Bai
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuanqi Zhou
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junjie Ao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenhua Wang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haimou Zhang
- School of Life Science, Hubei University, Wuhan 430062, China
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18
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Saha J, Sengupta A, Gupta K, Gupta B. Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress. Comput Biol Chem 2014; 54:18-32. [PMID: 25531538 DOI: 10.1016/j.compbiolchem.2014.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
Abstract
ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and O. sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, 'ABCE' has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.
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Affiliation(s)
- Jayita Saha
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Atreyee Sengupta
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India; Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Kamala Gupta
- Department of Biological Sciences (Section Botany), Presidency University, 86/1 College Street, Kolkata 700073, India.
| | - Bhaskar Gupta
- Department of Biological Sciences (Section Biotechnology), Presidency University, 86/1 College Street, Kolkata 700073, India.
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ATP-binding cassette transporter enhances tolerance to DDT in Tetrahymena. SCIENCE CHINA-LIFE SCIENCES 2014; 58:297-304. [DOI: 10.1007/s11427-014-4743-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/04/2014] [Indexed: 02/03/2023]
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Genome-wide identification, characterization and phylogenetic analysis of 50 catfish ATP-binding cassette (ABC) transporter genes. PLoS One 2013; 8:e63895. [PMID: 23696857 PMCID: PMC3655950 DOI: 10.1371/journal.pone.0063895] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/09/2013] [Indexed: 12/23/2022] Open
Abstract
Background Although a large set of full-length transcripts was recently assembled in catfish, annotation of large gene families, especially those with duplications, is still a great challenge. Most often, complexities in annotation cause mis-identification and thereby much confusion in the scientific literature. As such, detailed phylogenetic analysis and/or orthology analysis are required for annotation of genes involved in gene families. The ATP-binding cassette (ABC) transporter gene superfamily is a large gene family that encodes membrane proteins that transport a diverse set of substrates across membranes, playing important roles in protecting organisms from diverse environment. Methodology/Principal Findings In this work, we identified a set of 50 ABC transporters in catfish genome. Phylogenetic analysis allowed their identification and annotation into seven subfamilies, including 9 ABCA genes, 12 ABCB genes, 12 ABCC genes, 5 ABCD genes, 2 ABCE genes, 4 ABCF genes and 6 ABCG genes. Most ABC transporters are conserved among vertebrates, though cases of recent gene duplications and gene losses do exist. Gene duplications in catfish were found for ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 and ABCG2. Conclusion/Significance The whole set of catfish ABC transporters provide the essential genomic resources for future biochemical, toxicological and physiological studies of ABC drug efflux transporters. The establishment of orthologies should allow functional inferences with the information from model species, though the function of lineage-specific genes can be distinct because of specific living environment with different selection pressure.
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Dermauw W, Osborne EJ, Clark RM, Grbić M, Tirry L, Van Leeuwen T. A burst of ABC genes in the genome of the polyphagous spider mite Tetranychus urticae. BMC Genomics 2013; 14:317. [PMID: 23663308 PMCID: PMC3724490 DOI: 10.1186/1471-2164-14-317] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/25/2013] [Indexed: 12/20/2022] Open
Abstract
Background The ABC (ATP-binding cassette) gene superfamily is widespread across all living species. The majority of ABC genes encode ABC transporters, which are membrane-spanning proteins capable of transferring substrates across biological membranes by hydrolyzing ATP. Although ABC transporters have often been associated with resistance to drugs and toxic compounds, within the Arthropoda ABC gene families have only been characterized in detail in several insects and a crustacean. In this study, we report a genome-wide survey and expression analysis of the ABC gene superfamily in the spider mite, Tetranychus urticae, a chelicerate ~ 450 million years diverged from other Arthropod lineages. T. urticae is a major agricultural pest, and is among of the most polyphagous arthropod herbivores known. The species resists a staggering array of toxic plant secondary metabolites, and has developed resistance to all major classes of pesticides in use for its control. Results We identified 103 ABC genes in the T. urticae genome, the highest number discovered in a metazoan species to date. Within the T. urticae ABC gene set, all members of the eight currently described subfamilies (A to H) were detected. A phylogenetic analysis revealed that the high number of ABC genes in T. urticae is due primarily to lineage-specific expansions of ABC genes within the ABCC, ABCG and ABCH subfamilies. In particular, the ABCC subfamily harbors the highest number of T. urticae ABC genes (39). In a comparative genomic analysis, we found clear orthologous relationships between a subset of T. urticae ABC proteins and ABC proteins in both vertebrates and invertebrates known to be involved in fundamental cellular processes. These included members of the ABCB-half transporters, and the ABCD, ABCE and ABCF families. Furthermore, one-to-one orthologues could be distinguished between T. urticae proteins and human ABCC10, ABCG5 and ABCG8, the Drosophila melanogaster sulfonylurea receptor and ecdysone-regulated transporter E23. Finally, expression profiling revealed that ABC genes in the ABCC, ABCG ABCH subfamilies were differentially expressed in multi-pesticide resistant mite strains and/or in mites transferred to challenging (toxic) host plants. Conclusions In this study we present the first comprehensive analysis of ABC genes in a polyphagous arthropod herbivore. We demonstrate that the broad plant host range and high levels of pesticide resistance in T. urticae are associated with lineage-specific expansions of ABC genes, many of which respond transcriptionally to xenobiotic exposure. This ABC catalogue will serve as a basis for future biochemical and toxicological studies. Obtaining functional evidence that these ABC subfamilies contribute to xenobiotic tolerance should be the priority of future research.
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Affiliation(s)
- Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent B-9000, Belgium.
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Juganson K, Mortimer M, Ivask A, Kasemets K, Kahru A. Extracellular conversion of silver ions into silver nanoparticles by protozoan Tetrahymena thermophila. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2013; 15:244-250. [PMID: 24592441 DOI: 10.1039/c2em30731f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the current study, cell-free exudates of the ciliated protozoan Tetrahymena thermophila were shown to progressively convert silver nitrate to silver nanoparticles (Ag NPs) under illumination at ambient temperature. The formation of Ag NPs in the reaction mixture was evidenced by gradual colour changes, appearance of a specific absorbance peak (420–450 nm) and visualization using scanning electron microscopy coupled to an energy-dispersive X-ray spectrometer. After 2 h of incubation the mean hydrodynamic size of the Ag NPs was 70 nm. Seven days of incubation resulted in larger agglomerates and a significant decrease in silver toxicity to T. thermophila, accompanied by about 100-fold reduction in the silver ion concentration. Protein analysis indicated an extensive extracellular protein binding by the Ag NPs formed in the protozoan exudates. As protozoa are important components in wastewater treatment, their ability to sequester silver ions into a less bioavailable and less toxic form of silver (e.g. NPs) may be one of the adaption mechanisms of ciliate survival in contaminated environments.
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Abstract
Within the past decade, genomic studies have emerged as essential and highly productive tools to explore the biology of Tetrahymena thermophila. The current major resources, which have been extensively mined by the research community, are the annotated macronuclear genome assembly, transcriptomic data and the databases that house this information. Efforts in progress will soon improve these data sources and expand their scope, including providing annotated micronuclear and comparative genomic sequences. Future studies of Tetrahymena cell and molecular biology, development, physiology, evolution and ecology will benefit greatly from these resources and the advanced genomic technologies they enable.
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Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Badger JH, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 2011; 12:R100. [PMID: 22004680 PMCID: PMC3341644 DOI: 10.1186/gb-2011-12-10-r100] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 09/15/2011] [Accepted: 10/17/2011] [Indexed: 01/09/2023] Open
Abstract
Background Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism. Results We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio. Conclusions Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.
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Affiliation(s)
- Robert S Coyne
- Genomic Medicine, J Craig Venter Institute, Rockville, MD 20850, USA.
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