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Pan Y, Deng R, Jin C, Li Y, Ren B, Hou B, Wang C, Yang X, Hursthouse A. Isolation and Identification of Highly Sb-Resistant Rhodotorula glutinis Strain J5 and its Mechanism of Resistance to Sb(III). Curr Microbiol 2024; 81:335. [PMID: 39215822 DOI: 10.1007/s00284-024-03867-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Sb-resistant strains can detoxify antimony through metabolic mechanisms such as oxidation and affect the migration, transformation, and ultimate fate of antimony in the environment. In this study, a strain of Sb-resistant fungi, Rhodotorula glutinis sp. Strain J5, was isolated from Xikuangshan mine and its growth characteristics, gene expression differences, and functional annotation under Sb(III) stress were further investigated to reveal the mechanism of resistance to Sb(III). We identified strain J5 as belonging to the Rhodotorula glutinis species optimally growing at pH 5.0 and at 28 °C of temperature. According to gene annotation and differential expression, the resistance mechanism of Strain J5 includes: reducing the endocytosis of antimony by aquaporin AQP8 and transmembrane transporter pst, enhancing the efflux of Sb(III) by the gene expression of acr2, acr3 and ABC, improving the oxidation of Sb(III) by iron-sulfur protein and Superoxide dismutase (SOD), glutathione (GSH) and cysteine (Cys) chelation, methylation of methyltransferase and N-methyltransferase, accelerating cell damage repair and EPS synthesis and other biochemical reaction mechanisms. FT-IR analysis shows that the -OH, -COOH, -NH, -PO, C-O, and other active groups of Strain J5 can be complexed with Sb(III), resulting in chemical adsorption. Strain J5 displays significant resistance to Sb(III) with the MIC of 1300 mg/L, playing a crucial role in the global biochemical transformation of antimony and its potential application in soil microbial remediation.
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Affiliation(s)
- Yulin Pan
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Renjian Deng
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China.
| | - Changsheng Jin
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
- School of Life Science, Shaoxing University, Huancheng West Road 508, Shaoxing, 312000, China
| | - Yinfu Li
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Bozhi Ren
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Baolin Hou
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Chuang Wang
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xiuzhen Yang
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Andrew Hursthouse
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
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2
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Li M, Boisson-Dernier A, Bertoldi D, Ardini F, Larcher R, Grotti M, Varotto C. Elucidation of arsenic detoxification mechanism in Marchantia polymorpha: The role of ACR3. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134088. [PMID: 38555672 DOI: 10.1016/j.jhazmat.2024.134088] [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: 01/18/2024] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
The arsenic-specific ACR3 transporter plays pivotal roles in As detoxification in yeast and a group of ancient tracheophytes, the ferns. Despite putative ACR3 genes being present in the genomes of bryophytes, whether they have the same relevance also in this lineage is currently unknown. In this study, we characterized the MpACR3 gene from the bryophyte Marchantia polymorpha L. through a multiplicity of functional approaches ranging from phylogenetic reconstruction, expression analysis, loss- and gain-of-function as well as genetic complementation with an MpACR3 gene tagged with a fluorescent protein. Genetic complementation demonstrates that MpACR3 plays a pivotal role in As tolerance in M. polymorpha, with loss-of-function Mpacr3 mutants being hypersensitive and MpACR3 overexpressors more tolerant to As. Additionally, MpACR3 activity regulates intracellular As concentration, affects its speciation and controls the levels of intracellular oxidative stress. The MpACR3::3xCitrine appears to localize at the plasma membrane and possibly in other endomembrane systems. Taken together, these results demonstrate the pivotal function of ACR3 detoxification in both sister lineages of land plants, indicating that it was present in the common ancestor to all embryophytes. We propose that Mpacr3 mutants could be used in developing countries as low-cost and low-technology visual bioindicators to detect As pollution in water.
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Affiliation(s)
- Mingai Li
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, San Michele all'Adige, 38098 Trento, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| | - Aurélien Boisson-Dernier
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, 400 Route des Chappes, BP167, 06903 Sophia Antipolis Cedex, France
| | - Daniela Bertoldi
- Department of Food and Transformation, Technology Transfer Centre of Fondazione Edmund Mach, E. Mach 1, San Michele all'Adige, 38098 TN, Italy
| | - Francisco Ardini
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, Genoa, Italy
| | - Roberto Larcher
- Department of Food and Transformation, Technology Transfer Centre of Fondazione Edmund Mach, E. Mach 1, San Michele all'Adige, 38098 TN, Italy
| | - Marco Grotti
- Department of Chemistry and Industrial Chemistry, University of Genoa, Via Dodecaneso 31, Genoa, Italy
| | - Claudio Varotto
- Biodiversity, Ecology and Environment Area, Research and Innovation Centre, Fondazione Edmund Mach, via Mach 1, San Michele all'Adige, 38098 Trento, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
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3
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Li L, Tian J, Huang K, Xue X, Chen J, Guan F, Zhang T, Sun Y, He C, Zeng X, Su S. Metal-Binding Protein TaGlo1 Improves Fungal Resistance to Arsenite (As III) and Methylarsenite (MAs III) in Paddy Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7469-7479. [PMID: 38557082 DOI: 10.1021/acs.est.3c11043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Trivalent arsenicals such as arsenite (AsIII) and methylarsenite (MAsIII) are thought to be ubiquitous in flooded paddy soils and have higher toxicity than pentavalent forms. Fungi are widely prevalent in the rice rhizosphere, and the latter is considered a hotspot for As uptake. However, few studies have focused on alleviating As toxicity in paddy soils using fungi. In this study, we investigated the mechanism by which the protein TaGlo1, derived from the As-resistant fungal strain Trichoderma asperellum SM-12F1, mitigates AsIII and MAsIII toxicity in paddy soils. Taglo1 gene expression in Escherichia coli BL21 conferred strong resistance to AsIII and MAsIII, while purified TaGlo1 showed a high affinity for AsIII and MAsIII. Three cysteine residues (Cys13, Cys18, and Cys71) play crucial roles in binding with AsIII, while only two (Cys13 and Cys18) play crucial roles for MAsIII binding. TaGlo1 had a stronger binding strength for MAsIII than AsIII. Importantly, up to 90.2% of the homologous TaGlo1 proteins originate from fungi by GenBank searching. In the rhizospheres of 14 Chinese paddy soils, Taglo1 was widely distributed and its gene abundance increased with porewater As. This study highlights the potential of fungi to mitigate As toxicity and availability in the soil-rice continuum and suggests future microbial strategies for bioremediation.
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Affiliation(s)
- Lijuan Li
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Ximei Xue
- Institute of Urban Environment, Key Laboratory of Urban Environment and Health, Chinese Academy of Sciences, Xiamen 361021, P. R. China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Tuo Zhang
- School of Environmental and Life Science, Nanning Normal University, Nanning 530100, P. R. China
| | - Yifei Sun
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Chao He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Environment, MARA, Beijing 100081, P. R. China
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4
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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5
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Zhao F, Han Y, Shi H, Wang G, Zhou M, Chen Y. Arsenic in the hyperaccumulator Pteris vittata: A review of benefits, toxicity, and metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165232. [PMID: 37392892 DOI: 10.1016/j.scitotenv.2023.165232] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023]
Abstract
Arsenic (As) is a toxic metalloid, elevated levels of which in soils are becoming a major global environmental issue that poses potential health risks to humans. Pteris vittata, the first known As hyperaccumulator, has been successfully used to remediate As-polluted soils. Understanding why and how P. vittata hyperaccumulates As is the core theoretical basis of As phytoremediation technology. In this review, we highlight the beneficial effects of As in P. vittata, including growth promotion, elemental defense, and other potential benefits. The stimulated growth of P. vittata induced by As can be defined as As hormesis, but differs from that in non-hyperaccumulators in some aspects. Furthermore, the As coping mechanisms of P. vittata, including As uptake, reduction, efflux, translocation, and sequestration/detoxification are discussed. We hypothesize that P. vittata has evolved strong As uptake and translocation capacities to obtain beneficial effects from As, which gradually leads to As accumulation. During this process, P. vittata has developed a strong As vacuolar sequestration ability to detoxify overloaded As, which enables it to accumulate extremely high As concentrations in its fronds. This review also provides insights into several important research gaps that need to be addressed to advance our understanding of As hyperaccumulation in P. vittata from the perspective of the benefits of As.
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Affiliation(s)
- Fei Zhao
- School of Environment, Nanjing Normal University, Nanjing 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Yu Han
- School of Environment, Nanjing Normal University, Nanjing 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Hongyi Shi
- School of Environment, Nanjing Normal University, Nanjing 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Guoxiang Wang
- School of Environment, Nanjing Normal University, Nanjing 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China
| | - Mingxi Zhou
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, 37005 Ceske Budejovice, Czech Republic.
| | - Yanshan Chen
- School of Environment, Nanjing Normal University, Nanjing 210023, China; Jiangsu Engineering Lab of Water and Soil Eco-remediation, Nanjing Normal University, Nanjing 210023, China.
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6
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Wen Y, Chairattanawat C, Vo KTX, Liu J, Zhang J, Pan T, Kim DY, Martinoia E, Zhong CY, Wang MH, Jeon JS, Song WY. VOZ1 and VOZ2 transcription factors regulate arsenic tolerance and distribution in rice and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1209860. [PMID: 37799560 PMCID: PMC10548236 DOI: 10.3389/fpls.2023.1209860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/23/2023] [Indexed: 10/07/2023]
Abstract
Rice is the major source of arsenic (As) intake in humans, as this staple crop readily accumulates As in the grain. Identifying the genes and molecular mechanisms underlying As accumulation and tolerance is a crucial step toward developing rice with reduced As levels. We identified 25 rice genes that improve As tolerance in yeast cells by expressing a complementary DNA (cDNA) library generated from As-treated rice roots. Among them, a zinc finger-type transcription factor VASCULAR PLANT ONE- ZINC FINGER 1 (OsVOZ1) (OsVOZ1) conferred the most pronounced As tolerance. OsVOZ1 inhibits As accumulation in yeast via activation of As efflux transporter Acr3p by post-transcriptional modification in yeast. The Arabidopsis voz1 voz2 double-knockout mutant exhibited As hypersensitivity, altered As concentrations in various tissues, and reduced As transport activity via the phloem. Arabidopsis and rice VOZs were highly expressed in phloem cells in various tissues, which are critical for As distribution in plant tissues. The double-knockdown and single-knockout plants of OsVOZ1 and OsVOZ2 reduced As accumulation in their seeds. These findings suggest that rice and Arabidopsis VOZs regulate the translocation of As into tissues by regulating the phloem loading of this element.
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Affiliation(s)
- Ying Wen
- Department of Horticulture, Foshan University, Foshan, Guangdong, China
| | - Chayanee Chairattanawat
- Department of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Jiayou Liu
- Department of Horticulture, Foshan University, Foshan, Guangdong, China
| | - Jie Zhang
- Department of Horticulture, Foshan University, Foshan, Guangdong, China
| | - Ting Pan
- Department of Horticulture, Foshan University, Foshan, Guangdong, China
| | - Do-Young Kim
- Advanced Bio-convergence Center, Pohang Technopark, Pohang, Republic of Korea
| | - Enrico Martinoia
- Institute of Plant Biology, University Zurich, Zurich, Switzerland
| | - Chun-Yan Zhong
- Zhaoqing Institute of Agricultural Sciences, Zhaoqing, China
| | - Mao-Hui Wang
- Zhaoqing Institute of Agricultural Sciences, Zhaoqing, China
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Won-Yong Song
- Department of Horticulture, Foshan University, Foshan, Guangdong, China
- Department of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
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7
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Lashani E, Amoozegar MA, Turner RJ, Moghimi H. Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments. Microorganisms 2023; 11:microorganisms11040891. [PMID: 37110315 PMCID: PMC10143001 DOI: 10.3390/microorganisms11040891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.
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Affiliation(s)
- Elham Lashani
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran;
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran;
- Correspondence: (M.A.A.); (H.M.); Tel.: +98-21-66415495 (H.M.)
| | - Raymond J. Turner
- Microbial Biochemistry Laboratory, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada;
| | - Hamid Moghimi
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran 14178-64411, Iran
- Correspondence: (M.A.A.); (H.M.); Tel.: +98-21-66415495 (H.M.)
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8
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Kugarajah V, Nisha KN, Jayakumar R, Sahabudeen S, Ramakrishnan P, Mohamed SB. Significance of microbial genome in environmental remediation. Microbiol Res 2023; 271:127360. [PMID: 36931127 DOI: 10.1016/j.micres.2023.127360] [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: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023]
Abstract
Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.
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Affiliation(s)
- Vaidhegi Kugarajah
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | | | - R Jayakumar
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India
| | - S Sahabudeen
- Department of Biotechnology, SRM Institute of Science and Technology, Kanchipuram Dist, Kattankulathur, Tamil Nadu, India; Medical Team, Doctoral Institute for Evidence Based Policy, Tokyo, Japan
| | - P Ramakrishnan
- Department of Nanobiomaterials, Institute for Biomedical Engineering, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602015, India.
| | - S B Mohamed
- Department of Materials Science, School of Technology, Central University of Tamil Nadu, Thiruvarur 610005, Tamil Nadu, India.
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Friedrich A, Gounot JS, Tsouris A, Bleykasten C, Freel K, Caradec C, Schacherer J. Contrasting Genomic Evolution Between Domesticated and Wild Kluyveromyces lactis Yeast Populations. Genome Biol Evol 2023; 15:evad004. [PMID: 36634937 PMCID: PMC9897184 DOI: 10.1093/gbe/evad004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of Kluyveromyces lactis, a yeast species well known for its involvement in dairy processes and also present in natural environments. Using a combination of short- and long-read sequencing strategies, we investigated the genomic variability of 41 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10-2) compared with other species such as Saccharomyces cerevisiae (θw = 1.6 × 10-2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10-3), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation, and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.
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Affiliation(s)
- Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | | | - Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | | | - Kelle Freel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | - Claudia Caradec
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg 67000, France
- Institut Universitaire de France (IUF), Paris 75005, France
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10
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Castro-Severyn J, Pardo-Esté C, Araya-Durán I, Gariazzo V, Cabezas C, Valdés J, Remonsellez F, Saavedra CP. Biochemical, genomic and structural characteristics of the Acr3 pump in Exiguobacterium strains isolated from arsenic-rich Salar de Huasco sediments. Front Microbiol 2022; 13:1047283. [PMID: 36406427 PMCID: PMC9671657 DOI: 10.3389/fmicb.2022.1047283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Arsenic is a highly toxic metalloid of major concern for public safety. However, microorganisms have several resistance mechanisms, particularly the expression of arsenic pumps is a critical component for bacterial ability to expel it and decrease intracellular toxicity. In this study, we aimed to characterize the biochemical, structural, and genomic characteristics of the Acr3 pump among a group of Exiguobacterium strains isolated from different sites of the arsenic-rich Salar de Huasco (SH) ecosystem. We also determined whether the differences in As(III) resistance levels presented by the strains could be attributed to changes in the sequence or structure of this protein. In this context, we found that based on acr3 sequences the strains isolated from the SH grouped together phylogenetically, even though clustering based on gene sequence identity did not reflect the strain’s geographical origin. Furthermore, we determined the genetic context of the acr3 sequences and found that there are two versions of the organization of acr3 gene clusters, that do not reflect the strain’s origin nor arsenic resistance level. We also contribute to the knowledge regarding structure of the Acr3 protein and its possible implications on the functionality of the pump, finding that although important and conserved components of this family of proteins are present, there are several changes in the amino acidic sequences that may affect the interactions among amino acids in the 3D model, which in fact are evidenced as changes in the structure and residues contacts. Finally, we demonstrated through heterologous expression that the Exiguobacterium Acr3 pump does indeed improve the organisms As resistance level, as evidenced in the complemented E. coli strains. The understanding of arsenic detoxification processes in prokaryotes has vast biotechnological potential and it can also provide a lot of information to understand the processes of evolutionary adaptation.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Ingrid Araya-Durán
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valentina Gariazzo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Carolina Cabezas
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta, Chile
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Claudia P. Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- *Correspondence: Claudia P. Saavedra,
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11
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Song X, Li Y, Stirling E, Zhao K, Wang B, Zhu Y, Luo Y, Xu J, Ma B. AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation. NAR Genom Bioinform 2022; 4:lqac080. [PMID: 36330044 PMCID: PMC9623898 DOI: 10.1093/nargab/lqac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/02/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.
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Affiliation(s)
- Xinwei Song
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China,Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yiqun Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China,Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China,Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China,Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Binhao Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China,Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100000, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing 210000, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310000, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310000, China
| | - Bin Ma
- To whom correspondence should be addressed. Tel: +86 13282198979;
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12
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Zhang J, Liu J, Zheng F, Yu M, Shabala S, Song WY. Comparative Analysis of Arsenic Transport and Tolerance Mechanisms: Evolution from Prokaryote to Higher Plants. Cells 2022; 11:cells11172741. [PMID: 36078150 PMCID: PMC9454679 DOI: 10.3390/cells11172741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Arsenic (As) is a toxic metalloid for all living organisms and can cause serious harm to humans. Arsenic is also toxic to plants. To alleviate As toxicity, all living organisms (from prokaryotes to higher plants) have evolved comprehensive mechanisms to reduce cytosolic As concentration through the set of As transporters localized at the plasma and tonoplast membranes, which operate either in arsenite As(III) extrusion out of cells (via ArsB, ACR3, and aquaporins) or by sequestering arsenic into vacuoles (by ABC transporters). In addition, a special arsenate resistance mechanism found in some bacterial systems has evolved in an As hyperaccumulating fern Pteris vittata, which involves transforming arsenate As(V) to an As(V) phosphoglycerate derivative by a glyceraldehyde 3-phosphate dehydrogenase and transporting this complex by an efflux transporter. In the present review, we summarize the evolution of these arsenic resistance mechanisms from prokaryotes to eukaryotes and discuss future approaches that could be utilized to better understand and improve As resistance mechanisms in plants.
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Affiliation(s)
- Jie Zhang
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Jiayou Liu
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Fubin Zheng
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Min Yu
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
| | - Sergey Shabala
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, 7001, Australia
- School of Biological Science, University of Western Australia, Perth 6009, Australia
- Correspondence: (S.S.); (W.-Y.S.)
| | - Won-Yong Song
- International Centre for Environmental Membrane Biology, Department of Horticulture, School of Food Science and Engineering, Foshan University, Foshan 528011, China
- Correspondence: (S.S.); (W.-Y.S.)
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13
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Stefanini I, Di Paola M, Liti G, Marranci A, Sebastiani F, Casalone E, Cavalieri D. Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19138119. [PMID: 35805774 PMCID: PMC9266342 DOI: 10.3390/ijerph19138119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/25/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023]
Abstract
Arsenic is one of the most prevalent toxic elements in the environment, and its toxicity affects every organism. Arsenic resistance has mainly been observed in microorganisms, and, in bacteria, it has been associated with the presence of the Ars operon. In Saccharomyces cerevisiae, three genes confer arsenic resistance: ARR1, ARR2, and ARR3. Unlike bacteria, in which the presence of the Ars genes confers per se resistance to arsenic, most of the S. cerevisiae isolates present the three ARR genes, regardless of whether the strain is resistant or sensitive to arsenic. To assess the genetic features that make natural S. cerevisiae strains resistant to arsenic, we used a combination of comparative genomic hybridization, whole-genome sequencing, and transcriptomics profiling with microarray analyses. We observed that both the presence and the genomic location of multiple copies of the whole cluster of ARR genes were central to the escape from subtelomeric silencing and the acquisition of resistance to arsenic. As a result of the repositioning, the ARR genes were expressed even in the absence of arsenic. In addition to their relevance in improving our understanding of the mechanism of arsenic resistance in yeast, these results provide evidence for a new cluster of functionally related genes that are independently duplicated and translocated.
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Affiliation(s)
- Irene Stefanini
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy;
| | - Monica Di Paola
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
| | - Gianni Liti
- National Centre for Scientific Research (CNRS), National Institute of Health and Medical Research (INSERM), Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, 06103 Nice, France;
| | - Andrea Marranci
- Core Research Laboratory, Oncogenomics Unit, Istituto di Fisiologia Clinica, Institute for Cancer Research and Pre-vention (ISPRO), 56124 Pisa, Italy;
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Sesto Fiorentino, 50019 Florence, Italy;
| | - Enrico Casalone
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, 50019 Florence, Italy; (M.D.P.); (E.C.)
- Correspondence:
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14
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Isik E, Balkan Ç, Karl V, Karakaya HÇ, Hua S, Rauch S, Tamás MJ, Koc A. Identification of novel arsenic resistance genes in yeast. Microbiologyopen 2022; 11:e1284. [PMID: 35765185 PMCID: PMC9055376 DOI: 10.1002/mbo3.1284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Arsenic is a toxic metalloid that affects human health by causing numerous diseases and by being used in the treatment of acute promyelocytic leukemia. Saccharomyces cerevisiae (budding yeast) has been extensively utilized to elucidate the molecular mechanisms underlying arsenic toxicity and resistance in eukaryotes. In this study, we applied a genomic DNA overexpression strategy to identify yeast genes that provide arsenic resistance in wild-type and arsenic-sensitive S. cerevisiae cells. In addition to known arsenic-related genes, our genetic screen revealed novel genes, including PHO86, VBA3, UGP1, and TUL1, whose overexpression conferred resistance. To gain insights into possible resistance mechanisms, we addressed the contribution of these genes to cell growth, intracellular arsenic, and protein aggregation during arsenate exposure. Overexpression of PHO86 resulted in higher cellular arsenic levels but no additional effect on protein aggregation, indicating that these cells efficiently protect their intracellular environment. VBA3 overexpression caused resistance despite higher intracellular arsenic and protein aggregation levels. Overexpression of UGP1 led to lower intracellular arsenic and protein aggregation levels while TUL1 overexpression had no impact on intracellular arsenic or protein aggregation levels. Thus, the identified genes appear to confer arsenic resistance through distinct mechanisms but the molecular details remain to be elucidated.
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Affiliation(s)
- Esin Isik
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
| | - Çiğdem Balkan
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
| | - Vivien Karl
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | | | - Sansan Hua
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Sebastien Rauch
- Water Environment Technology, Department of Architecture and Civil EngineeringChalmers University of TechnologyGothenburgSweden
| | - Markus J. Tamás
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Ahmet Koc
- Department of Molecular Biology and GeneticsIzmir Institute of TechnologyIzmirTurkey
- Department of Genetics, School of MedicineInonu UniversityMalatyaTurkey
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15
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Zhang W, Miao AJ, Wang NX, Li C, Sha J, Jia J, Alessi DS, Yan B, Ok YS. Arsenic bioaccumulation and biotransformation in aquatic organisms. ENVIRONMENT INTERNATIONAL 2022; 163:107221. [PMID: 35378441 DOI: 10.1016/j.envint.2022.107221] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Arsenic exists universally in freshwater and marine environments, threatening the survival of aquatic organisms and human health. To elucidate arsenic bioaccumulation and biotransformation processes in aquatic organisms, this review evaluates the dissolved uptake, dietary assimilation, biotransformation, and elimination of arsenic in aquatic organisms and discusses the major factors influencing these processes. Environmental factors such as phosphorus concentration, pH, salinity, and dissolved organic matter influence arsenic absorption from aquatic systems, whereas ingestion rate, gut passage time, and gut environment affect the assimilation of arsenic from foodstuffs. Arsenic bioaccumulation and biotransformation mechanisms differ depending on specific arsenic species and the involved aquatic organism. Although some enzymes engaged in arsenic biotransformation are known, deciphering the complicated synthesis and degradation pathway of arsenobetaine remains a challenge. The elimination of arsenic involves many processes, such as fecal excretion, renal elimination, molting, and reproductive processes. This review facilitates our understanding of the environmental behavior and biological fate of arsenic and contributes to regulation of the environmental risk posed by arsenic pollution.
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Affiliation(s)
- Wei Zhang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Ai-Jun Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Ning-Xin Wang
- School of Environmental Engineering, Nanjing Institute of Technology, Nanjing 211167, China
| | - Chengjun Li
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jun Sha
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jianbo Jia
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Bing Yan
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Yong Sik Ok
- Korea Biochar Research Center, APRU Sustainable Waste Management Program & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea.
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16
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Wang HT, Ma L, Zhu D, Ding J, Li G, Jin BJ, Shao YH, Zhang WX, Song MY, Fu SL. Responses of earthworm Metaphire vulgaris gut microbiota to arsenic and nanoplastics contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150279. [PMID: 34600205 DOI: 10.1016/j.scitotenv.2021.150279] [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: 06/08/2021] [Revised: 08/13/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
The growing contamination of arsenic and plastics has severely effects on the soil fauna health, including shifts of gut microbiota community. A few studies have focused on effects of microplastics and metal(loid) in soil and fauna gut microbiome. However, the environmental effect of nanoplastics and arsenic on the earthworm gut microbiota, especially on arsenic biotransformation in the gut, remain largely unknown. Here, a microcosm study was performed to explore the effects of nanoplastics and arsenic on the microbiota characteristics in earthworm Metaphire vulgaris gut using Illumina high throughput sequencing, and to investigate changes in the gut microbiota-mediated arsenic biotransformation genes (ABGs) by using high-throughput quantitative PCR. Our results demonstrated that the concentration of arsenic in the earthworm body tissues after exposure to arsenic and nanoplastics was significantly lower from that with arsenic alone exposure. Moreover, the clearly different bacterial community was observed in the soil compared with the earthworm gut, which was dominated by Proteobacteria, Actinobacteria, and Firmicutes at phylum level. Arsenic exposure significantly disturbed bacterial community structure in the earthworm gut, but exposure to nanoplastics did not induce gut microbiota changes. More interestingly, nanoplastics can relieve adverse effect of arsenic on the gut microbiota possibly by adsorbing arsenic. In addition, a total of 16 ABGs were detected, and predominant genes involved in arsenic reduction and transport process were observed in the earthworm guts. In short, this study provides a new picture of the effects of nanoplastics and arsenic on the gut microbiota and arsenic biotransformation in soil fauna gut.
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Affiliation(s)
- Hong-Tao Wang
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China
| | - Lei Ma
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China.
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, Yantai 264005, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Bing-Jie Jin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuan-Hu Shao
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China
| | - Wei-Xin Zhang
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China
| | - Meng-Ya Song
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China
| | - Sheng-Lei Fu
- College of Geography and Environmental Science, Henan University, Kaifeng 475004, China; Key Laboratory of Geospatial Technology for the Middle and Lower Yellow River Regions (Henan University), Ministry of Education, Kaifeng 475004, China.
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17
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A large transposable element mediates metal resistance in the fungus Paecilomyces variotii. Curr Biol 2022; 32:937-950.e5. [PMID: 35063120 DOI: 10.1016/j.cub.2021.12.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/11/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022]
Abstract
The horizontal transfer of large gene clusters by mobile elements is a key driver of prokaryotic adaptation in response to environmental stresses. Eukaryotic microbes face similar stresses; however, a parallel role for mobile elements has not been established. A stress faced by many microorganisms is toxic metal ions in their environment. In fungi, identified mechanisms for protection against metals generally rely on genes that are dispersed within an organism's genome. Here, we discover a large (∼85 kb) region that confers tolerance to five metal/metalloid ions (arsenate, cadmium, copper, lead, and zinc) in the genomes of some, but not all, strains of a fungus, Paecilomyces variotii. We name this region HEPHAESTUS (Hφ) and present evidence that it is mobile within the P. variotii genome with features characteristic of a transposable element. HEPHAESTUS contains the greatest complement of host-beneficial genes carried by a transposable element in eukaryotes, suggesting that eukaryotic transposable elements might play a role analogous to bacteria in the horizontal transfer of large regions of host-beneficial DNA. Genes within HEPHAESTUS responsible for individual metal tolerances include those encoding a P-type ATPase transporter-PcaA-required for cadmium and lead tolerance, a transporter-ZrcA-providing tolerance to zinc, and a multicopper oxidase-McoA-conferring tolerance to copper. In addition, a subregion of Hφ confers tolerance to arsenate. The genome sequences of other fungi in the Eurotiales contain further examples of HEPHAESTUS, suggesting that it is responsible for independently assembling tolerance to a diverse array of ions, including chromium, mercury, and sodium.
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18
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Wu J, Liang J, Björn LO, Li J, Shu W, Wang Y. Phosphorus-arsenic interaction in the 'soil-plant-microbe' system and its influence on arsenic pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149796. [PMID: 34464787 DOI: 10.1016/j.scitotenv.2021.149796] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Elevated arsenic (As) in soil is of public concern due to the carcinogenicity. Phosphorus (P) strongly influences the adsorption, absorption, transport, and transformation of As in the soil and in organisms due to the similarity of the chemical properties of P and As. In soil, P, particularly inorganic P, can release soil-retained As (mostly arsenate) by competing for adsorption sites. In plant and microbial systems, P usually reduces As (mainly arsenate) uptake and affects As biotransformation by competing for As transporters. The intensity and pattern of PAs interaction are highly dependent on the forms of As and P, and strongly influenced by various biotic and abiotic factors. An understanding of the PAs interaction in 'soil-plant-microbe' systems is of great value to prevent soil As from entering the human food chain. Here, we review PAs interactions and the main influential factors in soil, plant, and microbial subsystems and their effects on the As release, absorption, transformation, and transport in the 'soil-plant-microbe' system. We also analyze the application potential of P fertilization as a control for As pollution and suggest the research directions that need to be followed in the future.
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Affiliation(s)
- Jingwen Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jieliang Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lars Olof Björn
- Department of Biology, Lund University, Lund SE-22362, Sweden
| | - Jintian Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wensheng Shu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yutao Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitor, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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19
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Romero AM, Maciaszczyk-Dziubinska E, Mombeinipour M, Lorentzon E, Aspholm E, Wysocki R, Tamás MJ. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6551893. [PMID: 35323907 PMCID: PMC9041338 DOI: 10.1093/femsyr/foac018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/23/2022] Open
Abstract
In a high-throughput yeast two-hybrid screen of predicted coiled-coil motif interactions in the Saccharomyces cerevisiae proteome, the protein Etp1 was found to interact with the yeast AP-1-like transcription factors Yap8, Yap1 and Yap6. Yap8 plays a crucial role during arsenic stress since it regulates expression of the resistance genes ACR2 and ACR3. The function of Etp1 is not well understood but the protein has been implicated in transcription and protein turnover during ethanol stress, and the etp1∆ mutant is sensitive to ethanol. In this current study, we investigated whether Etp1 is implicated in Yap8-dependent functions. We show that Etp1 is required for optimal growth in the presence of trivalent arsenite and for optimal expression of the arsenite export protein encoded by ACR3. Since Yap8 is the only known transcription factor that regulates ACR3 expression, we investigated whether Etp1 regulates Yap8. Yap8 ubiquitination, stability, nuclear localization and ACR3 promoter association were unaffected in etp1∆ cells, indicating that Etp1 affects ACR3 expression independently of Yap8. Thus, Etp1 impacts gene expression under arsenic and other stress conditions but the mechanistic details remain to be elucidated.
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Affiliation(s)
| | | | - Mandana Mombeinipour
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emma Lorentzon
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Emelie Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-405 30 Göteborg, Sweden
| | - Robert Wysocki
- Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Markus J Tamás
- Corresponding author: Department of Chemistry and Molecular Biology, University of Gothenburg, PO Box 462, S-405 30 Göteborg, Sweden. Tel: +46-31-786-2548; E-mail:
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20
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Chen Y, Wang HY, Chen YF. The transcription factor MYB40 is a central regulator in arsenic resistance in Arabidopsis. PLANT COMMUNICATIONS 2021; 2:100234. [PMID: 34778748 PMCID: PMC8577101 DOI: 10.1016/j.xplc.2021.100234] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 06/01/2023]
Abstract
Arsenic is a metalloid that is toxic to plants. Arsenate (As(V)), the prevalent chemical form of arsenic, is a phosphate (Pi) analog and is incorporated into plant cells via Pi transporters. Here, we found that the MYB40 transcription factor played important roles in the control of Arabidopsis As(V) resistance. The expression of MYB40 was induced by As(V) stress. MYB40-overexpressing lines had an obvious As(V)-resistant phenotype and a reduced As(V)/Pi uptake rate, whereas myb40 mutants were sensitive to As(V) stress. Upon exposure to As(V), MYB40 directly repressed the expression of PHT1;1, which encodes a main Pi transporter. The As(V)-resistant phenotypes of MYB40-overexpressing lines were impaired by overexpression of PHT1;1, demonstrating an epistatic genetic relationship between MYB40 and PHT1;1. Moreover, overexpression of MYB40 enhanced, and disruption of MYB40 reduced, thiol-peptide contents. Upon exposure to As(V), MYB40 positively regulated the expression of PCS1, which encodes a phytochelatin synthase, and ABCC1 and ABCC2, which encode the major vacuolar phytochelatin transporters. Together, our data demonstrate that AtMYB40 acts as a central regulator of As(V) responses, providing a genetic strategy for enhancing plant As(V) tolerance and reducing As(V) uptake to improve food safety.
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Affiliation(s)
- Yun Chen
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong-Yang Wang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi-Fang Chen
- College of Biological Sciences, China Agricultural University, Beijing, China
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21
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Newsome L, Falagán C. The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health. GEOHEALTH 2021; 5:e2020GH000380. [PMID: 34632243 PMCID: PMC8490943 DOI: 10.1029/2020gh000380] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/13/2023]
Abstract
Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.
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Affiliation(s)
- Laura Newsome
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
| | - Carmen Falagán
- Camborne School of Mines and Environment and Sustainability InstituteUniversity of ExeterPenrynUK
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22
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Deng R, Chen Y, Deng X, Huang Z, Zhou S, Ren B, Jin G, Hursthouse A. A Critical Review of Resistance and Oxidation Mechanisms of Sb-Oxidizing Bacteria for the Bioremediation of Sb(III) Pollution. Front Microbiol 2021; 12:738596. [PMID: 34557178 PMCID: PMC8453088 DOI: 10.3389/fmicb.2021.738596] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/30/2021] [Indexed: 12/03/2022] Open
Abstract
Antimony (Sb) is a priority pollutant in many countries and regions due to its chronic toxicity and potential carcinogenicity. Elevated concentrations of Sb in the environmental originating from mining and other anthropogenic sources are of particular global concern, so the prevention and control of the source of pollution and environment remediation are urgent. It is widely accepted that indigenous microbes play an important role in Sb speciation, mobility, bioavailability, and fate in the natural environment. Especially, antimony-oxidizing bacteria can promote the release of antimony from ore deposits to the wider environment. However, it can also oxidize the more toxic antimonite [Sb(III)] to the less-toxic antimonate [Sb(V)], which is considered as a potentially environmentally friendly and efficient remediation technology for Sb pollution. Therefore, understanding its biological oxidation mechanism has great practical significance to protect environment and human health. This paper reviews studies of the isolation, identification, diversity, Sb(III) resistance mechanisms, Sb(III) oxidation characteristics and mechanism and potential application of Sb-oxidizing bacteria. The aim is to provide a theoretical basis and reference for the diversity and metabolic mechanism of Sb-oxidizing bacteria, the prevention and control of Sb pollution sources, and the application of environment treatment for Sb pollution.
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Affiliation(s)
- Renjian Deng
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Yilin Chen
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Xinpin Deng
- Hunan 402 Geological Prospecting Part, Changsha, China
| | - Zhongjie Huang
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Saijun Zhou
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Bozhi Ren
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Guizhong Jin
- Hsikwangshan Twinkling Star Co., Ltd., Lengshuijiang, China
| | - Andrew Hursthouse
- School of Civil Engineering, Hunan University of Science and Technology, Xiangtan, China
- School of Computing, Engineering and Physical Sciences, The University of the West of Scotland, Paisley, United Kingdom
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23
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Foflonker F, Blaby-Haas CE. Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery. Mol Biol Evol 2021; 38:650-662. [PMID: 32886760 PMCID: PMC7826186 DOI: 10.1093/molbev/msaa221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.
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24
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Hagee D, Abu Hardan A, Botero J, Arnone JT. Genomic clustering within functionally related gene families in Ascomycota fungi. Comput Struct Biotechnol J 2020; 18:3267-3277. [PMID: 33209211 PMCID: PMC7653285 DOI: 10.1016/j.csbj.2020.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022] Open
Abstract
Multiple mechanisms collaborate for proper regulation of gene expression. One layer of this regulation is through the clustering of functionally related genes at discrete loci throughout the genome. This phenomenon occurs extensively throughout Ascomycota fungi and is an organizing principle for many gene families whose proteins participate in diverse molecular functions throughout the cell. Members of this phylum include organisms that serve as model systems and those of interest medically, pharmaceutically, and for industrial and biotechnological applications. In this review, we discuss the prevalence of functional clustering through a broad range of organisms within the phylum. Position effects on transcription, genomic locations of clusters, transcriptional regulation of clusters, and selective pressures contributing to the formation and maintenance of clusters are addressed, as are common methods to identify and characterize clusters.
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Affiliation(s)
- Danielle Hagee
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Ahmad Abu Hardan
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Juan Botero
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - James T. Arnone
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
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25
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Onetto CA, Schmidt SA, Roach MJ, Borneman AR. Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice. FEMS Yeast Res 2020; 20:5902852. [DOI: 10.1093/femsyr/foaa052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/04/2020] [Indexed: 12/24/2022] Open
Abstract
ABSTRACT
Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.
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Affiliation(s)
- Cristobal A Onetto
- The Australian Wine Research Institute, Glen Osmond, PO Box 197, Adelaide, SA, 5064, Australia
| | - Simon A Schmidt
- The Australian Wine Research Institute, Glen Osmond, PO Box 197, Adelaide, SA, 5064, Australia
| | - Michael J Roach
- The Australian Wine Research Institute, Glen Osmond, PO Box 197, Adelaide, SA, 5064, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, Glen Osmond, PO Box 197, Adelaide, SA, 5064, Australia
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26
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Thakre PK, Golla U, Biswas A, Tomar RS. Identification of Histone H3 and H4 Amino Acid Residues Important for the Regulation of Arsenite Stress Signaling in Saccharomyces cerevisiae. Chem Res Toxicol 2020; 33:817-833. [PMID: 32032493 DOI: 10.1021/acs.chemrestox.9b00471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arsenic is an environmental carcinogen that causes many diseases in humans, including cancers and organ failures, affecting millions of people in the world. Arsenic trioxide is a drug used for the treatment of acute promyelocytic leukemia (APL). In the present study, we screened the synthetic histone H3 and H4 library in the presence of arsenite to understand the role of histone residues in arsenic toxicity. We identified residues of histone H3 and H4 crucial for arsenite stress response. The residues H3T3, H3G90, H4K5, H4G13, and H4R95 are required for the activation of Hog1 kinase in response to arsenite exposure. We showed that a reduced level of Hog1 activation increases the intracellular arsenic content in these histone mutants through the Fps1 channel. We have also noticed the reduced expression of ACR3 exporter in the mutants. The growth defect of mutants caused by arsenite exposure was suppressed in hyperosmotic conditions, in a higher concentration of glucose, and upon deletion of the FPS1 gene. The arsenite sensitive histone mutants also showed a lack of H3K4 methylation and reduced H4K16 acetylation. Altogether, we have identified the key residues in histone H3 and H4 proteins important for the regulation of Hog1 signaling, Fps1 activity, and ACR3 expression during arsenite stress.
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Affiliation(s)
- Pilendra Kumar Thakre
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Upendarrao Golla
- Division of Hematology and Oncology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Ashis Biswas
- Environmental Geochemistry Laboratory, Department of Earth and Environmental Sciences (EES), Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462066, India
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27
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Phenotypic and genomic analysis of multiple heavy metal–resistant Micrococcus luteus strain AS2 isolated from industrial waste water and its potential use in arsenic bioremediation. Appl Microbiol Biotechnol 2020; 104:2243-2254. [DOI: 10.1007/s00253-020-10351-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/23/2019] [Accepted: 01/05/2020] [Indexed: 12/23/2022]
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28
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Guerra-Moreno A, Prado MA, Ang J, Schnell HM, Micoogullari Y, Paulo JA, Finley D, Gygi SP, Hanna J. Thiol-based direct threat sensing by the stress-activated protein kinase Hog1. Sci Signal 2019; 12:12/609/eaaw4956. [PMID: 31772124 DOI: 10.1126/scisignal.aaw4956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The yeast stress-activated protein kinase Hog1 is best known for its role in mediating the response to osmotic stress, but it is also activated by various mechanistically distinct environmental stressors, including heat shock, endoplasmic reticulum stress, and arsenic. In the osmotic stress response, the signal is sensed upstream and relayed to Hog1 through a kinase cascade. Here, we identified a mode of Hog1 function whereby Hog1 senses arsenic through a direct physical interaction that requires three conserved cysteine residues located adjacent to the catalytic loop. These residues were essential for Hog1-mediated protection against arsenic, were dispensable for the response to osmotic stress, and promoted the nuclear localization of Hog1 upon exposure of cells to arsenic. Hog1 promoted arsenic detoxification by stimulating phosphorylation of the transcription factor Yap8, promoting Yap8 nuclear localization, and stimulating the transcription of the only known Yap8 targets, ARR2 and ARR3, both of which encode proteins that promote arsenic efflux. The related human kinases ERK1 and ERK2 also bound to arsenic in vitro, suggesting that this may be a conserved feature of some members of the mitogen-activated protein kinase (MAPK) family. These data provide a mechanistic basis for understanding how stress-activated kinases can sense distinct threats and perform highly specific adaptive responses.
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Affiliation(s)
- Angel Guerra-Moreno
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Jessie Ang
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Helena M Schnell
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yagmur Micoogullari
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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29
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Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
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30
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Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G. Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. Front Microbiol 2019; 10:1514. [PMID: 31333619 PMCID: PMC6620896 DOI: 10.3389/fmicb.2019.01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2T, and Thioalkalivibrio thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lucia Cavalca
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Milena Colombo
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - J Merijn Schuurmans
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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31
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Sher S, Rehman A. Use of heavy metals resistant bacteria-a strategy for arsenic bioremediation. Appl Microbiol Biotechnol 2019; 103:6007-6021. [PMID: 31209527 DOI: 10.1007/s00253-019-09933-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 01/26/2023]
Abstract
A large number of industries release their untreated wastes in the environment causing an increase in the concentration of toxic pollutants including heavy metal ions in ground and drinking water which is above the WHO limit. The presence of toxic pollutants in the industrial wastes pollutes our environment. Arsenic (As) is a ubiquitous toxic metalloid. Its amount varies in different parts on the earth, and its concentration is increasing in our environment day by day both by natural and anthropogenic activities. It is found in two forms; one is arsenate (As5+) and other is arsenite (As3+) and the latter is more toxic due to high mobility across the cell membrane. The long-term use of arsenic-containing water causes arsenicosis. High arsenic consumption, revealed by skin harms, color change, and spots on hands and feet, may cause skin cancer and affect lungs and kidneys. Hypertension, a state of high blood pressure, and lack of insulin which causes diabetes and many other disorders which relate to reproduction are the consequences of arsenic contamination. Several methods have been employed to decontaminate arsenic pollution, but the bioremediation by using biomass of bacteria, algae, fungi, and yeasts is the most compromising approach and has gained much attention from researchers in the last few decades. The microbial detoxification of arsenic can be achieved by reduction, oxidation, and methylation. High bioremediation potential and feasibility of the process make bacteria an impending foundation for green chemistry to exterminate arsenic in the environment.
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Affiliation(s)
- Shahid Sher
- Department of Microbiology and Molecular Genetics, University of the Punjab, New Campus, Lahore, 54590, Pakistan
| | - Abdul Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, New Campus, Lahore, 54590, Pakistan.
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32
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Garbinski LD, Rosen BP, Chen J. Pathways of arsenic uptake and efflux. ENVIRONMENT INTERNATIONAL 2019; 126:585-597. [PMID: 30852446 PMCID: PMC6472914 DOI: 10.1016/j.envint.2019.02.058] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 05/19/2023]
Abstract
Arsenic is a non-essential, environmentally ubiquitous toxic metalloid. In response to this pervasive environmental challenge, organisms evolved mechanisms to confer resistance to arsenicals. Inorganic pentavalent arsenate is taken into most cells adventitiously by phosphate uptake systems. Similarly, inorganic trivalent arsenite is taken into most cells adventitiously, primarily via aquaglyceroporins or sugar permeases. The most common strategy for tolerance to both inorganic and organic arsenicals is by efflux that extrude them from the cytosol. These efflux transporters span across kingdoms and belong to various families such as aquaglyceroporins, major facilitator superfamily (MFS) transporters, ATP-binding cassette (ABC) transporters and potentially novel, yet to be discovered families. This review will outline the properties and substrates of known arsenic transport systems, the current knowledge gaps in the field, and aims to provide insight into the importance of arsenic transport in the context of the global arsenic biogeocycle and human health.
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Affiliation(s)
- Luis D Garbinski
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
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33
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Wawrzycka D, Sadlak J, Maciaszczyk-Dziubinska E, Wysocki R. Rsp5-dependent endocytosis and degradation of the arsenite transporter Acr3 requires its N-terminal acidic tail as an endocytic sorting signal and arrestin-related ubiquitin-ligase adaptors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:916-925. [PMID: 30776335 DOI: 10.1016/j.bbamem.2019.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 01/15/2023]
Abstract
The yeast plasma membrane transporter Acr3 mediates efflux of toxic arsenite and antimonite. Here, we investigated the mechanisms of Acr3 turnover. We found that after arrival and residence at the plasma membrane, Acr3 is subjected to internalization followed by proteolysis in the vacuole. Endocytic degradation of Acr3 is promoted by the ubiquitin ligase Rsp5 and requires polyubiquitination of Acr3 at multiple lysine residues via lysine 63-linked ubiquitin chains. The turnover of Acr3 also depends on two arrestin-related proteins, Art3/Aly2 and Art4/Rod1, that enable recruitment of Rsp5 to its targets. Finally, we found that a short acidic patch located in the N-terminal tail of Acr3 is needed for its ubiquitination and internalization. We propose that this motif serves as an endocytic signal that facilitates binding of the arrestin-Rsp5 complexes to the Acr3 cargo.
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Affiliation(s)
- Donata Wawrzycka
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Joanna Sadlak
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | | | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ. Proteomic characterization of the arsenic response locus in S. cerevisiae. Epigenetics 2019; 14:130-145. [PMID: 30739529 PMCID: PMC6557609 DOI: 10.1080/15592294.2019.1580110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022] Open
Abstract
Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a conserved pathway ranging from prokaryotes to higher eukaryotes. The goal of this study was to identify how transcription from the arsenic response locus is regulated in an arsenic dependent manner. An affinity enrichment strategy called CRISPR-Chromatin Affinity Purification with Mass Spectrometry (CRISPR-ChAP-MS) was used, which provides for the proteomic characterization of a targeted locus. CRISPR-ChAP-MS was applied to the promoter regions of the activated arsenic response locus and uncovered 40 nuclear-annotated proteins showing enrichment. Functional assays identified the histone acetyltransferase SAGA and the chromatin remodelling complex SWI/SNF to be required for activation of the locus. Furthermore, SAGA and SWI/SNF were both found to specifically organize the chromatin structure at the arsenic response locus for activation of gene transcription. This study provides the first proteomic characterization of an arsenic response locus and key insight into the mechanisms of transcriptional activation that are necessary for detoxification of arsenic from the cell.
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Affiliation(s)
- Kirk L. West
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephanie D. Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s Research Institute, Little Rock, AR, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rick D. Edmondson
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children’s Research Institute, Little Rock, AR, USA
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Zhao Y, Su JQ, Ye J, Rensing C, Tardif S, Zhu YG, Brandt KK. AsChip: A High-Throughput qPCR Chip for Comprehensive Profiling of Genes Linked to Microbial Cycling of Arsenic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:798-807. [PMID: 30532956 DOI: 10.1021/acs.est.8b03798] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Arsenic (As) is a ubiquitous toxic element adversely affecting human health. Microbe-mediated cycling of As is largely mediated by detoxification and energy metabolism in microorganisms. We here report the development of a novel high-throughput qPCR (HT-qPCR) chip (AsChip) for comprehensive profiling of genes involved in microbial As cycling (here collectively termed "As genes"). AsChip contained 81 primer sets targeting 19 As genes and the 16S rRNA gene as a reference gene. Gene amplicon sequencing showed high identity (>96%) of newly designed primers corresponding to their targets. AsChip displayed high sensitivity (plasmid template serial dilution test; r = -0.99), with more than 96% of all PCR assays yielding true positive signals. R2 coefficients for standard curves and PCR amplification efficiencies averaged 0.98 and 0.99, respectively. A high correlation between CT values obtained by AsChip and conventional qPCR was obtained ( r = 0.962, P < 0.001). Finally, we successfully applied AsChip on soil samples from a chromium-copper-arsenic-contaminated field site and identified diverse As genes with total abundance average of 0.4 As gene copies per 16S rRNA. Our results indicate that AsChip constitutes a robust tool for comprehensive quantitative profiling of As genes in environmental samples.
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Affiliation(s)
- Yi Zhao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences , University of Copenhagen , Thorvaldsenvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health , Institute of Urban Environment , Chinese Academy of Science , 1799 Jimei Road , Xiamen 361021 , China
| | - Jun Ye
- Key Laboratory of Urban Environment and Health , Institute of Urban Environment , Chinese Academy of Science , 1799 Jimei Road , Xiamen 361021 , China
| | - Christopher Rensing
- Key Laboratory of Urban Environment and Health , Institute of Urban Environment , Chinese Academy of Science , 1799 Jimei Road , Xiamen 361021 , China
- Institute of Environmental Microbiology, College of Resources and Environment , Fujian Agriculture and Forestry University , Fuzhou 350002 , Fujian China
| | - Stacie Tardif
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences , University of Copenhagen , Thorvaldsenvej 40 , DK-1871 Frederiksberg C , Denmark
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health , Institute of Urban Environment , Chinese Academy of Science , 1799 Jimei Road , Xiamen 361021 , China
- State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing 100085 , China
| | - Kristian Koefoed Brandt
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences , University of Copenhagen , Thorvaldsenvej 40 , DK-1871 Frederiksberg C , Denmark
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36
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Chi L, Bian X, Gao B, Tu P, Ru H, Lu K. The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and Its Functional Metagenome. Toxicol Sci 2018; 160:193-204. [PMID: 28973555 DOI: 10.1093/toxsci/kfx174] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Multiple environmental factors induce dysbiosis in the gut microbiome and cause a variety of human diseases. Previously, we have first demonstrated that arsenic alters the composition of the gut microbiome. However, the functional impact of arsenic on the gut microbiome has not been adequately assessed, particularly at environmentally relevant concentrations. In this study, we used 16S rRNA sequencing and metagenomics sequencing to investigate how exposure to 100 ppb arsenic for 13 weeks alters the composition and functional capacity of the gut microbiome in mice. Arsenic exposure altered the alpha and beta diversities as well as the composition profile of the gut microbiota. Metagenomics data revealed that the abundances of genes involved in carbohydrate metabolism, especially pyruvate fermentation, short-chain fatty acid synthesis, and starch utilization, and were significantly changed. Moreover, lipopolysaccharide biosynthesis genes, multiple stress response genes, and DNA repair genes were significantly increased in the gut microbiome of arsenic-exposed mice. The genes involved in the production or processing of multiple vitamins, including folic acid and vitamins B6, B12, and K2, were also enriched in arsenic-treated mice. In, addition, genes involved in multidrug resistance and conjugative transposon proteins were highly increased after treatment with arsenic. In conclusion, we demonstrate that arsenic exposure, at an environmentally relevant dose, not only perturbed the communal composition of the gut microbiome but also profoundly altered a variety of important bacterial functional pathways.
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Affiliation(s)
- Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519
| | - Xiaoming Bian
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519
| | - Bei Gao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519.,Department of Molecular and Cellular Biology, NIH West Coast Metabolomics Center, University of California, Davis, Davis, California 95616
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina 27607
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27519
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Mild Telomere Dysfunction as a Force for Altering the Adaptive Potential of Subtelomeric Genes. Genetics 2017; 208:537-548. [PMID: 29242289 DOI: 10.1534/genetics.117.300607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/08/2017] [Indexed: 11/18/2022] Open
Abstract
Subtelomeric regions have several unusual characteristics, including complex repetitive structures, increased rates of evolution, and enrichment for genes involved in niche adaptation. The adaptive telomere failure hypothesis suggests that certain environmental stresses can induce a low level of telomere failure, potentially leading to elevated subtelomeric recombination that could result in adaptive mutational changes within subtelomeric genes. Here, we tested a key prediction of the adaptive telomere failure hypothesis-that telomere dysfunction mild enough to have little or no overall effect on cell fitness could still lead to substantial increases in the mutation rates of subtelomeric genes. Our results show that a mutant of Kluyveromyces lactis with stably short telomeres produced a large increase in the frequency of mutations affecting the native subtelomeric β-galactosidase (LAC4) gene. All lac4 mutants examined from strains with severe telomere dysfunction underwent terminal deletion/duplication events consistent with being due to break-induced replication. In contrast, although cells with mild telomere dysfunction also exhibited similar terminal deletion and duplication events, up to 50% of lac4 mutants from this background unexpectedly contained base changes within the LAC4 coding region. This mutational bias for producing base changes demonstrates that mild telomere dysfunction can be well suited as a force for altering the adaptive potential of subtelomeric genes.
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Chen Y, Hua CY, Jia MR, Fu JW, Liu X, Han YH, Liu Y, Rathinasabapathi B, Cao Y, Ma LQ. Heterologous Expression of Pteris vittata Arsenite Antiporter PvACR3;1 Reduces Arsenic Accumulation in Plant Shoots. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10387-10395. [PMID: 28834681 DOI: 10.1021/acs.est.7b03369] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Arsenic (As) is a toxic carcinogen so it is crucial to decrease As accumulation in crops to reduce its risk to human health. Arsenite (AsIII) antiporter ACR3 protein is critical for As metabolism in organisms, but it is lost in flowering plants. Here, a novel ACR3 gene from As-hyperaccumulator Pteris vittata, PvACR3;1, was cloned and expressed in Saccharomyces cerevisiae (yeast), Arabidopsis thaliana (model plant), and Nicotiana tabacum (tobacco). Yeast experiments showed that PvACR3;1 functioned as an AsIII-antiporter to mediate AsIII efflux to an external medium. At 5 μM AsIII, PvACR3;1 transgenic Arabidopsis accumulated 14-29% higher As in the roots and 55-61% lower As in the shoots compared to WT control, showing lower As translocation. Besides, transgenic tobacco under 5 μM AsIII or AsV also showed similar results, indicating that expressing PvACR3;1 gene increased As retention in plant roots. Moreover, observation of PvACR3;1-green fluorescent protein fusions in transgenic Arabidopsis showed that PvACR3;1 protein localized to the vacuolar membrane, indicating that PvACR3;1 mediated AsIII sequestration into vacuoles, consistent with increased root As. In addition, soil experiments showed ∼22% lower As in the shoots of transgenic tobacco than control. Thus, our study provides a potential strategy to limit As accumulation in plant shoots, representing the first report to decrease As translocation by sequestrating AsIII into vacuoles, shedding light on engineering low-As crops to improve food safety.
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Affiliation(s)
- Yanshan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Chen-Yu Hua
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Meng-Ru Jia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Jing-Wei Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Xue Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Yong-He Han
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
- Quangang Petrochemical Research Institute, Fujian Normal University , Quanzhou, Fujian 326801, China
| | - Yungen Liu
- Research Institute of Rural Sewage Treatment, South West Forestry University , Yunnan 650224, China
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida , Gainesville, Florida 32611, United States
| | - Yue Cao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
| | - Lena Q Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Jiangsu 210023, China
- Soil and Water Science Department, University of Florida , Gainesville, Florida 32611, United States
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Chauhan NS, Nain S, Sharma R. Identification of Arsenic Resistance Genes from Marine Sediment Metagenome. Indian J Microbiol 2017; 57:299-306. [PMID: 28904414 DOI: 10.1007/s12088-017-0658-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 02/02/2023] Open
Abstract
A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids. The clones harbored inserts of 8.848 Kb and 6.771 Kb, respectively. Both the clones possess A + T rich nucleotide sequence with similarity to sequences from marine psychrophilic bacteria. Sequence and transposon-mutagenesis based analysis revealed the presence of a putative arsenate reductase (ArsC), a putative arsenite efflux pump (ArsB/ACR) and a putative NADPH-dependent FMN reductase (ArsH) in both the clones and also a putative transcriptional regulatory protein (ArsR) in pA7. The increased resistance of clone A7 to As(V), As(III) and Sb(III) indicates functional expression of ArsC and ArsB proteins from pA7. The absence of increased As(V) resistance in clone A12 may be due to the expression of a possible inactive ArsC, as conserved Arg60 residue in this protein was replaced by Glu60, while the absence of Sb(III) resistance may be due to the presence of an ACR3p-type arsenite pump, which is known to lack antimony transport ability.
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Affiliation(s)
- Nar Singh Chauhan
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Department of Biochemistry, Present Address: Maharishi Dayanand University, Rohtak, Haryana India
| | - Sonam Nain
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
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40
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Mediator, SWI/SNF and SAGA complexes regulate Yap8-dependent transcriptional activation of ACR2 in response to arsenate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:472-481. [DOI: 10.1016/j.bbagrm.2017.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/30/2017] [Accepted: 02/01/2017] [Indexed: 01/12/2023]
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41
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Johnson AJ, Veljanoski F, O'Doherty PJ, Zaman MS, Petersingham G, Bailey TD, Münch G, Kersaitis C, Wu MJ. Molecular insight into arsenic toxicity via the genome-wide deletion mutant screening of Saccharomyces cerevisiae. Metallomics 2016; 8:228-35. [PMID: 26688044 DOI: 10.1039/c5mt00261c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Arsenic is omnipresent in soil, air, food and water. Chronic exposure to arsenic is a serious problem to human health. In-depth understanding of this metalloid's toxicity is a fundamental step towards development of arsenic-free foods and measures for bioremediation. By screening the complete set of gene deletion mutants (4873) of Saccharomyces cerevisiae, this study uncovered 75 sensitive and 39 resistant mutants against arsenite [As(III)]. Functional analysis of the corresponding genes revealed the molecular details for its uptake, toxicity and detoxification. On the basis of the hypersensitivity of yap3Δ, the transcription factor, Yap3p, is for the first time linked to the cell's detoxification against As(III). Apart from confirming the previously described role of the mitogen-activated protein kinase (MAPK) Hog1 pathway in combating arsenic toxicity, the results show that the regulatory subunits (Ckb1p and Ckb2p) of protein kinase CK2 are also involved in the process, suggesting possible crosstalk between the two key protein kinases. The sensitivity to As(III) conferred by deletion of the genes involved in protein degradation and chromatin remodelling demonstrates protein damage is the key mode of toxicity for the metalloid. Furthermore, the resistant phenotype of fps1Δ, snf3Δ and pho81Δ against As(III) links arsenic uptake with the corresponding plasma membrane-bound transporters-aquaglyceroporin (Fps1p), hexose (Snf3p) and phosphate transporters. The molecular details obtained in this screen for As(III) uptake, detoxification and toxicity provide the basis for future investigations into arsenic-related problems in the environment, agriculture and human health.
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Affiliation(s)
- Adam J Johnson
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Filip Veljanoski
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Patrick J O'Doherty
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Mohammad S Zaman
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Gayani Petersingham
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Trevor D Bailey
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Gerald Münch
- Department of Pharmacology, School of Medicine and Molecular Medicine Research Group, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Cindy Kersaitis
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Ming J Wu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
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Wawrzycka D, Markowska K, Maciaszczyk-Dziubinska E, Migocka M, Wysocki R. Transmembrane topology of the arsenite permease Acr3 from Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:117-125. [PMID: 27836640 DOI: 10.1016/j.bbamem.2016.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 11/03/2016] [Accepted: 11/06/2016] [Indexed: 10/20/2022]
Abstract
Acr3 is a plasma membrane transporter, a member of the bile/arsenite/riboflavin transporter (BART) superfamily, which confers high-level resistance to arsenicals in the yeast Saccharomyces cerevisiae. We have previously shown that the yeast Acr3 acts as a low affinity As(III)/H+ and Sb(III)/H+ antiporter. We have also identified several amino acid residues that are localized in putative transmembrane helices (TM) and appeared to be critical for the Acr3 activity. In the present study, the topology of Acr3 was investigated by insertion of glycosylation and factor Xa protease cleavage sites at predicted hydrophilic regions. The analysis of the glycosylation pattern and factor Xa cleavage products of resulting Acr3 fusion constructs provide evidence supporting a topological model of Acr3 with 10 TM segments and cytoplasmically oriented N- and C-terminal domains. Next, we investigated the role of the hydrophilic loop connecting TM8 and TM9, the large size of which is unique to members of the yeast Acr3 family of metalloid transporters. We found that a 28 amino acid deletion in this region does not affect Acr3 folding, trafficking substrate binding, or transport activity. Finally, we constructed a homology-based structural model of Acr3 using the crystal structure of the Yersinia frederiksenii homologue of the human bile acid sodium symporter ASBT.
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Affiliation(s)
- Donata Wawrzycka
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Katarzyna Markowska
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | | | - Magdalena Migocka
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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43
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Genome-based insights into the resistome and mobilome of multidrug-resistant Aeromonas sp. ARM81 isolated from wastewater. Arch Microbiol 2016; 199:177-183. [PMID: 27590015 PMCID: PMC5216076 DOI: 10.1007/s00203-016-1285-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/20/2016] [Accepted: 08/27/2016] [Indexed: 11/26/2022]
Abstract
The draft genome of multidrug-resistant Aeromonas sp. ARM81 isolated from a wastewater treatment plant in Warsaw (Poland) was obtained. Sequence analysis revealed multiple genes conferring resistance to aminoglycosides, β-lactams or tetracycline. Three different β-lactamase genes were identified, including an extended-spectrum β-lactamase gene blaPER-1. The antibiotic susceptibility was experimentally tested. Genome sequencing also allowed us to investigate the plasmidome and transposable mobilome of ARM81. Four plasmids, of which two carry phenotypic modules (i.e., genes encoding a zinc transporter ZitB and a putative glucosyltransferase), and 28 putative transposase genes were identified. The mobility of three insertion sequences (isoforms of previously identified elements ISAs12, ISKpn9 and ISAs26) was confirmed using trap plasmids.
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44
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Merhej J, Thiebaut A, Blugeon C, Pouch J, Ali Chaouche MEA, Camadro JM, Le Crom S, Lelandais G, Devaux F. A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata. Front Microbiol 2016; 7:645. [PMID: 27242683 PMCID: PMC4860858 DOI: 10.3389/fmicb.2016.00645] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/18/2016] [Indexed: 01/15/2023] Open
Abstract
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption, and iron metabolism.
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Affiliation(s)
- Jawad Merhej
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Antonin Thiebaut
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Corinne Blugeon
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Juliette Pouch
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Mohammed El Amine Ali Chaouche
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Jean-Michel Camadro
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Stéphane Le Crom
- Évolution, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7138, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Gaëlle Lelandais
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Frédéric Devaux
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
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45
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Koechler S, Bertin PN, Plewniak F, Baltenweck R, Casiot C, Heipieper HJ, Bouchez O, Arsène-Ploetze F, Hugueney P, Halter D. Arsenite response in Coccomyxa sp. Carn explored by transcriptomic and non-targeted metabolomic approaches. Environ Microbiol 2016; 18:1289-300. [PMID: 26769162 DOI: 10.1111/1462-2920.13227] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/20/2015] [Accepted: 01/12/2016] [Indexed: 12/17/2022]
Abstract
Arsenic is a toxic metalloid known to generate an important oxidative stress in cells. In the present study, we focused our attention on an alga related to the genus Coccomyxa, exhibiting an extraordinary capacity to resist high concentrations of arsenite and arsenate. The integrated analysis of high-throughput transcriptomic data and non-targeted metabolomic approaches highlighted multiple levels of protection against arsenite. Indeed, Coccomyxa sp. Carn induced a set of transporters potentially preventing the accumulation of this metalloid in the cells and presented a distinct arsenic metabolism in comparison to another species more sensitive to that compound, i.e. Euglena gracilis, especially in regard to arsenic methylation. Interestingly, Coccomyxa sp. Carn was characterized by a remarkable accumulation of the strong antioxidant glutathione (GSH). Such observation could explain the apparent low oxidative stress in the intracellular compartment, as suggested by the transcriptomic analysis. In particular, the high amount of GSH in the cell could play an important role for the tolerance to arsenate, as suggested by its partial oxidation into oxidized glutathione in presence of this metalloid. Our results therefore reveal that this alga has acquired multiple and original defence mechanisms allowing the colonization of extreme ecosystems such as acid mine drainages.
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Affiliation(s)
- Sandrine Koechler
- Génétique Moléculaire, Génomique et Microbiologie, Département Microorganismes, Génomes, Environnement UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, Département Microorganismes, Génomes, Environnement UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, Département Microorganismes, Génomes, Environnement UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France
| | - Raymonde Baltenweck
- Unité Mixte de Recherche Santé de la Vigne et Qualité du Vin, Equipe Métabolisme secondaire de la vigne INRA, 68021, Colmar, France
| | - Corinne Casiot
- Hydrosciences Montpellier, UMR 5569 (CNRS, IRD, UM1, UM2), Université Montpellier 2, Place E. Bataillon, 34095, Montpellier Cedex 05, France
| | - Hermann J Heipieper
- Helmholtz Centre for Environmental Research - UFZ, Department Environmental Biotechnology, Permoserstr. 15, Leipzig, Germany
| | - Olivier Bouchez
- GeT-PlaGe (Plateforme Génomique) Campus INRA, 24 Chemin de Borde Rouge - Auzeville CS 52627, 31326, Castanet-Tolosan, France
| | - Florence Arsène-Ploetze
- Génétique Moléculaire, Génomique et Microbiologie, Département Microorganismes, Génomes, Environnement UMR7156 Université de Strasbourg/CNRS, 28 rue Goethe, 67083, Strasbourg Cedex, France
| | - Philippe Hugueney
- Unité Mixte de Recherche Santé de la Vigne et Qualité du Vin, Equipe Métabolisme secondaire de la vigne INRA, 68021, Colmar, France
| | - David Halter
- Unité Mixte de Recherche Santé de la Vigne et Qualité du Vin, Equipe Métabolisme secondaire de la vigne INRA, 68021, Colmar, France
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46
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Singh S, Parihar P, Singh R, Singh VP, Prasad SM. Heavy Metal Tolerance in Plants: Role of Transcriptomics, Proteomics, Metabolomics, and Ionomics. FRONTIERS IN PLANT SCIENCE 2016; 6:1143. [PMID: 26904030 PMCID: PMC4744854 DOI: 10.3389/fpls.2015.01143] [Citation(s) in RCA: 436] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 05/18/2023]
Abstract
Heavy metal contamination of soil and water causing toxicity/stress has become one important constraint to crop productivity and quality. This situation has further worsened by the increasing population growth and inherent food demand. It has been reported in several studies that counterbalancing toxicity due to heavy metal requires complex mechanisms at molecular, biochemical, physiological, cellular, tissue, and whole plant level, which might manifest in terms of improved crop productivity. Recent advances in various disciplines of biological sciences such as metabolomics, transcriptomics, proteomics, etc., have assisted in the characterization of metabolites, transcription factors, and stress-inducible proteins involved in heavy metal tolerance, which in turn can be utilized for generating heavy metal-tolerant crops. This review summarizes various tolerance strategies of plants under heavy metal toxicity covering the role of metabolites (metabolomics), trace elements (ionomics), transcription factors (transcriptomics), various stress-inducible proteins (proteomics) as well as the role of plant hormones. We also provide a glance of some strategies adopted by metal-accumulating plants, also known as "metallophytes."
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Affiliation(s)
- Samiksha Singh
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of AllahabadAllahabad, India
| | - Parul Parihar
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of AllahabadAllahabad, India
| | - Rachana Singh
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of AllahabadAllahabad, India
| | - Vijay P. Singh
- Department of Botany, Government Ramanuj Pratap Singhdev Post Graduate College, Sarguja UniversityBaikunthpur, India
| | - Sheo M. Prasad
- Ranjan Plant Physiology and Biochemistry Laboratory, Department of Botany, University of AllahabadAllahabad, India
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Laureau R, Loeillet S, Salinas F, Bergström A, Legoix-Né P, Liti G, Nicolas A. Extensive Recombination of a Yeast Diploid Hybrid through Meiotic Reversion. PLoS Genet 2016; 12:e1005781. [PMID: 26828862 PMCID: PMC4734685 DOI: 10.1371/journal.pgen.1005781] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
In somatic cells, recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events (LOH), allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection. However, inter-homolog recombination in somatic cells is rare, thus reducing potential genetic variation. Here, we explored the property of S. cerevisiae to enter the meiotic developmental program, induce meiotic Spo11-dependent double-strand breaks genome-wide and return to mitotic growth, a process known as Return To Growth (RTG). Whole genome sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid strain demonstrates that the RTGs are bona fide diploids with mosaic recombined genome, derived from either parental origin. Individual RTG genome-wide genotypes are comprised of 5 to 87 homozygous regions due to the loss of heterozygous (LOH) events of various lengths, varying between a few nucleotides up to several hundred kilobases. Furthermore, we show that reiteration of the RTG process shows incremental increases of homozygosity. Phenotype/genotype analysis of the RTG strains for the auxotrophic and arsenate resistance traits validates the potential of this procedure of genome diversification to rapidly map complex traits loci (QTLs) in diploid strains without undergoing sexual reproduction.
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Affiliation(s)
- Raphaëlle Laureau
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
| | - Sophie Loeillet
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
| | - Francisco Salinas
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Anders Bergström
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Patricia Legoix-Né
- Institut Curie, PSL Research University, Next Generation Sequencing Platform, Paris, France
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, CNRS, UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 3244, Paris, France
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48
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Arsenic Directly Binds to and Activates the Yeast AP-1-Like Transcription Factor Yap8. Mol Cell Biol 2015; 36:913-22. [PMID: 26711267 DOI: 10.1128/mcb.00842-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/23/2015] [Indexed: 11/20/2022] Open
Abstract
The AP-1-like transcription factor Yap8 is critical for arsenic tolerance in the yeast Saccharomyces cerevisiae. However, the mechanism by which Yap8 senses the presence of arsenic and activates transcription of detoxification genes is unknown. Here we demonstrate that Yap8 directly binds to trivalent arsenite [As(III)] in vitro and in vivo and that approximately one As(III) molecule is bound per molecule of Yap8. As(III) is coordinated by three sulfur atoms in purified Yap8, and our genetic and biochemical data identify the cysteine residues that form the binding site as Cys132, Cys137, and Cys274. As(III) binding by Yap8 does not require an additional yeast protein, and Yap8 is regulated neither at the level of localization nor at the level of DNA binding. Instead, our data are consistent with a model in which a DNA-bound form of Yap8 acts directly as an As(III) sensor. Binding of As(III) to Yap8 triggers a conformational change that in turn brings about a transcriptional response. Thus, As(III) binding to Yap8 acts as a molecular switch that converts inactive Yap8 into an active transcriptional regulator. This is the first report to demonstrate how a eukaryotic protein couples arsenic sensing to transcriptional activation.
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Guerra-Moreno A, Isasa M, Bhanu MK, Waterman DP, Eapen VV, Gygi SP, Hanna J. Proteomic Analysis Identifies Ribosome Reduction as an Effective Proteotoxic Stress Response. J Biol Chem 2015; 290:29695-706. [PMID: 26491016 DOI: 10.1074/jbc.m115.684969] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 11/06/2022] Open
Abstract
Stress responses are adaptive cellular programs that identify and mitigate potentially dangerous threats. Misfolded proteins are a ubiquitous and clinically relevant stress. Trivalent metalloids, such as arsenic, have been proposed to cause protein misfolding. Using tandem mass tag-based mass spectrometry, we show that trivalent arsenic results in widespread reorganization of the cell from an anabolic to a catabolic state. Both major pathways of protein degradation, the proteasome and autophagy, show increased abundance of pathway components and increased functional output, and are required for survival. Remarkably, cells also showed a down-regulation of ribosomes at the protein level. That this represented an adaptive response and not an adverse toxic effect was indicated by enhanced survival of ribosome mutants after arsenic exposure. These results suggest that a major source of toxicity of trivalent arsenic derives from misfolding of newly synthesized proteins and identifies ribosome reduction as a rapid, effective, and reversible proteotoxic stress response.
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Affiliation(s)
- Angel Guerra-Moreno
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Marta Isasa
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, and
| | - Meera K Bhanu
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - David P Waterman
- Rosenstiel Basic Medical Sciences Research Center and the Department of Biology, Brandeis University, Waltham, Massachusetts 02254
| | - Vinay V Eapen
- Rosenstiel Basic Medical Sciences Research Center and the Department of Biology, Brandeis University, Waltham, Massachusetts 02254
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, and
| | - John Hanna
- From the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115,
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50
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Cesaro P, Cattaneo C, Bona E, Berta G, Cavaletto M. The arsenic hyperaccumulating Pteris vittata expresses two arsenate reductases. Sci Rep 2015; 5:14525. [PMID: 26412036 PMCID: PMC4585942 DOI: 10.1038/srep14525] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/26/2015] [Indexed: 11/09/2022] Open
Abstract
Enzymatic reduction of arsenate to arsenite is the first known step in arsenate metabolism in all organisms. Although the presence of one mRNA arsenate reductase (PvACR2) has been characterized in gametophytes of P. vittata, no arsenate reductase protein has been directly observed in this arsenic hyperaccumulating fern, yet. In order to assess the possible presence of arsenate reductase in P. vittata, two recombinant proteins, ACR2-His6 and Trx-His6-S-Pv2.5-8 were prepared in Escherichia coli, purified and used to produce polyclonal antibodies. The presence of these two enzymes was evaluated by qRT-PCR, immunoblotting and direct MS analysis. Enzymatic activity was detected in crude extracts. For the first time we detected and identified two arsenate reductase proteins (PvACR2 and Pv2.5-8) in sporophytes and gametophytes of P. vittata. Despite an increase of the mRNA levels for both proteins in roots, no difference was observed at the protein level after arsenic treatment. Overall, our data demonstrate the constitutive protein expression of PvACR2 and Pv2.5-8 in P. vittata tissues and propose their specific role in the complex metabolic network of arsenic reduction.
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Affiliation(s)
- Patrizia Cesaro
- Università del Piemonte Orientale, DiSIT- Dipartimento di Scienze e Innovazione Tecnologica, viale T. Michel 11, 15121 - Alessandria, Novara, Vercelli - Italy
| | - Chiara Cattaneo
- Università del Piemonte Orientale, DiSIT- Dipartimento di Scienze e Innovazione Tecnologica, viale T. Michel 11, 15121 - Alessandria, Novara, Vercelli - Italy
| | - Elisa Bona
- Università del Piemonte Orientale, DiSIT- Dipartimento di Scienze e Innovazione Tecnologica, viale T. Michel 11, 15121 - Alessandria, Novara, Vercelli - Italy
| | - Graziella Berta
- Università del Piemonte Orientale, DiSIT- Dipartimento di Scienze e Innovazione Tecnologica, viale T. Michel 11, 15121 - Alessandria, Novara, Vercelli - Italy
| | - Maria Cavaletto
- Università del Piemonte Orientale, DiSIT- Dipartimento di Scienze e Innovazione Tecnologica, viale T. Michel 11, 15121 - Alessandria, Novara, Vercelli - Italy
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