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Ramnarine SDB, Ali O, Jayaraman J, Ramsubhag A. Early transcriptional changes of heavy metal resistance and multiple efflux genes in Xanthomonas campestris pv. campestris under copper and heavy metal ion stress. BMC Microbiol 2024; 24:81. [PMID: 38461228 PMCID: PMC10924375 DOI: 10.1186/s12866-024-03206-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/28/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Copper-induced gene expression in Xanthomonas campestris pv. campestris (Xcc) is typically evaluated using targeted approaches involving qPCR. The global response to copper stress in Xcc and resistance to metal induced damage is not well understood. However, homologs of heavy metal efflux genes from the related Stenotrophomonas genus are found in Xanthomonas which suggests that metal related efflux may also be present. METHODS AND RESULTS Gene expression in Xcc strain BrA1 exposed to 0.8 mM CuSO4.5H2O for 15 minutes was captured using RNA-seq analysis. Changes in expression was noted for genes related to general stress responses and oxidoreductases, biofilm formation, protein folding chaperones, heat-shock proteins, membrane lipid profile, multiple drug and efflux (MDR) transporters, and DNA repair were documented. At this timepoint only the cohL (copper homeostasis/tolerance) gene was upregulated as well as a chromosomal czcCBA efflux operon. An additional screen up to 4 hrs using qPCR was conducted using a wider range of heavy metals. Target genes included a cop-containing heavy metal resistance island and putative metal efflux genes. Several efflux pumps, including a copper resistance associated homolog from S. maltophilia, were upregulated under toxic copper stress. However, these pumps were also upregulated in response to other toxic heavy metals. Additionally, the temporal expression of the coh and cop operons was also observed, demonstrating co-expression of tolerance responses and later activation of part of the cop operon. CONCLUSIONS Overall, initial transcriptional responses focused on combating oxidative stress, mitigating protein damage and potentially increasing resistance to heavy metals and other biocides. A putative copper responsive efflux gene and others which might play a role in broader heavy metal resistance were also identified. Furthermore, the expression patterns of the cop operon in conjunction with other copper responsive genes allowed for a better understanding of the fate of copper ions in Xanthomonas. This work provides useful evidence for further evaluating MDR and other efflux pumps in metal-specific homeostasis and tolerance phenotypes in the Xanthomonas genus. Furthermore, non-canonical copper tolerance and resistance efflux pumps were potentially identified. These findings have implications for interpreting MIC differences among strains with homologous copLAB resistance genes, understanding survival under copper stress, and resistance in disease management.
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Affiliation(s)
- Stephen D B Ramnarine
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Omar Ali
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of The West Indies, St. Augustine campus, St. Augustine, Trinidad and Tobago, W. I.
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Yu Y, Xie Z, Yang J, Yang R, Li Y, Zhu Y, Zhao Y, Yang Q, Chen J, Alwathnani HA, Feng R, Rensing C, Herzberg M. Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130184. [PMID: 36270189 DOI: 10.1016/j.jhazmat.2022.130184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 05/25/2023]
Abstract
Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.
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Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhenchen Xie
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jigang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ruixiang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yongguan Zhu
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yanlin Zhao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jichen Chen
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Hend A Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle(Saale), Germany
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3
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Ares Á, Sakai S, Sasaki T, Shimamura S, Mitarai S, Nunoura T. Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Environ Microbiol 2022; 24:6144-6163. [PMID: 36284406 PMCID: PMC10092412 DOI: 10.1111/1462-2920.16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Sanae Sakai
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Toshio Sasaki
- Imaging section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Shigeru Shimamura
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Martin-Pozas T, Sanchez-Moral S, Cuezva S, Jurado V, Saiz-Jimenez C, Perez-Lopez R, Carrey R, Otero N, Giesemann A, Well R, Calaforra JM, Fernandez-Cortes A. Biologically mediated release of endogenous N 2O and NO 2 gases in a hydrothermal, hypoxic subterranean environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141218. [PMID: 32777502 DOI: 10.1016/j.scitotenv.2020.141218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO2-rich fluids. Anomalous concentrations of N2O and NO2 were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO2 and CH4 during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O2, temperature, and GHG concentration. Both the N2O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N2O and NO2 emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH2OH, NO, and NO2- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Raul Perez-Lopez
- Geological Hazard Division, Geological Survey of Spain (IGME), 28003 Madrid, Spain.
| | - Raul Carrey
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Neus Otero
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Anette Giesemann
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Jose M Calaforra
- Department of Biology and Geology, University of Almeria, 04120 Almeria, Spain.
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Rattanapolsan L, Nakbanpote W, Sangdee A. Zinc- and cadmium-tolerant endophytic bacteria from Murdannia spectabilis (Kurz) Faden. studied for plant growth-promoting properties, in vitro inoculation, and antagonism. Arch Microbiol 2020; 203:1131-1148. [PMID: 33206216 DOI: 10.1007/s00203-020-02108-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 01/28/2023]
Abstract
This research aims to isolate and identify Zn- and Cd-tolerant endophytic bacteria from Murdannia spectabilis, identify their properties with and without Zn and Cd stress, and to investigate the effect of bacterial inoculation in an in vitro system. Twenty-four isolates could survive on trypticase soya agar (TSA) supplemented with Zn (250-500 mg L-1) and/or Cd (20-50 mg L-1) that belonged to the genera Bacillus, Pantoea, Microbacterium, Curtobacterium, Chryseobacterium, Cupriavidus, Siphonobacter, and Pseudomonas. Each strain had different indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC) deaminase and siderophore production, nitrogen fixation, phosphate solubilization, and lignocellulosic enzyme characteristics. Cupriavidus plantarum MDR5 and Chryseobacterium sp. MDR7 were selected for inoculation into plantlets that were already occupied by Curtobacterium sp. TMIL due to them have a high tolerance for Zn and Cd while showing no pathogenicity. As determined via an in vitro system, Cupriavidus plantarum MDR5 remained in the plants to a greater extent than Chryseobacterium sp. MDR7, while Curtobacterium sp. TMIL was the dominant species. The Zn plus Cd treatment supported the persistence of Cupriavidus plantarum MDR5. Dual and mixed cultivation showed no antagonistic effects between the endophytes. Although the plant growth and Zn/Cd accumulation were not significantly affected by the Zn-/Cd-tolerant endophytes, the inoculation did not weaken the plants. Therefore, Cupriavidus plantarum MDR5 could be applied in a bioaugmentation process.
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Affiliation(s)
- Ladawan Rattanapolsan
- Department of Biology, Faculty of Science, Mahasarakham University, Khamriang, Kantarawichai, Maha Sarakham, 44150, Thailand
| | - Woranan Nakbanpote
- Department of Biology, Faculty of Science, Mahasarakham University, Khamriang, Kantarawichai, Maha Sarakham, 44150, Thailand.
| | - Aphidech Sangdee
- Department of Biology, Faculty of Science, Mahasarakham University, Khamriang, Kantarawichai, Maha Sarakham, 44150, Thailand
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Maertens L, Leys N, Matroule JY, Van Houdt R. The Transcriptomic Landscape of Cupriavidus metallidurans CH34 Acutely Exposed to Copper. Genes (Basel) 2020; 11:E1049. [PMID: 32899882 PMCID: PMC7563307 DOI: 10.3390/genes11091049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022] Open
Abstract
Bacteria are increasingly used for biotechnological applications such as bioremediation, biorecovery, bioproduction, and biosensing. The development of strains suited for such applications requires a thorough understanding of their behavior, with a key role for their transcriptomic landscape. We present a thorough analysis of the transcriptome of Cupriavidus metallidurans CH34 cells acutely exposed to copper by tagRNA-sequencing. C. metallidurans CH34 is a model organism for metal resistance, and its potential as a biosensor and candidate for metal bioremediation has been demonstrated in multiple studies. Several metabolic pathways were impacted by Cu exposure, and a broad spectrum of metal resistance mechanisms, not limited to copper-specific clusters, was overexpressed. In addition, several gene clusters involved in the oxidative stress response and the cysteine-sulfur metabolism were induced. In total, 7500 transcription start sites (TSSs) were annotated and classified with respect to their location relative to coding sequences (CDSs). Predicted TSSs were used to re-annotate 182 CDSs. The TSSs of 2422 CDSs were detected, and consensus promotor logos were derived. Interestingly, many leaderless messenger RNAs (mRNAs) were found. In addition, many mRNAs were transcribed from multiple alternative TSSs. We observed pervasive intragenic TSSs both in sense and antisense to CDSs. Antisense transcripts were enriched near the 5' end of mRNAs, indicating a functional role in post-transcriptional regulation. In total, 578 TSSs were detected in intergenic regions, of which 35 were identified as putative small regulatory RNAs. Finally, we provide a detailed analysis of the main copper resistance clusters in CH34, which include many intragenic and antisense transcripts. These results clearly highlight the ubiquity of noncoding transcripts in the CH34 transcriptome, many of which are putatively involved in the regulation of metal resistance.
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Affiliation(s)
- Laurens Maertens
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium;
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium;
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (N.L.)
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A Sensitive Magnetic Arsenite-Specific Biosensor Hosted in Magnetotactic Bacteria. Appl Environ Microbiol 2020; 86:AEM.00803-20. [PMID: 32385084 DOI: 10.1128/aem.00803-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/01/2020] [Indexed: 01/22/2023] Open
Abstract
According to the World Health Organization, arsenic is the water contaminant that affects the largest number of people worldwide. To limit its impact on the population, inexpensive, quick, and easy-to-use systems of detection are required. One promising solution could be the use of whole-cell biosensors, which have been extensively studied and could meet all these criteria even though they often lack sensitivity. Here, we investigated the benefit of using magnetotactic bacteria as cellular chassis to design and build sensitive magnetic bacterial biosensors. Promoters potentially inducible by arsenic were first identified in silico within the genomes of two magnetotactic bacteria strains, Magnetospirillum magneticum AMB-1 and Magnetospirillum gryphiswaldense MSR-1. The ArsR-dependent regulation was confirmed by reverse transcription-PCR experiments. Biosensors built by transcriptional fusion between the arsenic-inducible promoters and the bacterial luciferase luxCDABE operon gave an element-specific response in 30 min with an arsenite detection limit of 0.5 μM. After magnetic concentration, we improved the sensitivity of the biosensor by a factor of 50 to reach 10 nM, more than 1 order of magnitude below the recommended guidelines for arsenic in drinking water (0.13 μM). Finally, we demonstrated the successful preservation of the magnetic bacterium biosensors by freeze-drying.IMPORTANCE Whole-cell biosensors based on reporter genes can be designed for heavy metal detection but often require the optimization of their sensitivity and specific adaptations for practical use in the field. Magnetotactic bacteria as cellular hosts for biosensors are interesting models, as their intrinsic magnetism permits them to be easily concentrated and entrapped to increase the arsenic-response signal. This paves the way for the development of sensitive and immobilized whole-cell biosensors tailored for use in the field.
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
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Klonowska A, Moulin L, Ardley JK, Braun F, Gollagher MM, Zandberg JD, Marinova DV, Huntemann M, Reddy TBK, Varghese NJ, Woyke T, Ivanova N, Seshadri R, Kyrpides N, Reeve WG. Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil. BMC Genomics 2020; 21:214. [PMID: 32143559 PMCID: PMC7060636 DOI: 10.1186/s12864-020-6623-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. RESULTS The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. CONCLUSIONS STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.
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Affiliation(s)
- Agnieszka Klonowska
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
| | - Julie Kaye Ardley
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Florence Braun
- IRD, UMR LSTM-Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier cedex 5, France
| | | | - Jaco Daniel Zandberg
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Dora Vasileva Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, USA
| | | | | | | | - Wayne Gerald Reeve
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
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Durante-Rodríguez G, Fernández-Llamosas H, Alonso-Fernandes E, Fernández-Muñiz MN, Muñoz-Olivas R, Díaz E, Carmona M. ArxA From Azoarcus sp. CIB, an Anaerobic Arsenite Oxidase From an Obligate Heterotrophic and Mesophilic Bacterium. Front Microbiol 2019; 10:1699. [PMID: 31417512 PMCID: PMC6683785 DOI: 10.3389/fmicb.2019.01699] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/10/2019] [Indexed: 11/13/2022] Open
Abstract
Arsenic is a toxic element widely distributed in nature, but numerous bacteria are able to resist its toxicity mainly through the ars genes encoding an arsenate reductase and an arsenite efflux pump. Some “arsenotrophic” bacteria are also able to use arsenite as energy supplier during autotrophic growth by coupling anaerobic arsenite oxidation via the arx gene products to nitrate respiration or photosynthesis. Here, we have demonstrated that Azoarcus sp. CIB, a facultative anaerobic β-proteobacterium, is able to resist arsenic oxyanions both under aerobic and anaerobic conditions. Genome mining, gene expression, and mutagenesis studies revealed the presence of a genomic island that harbors the ars and arx clusters involved in arsenic resistance in strain CIB. Orthologous ars clusters are widely distributed in the genomes of sequenced Azoarcus strains. Interestingly, genetic and metabolic approaches showed that the arx cluster of the CIB strain encodes an anaerobic arsenite oxidase also involved in the use of arsenite as energy source. Hence, Azoarcus sp. CIB represents the prototype of an obligate heterotrophic bacterium able to use arsenite as an extra-energy source for anaerobic cell growth. The arsenic island of strain CIB supports the notion that metabolic and energetic skills can be gained by genetic mobile elements.
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Affiliation(s)
| | | | - Elena Alonso-Fernandes
- Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | | | - Riansares Muñoz-Olivas
- Departamento de Química Analítica, Facultad de Químicas, Universidad Complutense Madrid, Madrid, Spain
| | - Eduardo Díaz
- Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | - Manuel Carmona
- Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
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11
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Pothier MP, Hinz AJ, Poulain AJ. Insights Into Arsenite and Arsenate Uptake Pathways Using a Whole Cell Biosensor. Front Microbiol 2018; 9:2310. [PMID: 30333804 PMCID: PMC6176005 DOI: 10.3389/fmicb.2018.02310] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Despite its high toxicity and widespread occurrence in many parts of the world, arsenic (As) concentrations in decentralized water supplies such as domestic wells remain often unquantified. One limitation to effective monitoring is the high cost and lack of portability of current arsenic speciation techniques. Here, we present an arsenic biosensor assay capable of quantifying and determining the bioavailable fraction of arsenic species at environmentally relevant concentrations. First, we found that inorganic phosphate, a buffering agent and nutrient commonly found in most bioassay exposure media, was in fact limiting As(V) uptake, possibly explaining the variability in As(V) detection reported so far. Second, we show that the nature of the carbon source used in the bioassay differentially affects the response of the biosensor to As(III). Finally, our data support the existence of non-specific reduction pathways (non-ars encoded) that are responsible for the reduction of As(V) to As(III), allowing its detection by the biosensor. To validate our laboratory approach using field samples, we performed As(III) and As(V) standard additions on natural water samples collected from 17 lakes surrounding Giant Mine in Yellowknife (NWT), Canada. We found that legacy arsenic contamination in these lake water samples was accurately quantified by the biosensor. Interestingly, bioavailability of freshly added standards showed signs of matrix interference, indicative of dynamic interactions between As(III), As(V) and environmental constituents that have yet to be identified. Our results point toward dissolved organic carbon as possibly controlling these interactions, thus altering As bioavailability.
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Affiliation(s)
| | - Aaron J Hinz
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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12
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Teng Y, Wang X, Zhu Y, Chen W, Christie P, Li Z, Luo Y. Biodegradation of pentachloronitrobenzene by Cupriavidus sp. YNS-85 and its potential for remediation of contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:9538-9547. [PMID: 28238184 DOI: 10.1007/s11356-017-8640-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
Pentachloronitrobenzene (PCNB) is a toxic chlorinated nitroaromatic compound. However, only a few bacteria have been reported to be able to utilize PCNB. In the present study, one pentachloronitrobenzene (PCNB)-degrading bacterium, Cupriavidus sp. YNS-85, was isolated from a contaminated Panax notoginseng plantation. The strain co-metabolized 200 mg L-1 PCNB in aqueous solution with a removal rate of 73.8% after 5 days. The bacterium also degraded PCNB effectively under acid conditions (pH 4-6) and showed resistance to toxic trace elements (arsenic, copper, and cadmium). Its ability to utilize proposed PCNB intermediates as sole carbon sources was also confirmed. The soil microcosm experiment further demonstrated that bacterial bioaugmentation enhanced the removal of PCNB (37.8%) from soil and the accumulation of pentachloroaniline (89.3%) after 30 days. Soil enzyme activity and microbial community functional diversity were positively influenced after bioremediation. These findings indicate that Cupriavidus sp. YNS-85 may be a suitable inoculant for in situ bioremediation of PCNB-polluted sites, especially those with acid soils co-contaminated with heavy metal(loid)s.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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13
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Andres J, Bertin PN. The microbial genomics of arsenic. FEMS Microbiol Rev 2016; 40:299-322. [DOI: 10.1093/femsre/fuv050] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 12/17/2022] Open
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14
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Yan Y, Ye J, Xue XM, Zhu YG. Arsenic Demethylation by a C·As Lyase in Cyanobacterium Nostoc sp. PCC 7120. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14350-14358. [PMID: 26544154 DOI: 10.1021/acs.est.5b03357] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Arsenic, a ubiquitous toxic substance, exists mainly as inorganic forms in the environment. It is perceived that organoarsenicals can be demethylated and degraded into inorganic arsenic by microorganisms. Few studies have focused on the mechanism of arsenic demethylation in bacteria. Here, we investigated arsenic demethylation in a typical freshwater cyanobacterium Nostoc sp. PCC 7120. This bacterium was able to demethylate monomethylarsenite [MAs(III)] rapidly to arsenite [As(III)] and also had the ability to demethylate monomethylarsenate [MAs(V)] to As(III). The NsarsI encoding a C·As lyase responsible for MAs(III) demethylation was cloned from Nostoc sp. PCC 7120 and heterologously expressed in an As-hypersensitive strain Escherichia coli AW3110 (ΔarsRBC). Expression of NsarsI was shown to confer MAs(III) resistance through arsenic demethylation. The purified NsArsI was further identified and functionally characterized in vitro. NsArsI existed mainly as the trimeric state, and the kinetic data were well-fit to the Hill equation with K0.5 = 7.55 ± 0.33 μM for MAs(III), Vmax = 0.79 ± 0.02 μM min(-1), and h = 2.7. Both of the NsArsI truncated derivatives lacking the C-terminal 10 residues (ArsI10) or 23 residues (ArsI23) had a reduced ability of MAs(III) demethylation. These results provide new insights for understanding the important role of cyanobacteria in arsenic biogeochemical cycling in the environment.
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Affiliation(s)
- Yu Yan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Jun Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
| | - Xi-Mei Xue
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021, People's Republic of China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, People's Republic of China
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15
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Monsieurs P, Hobman J, Vandenbussche G, Mergeay M, Van Houdt R. Response of Cupriavidus metallidurans CH34 to Metals. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20594-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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16
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Effects of Arsenite Resistance on the Growth and Functional Gene Expression of Leptospirillum ferriphilum and Acidithiobacillus thiooxidans in Pure Culture and Coculture. BIOMED RESEARCH INTERNATIONAL 2015; 2015:203197. [PMID: 26064886 PMCID: PMC4443643 DOI: 10.1155/2015/203197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 11/18/2022]
Abstract
The response of iron-oxidizing Leptospirillum ferriphilum YSK and sulfur-oxidizing Acidithiobacillus thiooxidans A01 to arsenite under pure culture and coculture was investigated based on biochemical characterization (concentration of iron ion and pH value) and related gene expression. L. ferriphilum YSK and At. thiooxidans A01 in pure culture could adapt up to 400 mM and 800 mM As(III) after domestication, respectively, although arsenite showed a negative effect on both strains. The coculture showed a stronger sulfur and ferrous ion oxidation activity when exposed to arsenite. In coculture, the pH value showed no significant difference when under 500 mM arsenite stress, and the cell number of At. thiooxidans was higher than that in pure culture benefiting from the interaction with L. ferriphilum. The expression profile showed that the arsenic efflux system in the coculture was more active than that in pure culture, indicating that there is a synergetic interaction between At. thiooxidans A01 and L. ferriphilum YSK. In addition, a model was proposed to illustrate the interaction between arsenite and the ars operon in L. ferriphilum YSK and At. thiooxidans A01. This study will facilitate the effective application of coculture in the bioleaching process by taking advantage of strain-strain communication and coordination.
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17
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Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng. Antonie van Leeuwenhoek 2015; 107:749-58. [DOI: 10.1007/s10482-014-0369-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
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18
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Furnholm TR, Tisa LS. The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia. BMC Genomics 2014; 15:1092. [PMID: 25495525 PMCID: PMC4531530 DOI: 10.1186/1471-2164-15-1092] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 11/19/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb(2+), Al(+3), SeO2, Cu(2+), AsO4, and Zn(2+). With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. RESULTS Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. CONCLUSIONS Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils.
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Affiliation(s)
- Teal R Furnholm
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.
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19
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Fernández M, Udaondo Z, Niqui JL, Duque E, Ramos JL. Synergic role of the two ars operons in arsenic tolerance in Pseudomonas putida KT2440. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:483-489. [PMID: 25646541 DOI: 10.1111/1758-2229.12167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The chromosome of Pseudomonas putida KT2440 carries two clusters of genes, denoted ars1 and ars2, that are annotated as putative arsenic resistance operons. In this work, we present evidence that both operons encode functional arsenic-response regulatory genes as well as arsenic extrusion systems that confer resistance to both arsenite [As(III)] and arsenate [As(V)]. Transcriptional fusions of P(ars1) and P(ars2) to lacZ revealed that expression of both operons was induced by arsenite and arsenate. We generated single mutants in ars1 and ars2, which showed lower resistance to arsenic than the wild-type strain. A double ars1/ars2 was found to be highly sensitive to arsenic. Minimum inhibitory concentrations (MICs) for single mutants decreased two- to fourfold with respect to the parental strain, while in the double mutant the MIC decreased 128-fold for arsenite and 32-fold for arsenate. Bioinformatic analysis revealed that the ars2 resistance operon is part of the core genome of P. putida, while the ars1 operon appears to only occur in the KT2440 strain, suggesting that ars1 was acquired by horizontal gene transfer. The presence of ars1 in KT2440 may explain why it exhibits higher resistance to arsenic than other P. putida strains, which bear only the ars2 operon.
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20
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Estrada-de los Santos P, Solano-Rodríguez R, Matsumura-Paz LT, Vásquez-Murrieta MS, Martínez-Aguilar L. Cupriavidus plantarum sp. nov., a plant-associated species. Arch Microbiol 2014; 196:811-7. [DOI: 10.1007/s00203-014-1018-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/13/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
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21
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Morgante V, Mirete S, de Figueras CG, Postigo Cacho M, González-Pastor JE. Exploring the diversity of arsenic resistance genes from acid mine drainage microorganisms. Environ Microbiol 2014; 17:1910-25. [PMID: 24801164 DOI: 10.1111/1462-2920.12505] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 04/28/2014] [Accepted: 05/01/2014] [Indexed: 11/30/2022]
Abstract
The microbial communities from the Tinto River, a natural acid mine drainage environment, were explored to search for novel genes involved in arsenic resistance using a functional metagenomic approach. Seven pentavalent arsenate resistance clones were selected and analysed to find the genes responsible for this phenotype. Insights about their possible mechanisms of resistance were obtained from sequence similarities and cellular arsenic concentration. A total of 19 individual open reading frames were analysed, and each one was individually cloned and assayed for its ability to confer arsenic resistance in Escherichia coli cells. A total of 13 functionally active genes involved in arsenic resistance were identified, and they could be classified into different global processes: transport, stress response, DNA damage repair, phospholipids biosynthesis, amino acid biosynthesis and RNA-modifying enzymes. Most genes (11) encode proteins not previously related to heavy metal resistance or hypothetical or unknown proteins. On the other hand, two genes were previously related to heavy metal resistance in microorganisms. In addition, the ClpB chaperone and the RNA-modifying enzymes retrieved in this work were shown to increase the cell survival under different stress conditions (heat shock, acid pH and UV radiation). Thus, these results reveal novel insights about unidentified mechanisms of arsenic resistance.
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Affiliation(s)
- Verónica Morgante
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Salvador Mirete
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Carolina G de Figueras
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Marina Postigo Cacho
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - José E González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
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22
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Nadar SV, Yoshinaga M, Kandavelu P, Sankaran B, Rosen BP. Crystallization and preliminary X-ray crystallographic studies of the ArsI C-As lyase from Thermomonospora curvata. Acta Crystallogr F Struct Biol Commun 2014; 70:761-4. [PMID: 24915088 PMCID: PMC4051532 DOI: 10.1107/s2053230x14008814] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
Arsenic is a ubiquitous and carcinogenic environmental element that enters the biosphere primarily from geochemical sources, but also through anthropogenic activities. Microorganisms play an important role in the arsenic biogeochemical cycle by biotransformation of inorganic arsenic into organic arsenicals and vice versa. ArsI is a microbial nonheme ferrous-dependent dioxygenase that transforms toxic methylarsonous acid to the less toxic inorganic arsenite by C-As bond cleavage. An ArsI ortholog from the thermophilic bacterium Thermomonospora curvata was expressed, purified and crystallized. The crystals diffracted to 1.46 Å resolution and belonged to space group P4₃2₁2 or its enantiomer P4₁2₁2, with unit-cell parameters a=b=42.2, c=118.5 Å.
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Affiliation(s)
- S. Venkadesh Nadar
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
| | - Palani Kandavelu
- SER-CAT and the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
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A C⋅As lyase for degradation of environmental organoarsenical herbicides and animal husbandry growth promoters. Proc Natl Acad Sci U S A 2014; 111:7701-6. [PMID: 24821808 DOI: 10.1073/pnas.1403057111] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Arsenic is the most widespread environmental toxin. Substantial amounts of pentavalent organoarsenicals have been used as herbicides, such as monosodium methylarsonic acid (MSMA), and as growth enhancers for animal husbandry, such as roxarsone (4-hydroxy-3-nitrophenylarsonic acid) [Rox(V)]. These undergo environmental degradation to more toxic inorganic arsenite [As(III)]. We previously demonstrated a two-step pathway of degradation of MSMA to As(III) by microbial communities involving sequential reduction to methylarsonous acid [MAs(III)] by one bacterial species and demethylation from MAs(III) to As(III) by another. In this study, the gene responsible for MAs(III) demethylation was identified from an environmental MAs(III)-demethylating isolate, Bacillus sp. MD1. This gene, termed arsenic inducible gene (arsI), is in an arsenic resistance (ars) operon and encodes a nonheme iron-dependent dioxygenase with C ⋅ As lyase activity. Heterologous expression of ArsI conferred MAs(III)-demethylating activity and MAs(III) resistance to an arsenic-hypersensitive strain of Escherichia coli, demonstrating that MAs(III) demethylation is a detoxification process. Purified ArsI catalyzes Fe(2+)-dependent MAs(III) demethylation. In addition, ArsI cleaves the C ⋅ As bond in trivalent roxarsone and other aromatic arsenicals. ArsI homologs are widely distributed in prokaryotes, and we propose that ArsI-catalyzed organoarsenical degradation has a significant impact on the arsenic biogeocycle. To our knowledge, this is the first report of a molecular mechanism for organoarsenic degradation by a C ⋅ As lyase.
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Genomic responses to arsenic in the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2014; 9:e96826. [PMID: 24797411 PMCID: PMC4010505 DOI: 10.1371/journal.pone.0096826] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/11/2014] [Indexed: 12/02/2022] Open
Abstract
Arsenic is a ubiquitous contaminant and a toxic metalloid which presents two main redox states in nature: arsenite [AsIII] and arsenate [AsV]. Arsenic resistance in Synechocystis sp. strain PCC 6803 is mediated by the arsBHC operon and two additional arsenate reductases encoded by the arsI1 and arsI2 genes. Here we describe the genome-wide responses to the presence of arsenate and arsenite in wild type and mutants in the arsenic resistance system. Both forms of arsenic produced similar responses in the wild type strain, including induction of several stress related genes and repression of energy generation processes. These responses were transient in the wild type strain but maintained in time in an arsB mutant strain, which lacks the arsenite transporter. In contrast, the responses observed in a strain lacking all arsenate reductases were somewhat different and included lower induction of genes involved in metal homeostasis and Fe-S cluster biogenesis, suggesting that these two processes are targeted by arsenite in the wild type strain. Finally, analysis of the arsR mutant strain revealed that ArsR seems to only control 5 genes in the genome. Furthermore, the arsR mutant strain exhibited hypersentivity to nickel, copper and cadmium and this phenotype was suppressed by mutation in arsB but not in arsC gene suggesting that overexpression of arsB is detrimental in the presence of these metals in the media.
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Identification of a novel membrane transporter mediating resistance to organic arsenic in Campylobacter jejuni. Antimicrob Agents Chemother 2014; 58:2021-9. [PMID: 24419344 DOI: 10.1128/aac.02137-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although bacterial mechanisms involved in the resistance to inorganic arsenic are well understood, the molecular basis for organic arsenic resistance has not been described. Campylobacter jejuni, a major food-borne pathogen causing gastroenteritis in humans, is highly prevalent in poultry and is reportedly resistant to the arsenic compound roxarsone (4-hydroxy-3-nitrobenzenearsonic acid), which has been used as a feed additive in the poultry industry for growth promotion. In this study, we report the identification of a novel membrane transporter (named ArsP) that contributes to organic arsenic resistance in Campylobacter. ArsP is predicted to be a membrane permease containing eight transmembrane helices, distinct from other known arsenic transporters. Analysis of multiple C. jejuni isolates from various animal species revealed that the presence of an intact arsP gene is associated with elevated resistance to roxarsone. In addition, inactivation of arsP in C. jejuni resulted in 4- and 8-fold reductions in the MICs of roxarsone and nitarsone, respectively, compared to that for the wild-type strain. Furthermore, cloning of arsP into a C. jejuni strain lacking a functional arsP gene led to 16- and 64-fold increases in the MICs of roxarsone and nitarsone, respectively. Neither mutation nor overexpression of arsP affected the MICs of inorganic arsenic, including arsenite and arsenate, in Campylobacter. Moreover, acquisition of arsP in NCTC 11168 led to accumulation of less roxarsone than the wild-type strain lacking arsP. Together, these results indicate that ArsP functions as an efflux transporter specific for extrusion of organic arsenic and contributes to the resistance to these compounds in C. jejuni.
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Siripornadulsil S, Siripornadulsil W. Cadmium-tolerant bacteria reduce the uptake of cadmium in rice: potential for microbial bioremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2013; 94:94-103. [PMID: 23731867 DOI: 10.1016/j.ecoenv.2013.05.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 05/27/2023]
Abstract
We selected 24 bacterial isolates that could tolerate up to 2500 µM CdCl2 from the soil of rice fields downstream from a zinc-mineralized area contaminated with a high level of cadmium (Cd). In the presence of 500 µM CdCl2, all isolates grew slower and with a prolonged lag-phase compared to in the absence of Cd. Cd-binding capacity was high and ranged from 6.38 to 9.38 log[Cd(atom)]/cell. The stability of Cd complexes in bacteria was affected by 1mM EDTA. In 500 µM CdCl2, all isolates produced 0.7 to 4.8-fold more inorganic sulfide and 0.6 to 2.2-fold more thio-rich compounds containing SH groups. Out of 24 Cd-tolerant bacterial isolates, KKU2500-3, -8, -9 and -20 were able to promote the growth of Thai jasmine rice (Kao Hom Mali 105) seedlings in the presence of 200 µM CdCl2, and KKU2500-3 produced the highest numbers of fibrous root. Interestingly, these 4 isolates increased Cd tolerance and decreased the accumulation of Cd in rice by 61, 9, 6, and 17% when grown in the presence of 200 µM CdCl2. Of the 4 isolates, KKU2500-3 produced more inorganic sulfide when grown in CdCl2 at 500-2000 µM. XANES analyses indicated that this isolate precipitated a detectable amount of cadmium sulfide (CdS) when grown in 500 µM CdCl2. Thus, the isolate KKU2500-3 could possibly transform toxic, soluble CdCl2 into non-toxic, insoluble CdS. These 4Cd-tolerant bacterial isolates were identified via 16S rDNA sequencing and classified as Cupriavidus taiwanensis KKU2500-3 and Pseudomonas aeruginosa KKU2500-8, -9, and -20.
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Shen Z, Han J, Wang Y, Sahin O, Zhang Q. The contribution of ArsB to arsenic resistance in Campylobacter jejuni. PLoS One 2013; 8:e58894. [PMID: 23554953 PMCID: PMC3598800 DOI: 10.1371/journal.pone.0058894] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/07/2013] [Indexed: 11/21/2022] Open
Abstract
Arsenic, a toxic metalloid, exists in the natural environment and its organic form is approved for use as a feed additive for animal production. As a major foodborne pathogen of animal origin, Campylobacter is exposed to arsenic selection pressure in the food animal production environments. Previous studies showed that Campylobacter isolates from poultry were highly resistant to arsenic compounds and a 4-gene operon (containing arsP, arsR, arsC, and acr3) was associated with arsenic resistance in Campylobacter. However, this 4-gene operon is only present in some Campylobacter isolates and other arsenic resistance mechanisms in C. jejuni have not been characterized. In this study, we determined the role of several putative arsenic resistance genes including arsB, arsC2, and arsR3 in arsenic resistance in C. jejuni and found that arsB, but not the other two genes, contributes to the resistance to arsenite and arsenate. Inactivation of arsB in C. jejuni resulted in 8- and 4-fold reduction in the MICs of arsenite and arsenate, respectively, and complementation of the arsB mutant restored the MIC of arsenite. Additionally, overexpression of arsB in C. jejuni 11168 resulted in a 16-fold increase in the MIC of arsenite. PCR analysis of C. jejuni isolates from different animals hosts indicated that arsB and acr3 (the 4-gene operon) are widely distributed in various C. jejuni strains, suggesting that Campylobacter requires at least one of the two genes for adaptation to arsenic-containing environments. These results identify ArsB as an alternative mechanism for arsenic resistance in C. jejuni and provide new insights into the adaptive mechanisms of Campylobacter in animal food production environments.
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Affiliation(s)
- Zhangqi Shen
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Jing Han
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Yang Wang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Orhan Sahin
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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Liu M, Crosa JH. The regulator HlyU, the repeat-in-toxin gene rtxA1, and their roles in the pathogenesis of Vibrio vulnificus infections. Microbiologyopen 2012; 1:502-13. [PMID: 23233275 PMCID: PMC3535394 DOI: 10.1002/mbo3.48] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/27/2012] [Accepted: 08/06/2012] [Indexed: 12/19/2022] Open
Abstract
HlyU is a master regulator that plays an essential role in the virulence of the human pathogen Vibrio vulnificus. One of the most noteworthy characteristics of HlyU regulation in this organism is its positive control of the expression of the repeat-in-toxin (RtxA1) gene, one of the most important virulence factors accounting for the fulminating and damaging nature of V. vulnificus infections. In this work, we reviewed the latest studies of RtxA1 in this bacterium and highlight the mechanism of gene regulation of rtxA1 expression by HlyU under a broader gene regulatory network.
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Affiliation(s)
- Moqing Liu
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239, USA.
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Estrada-de los Santos P, Martínez-Aguilar L, López-Lara IM, Caballero-Mellado J. Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils. Syst Appl Microbiol 2012; 35:310-4. [DOI: 10.1016/j.syapm.2012.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 04/04/2012] [Accepted: 05/25/2012] [Indexed: 11/25/2022]
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Cupriavidus and Burkholderia species associated with agricultural plants that grow in alkaline soils. J Microbiol 2011; 49:867-76. [DOI: 10.1007/s12275-011-1127-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 07/08/2011] [Indexed: 01/11/2023]
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Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals 2011; 24:1133-51. [DOI: 10.1007/s10534-011-9473-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 06/15/2011] [Indexed: 10/18/2022]
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Goldfarb RD, Bennett CF, Butler M, Condon T, Parrillo JE. Targeting host E-selectin expression by antisense oligodeoxynucleotides as potential antiendotoxin therapy in vivo. Oligonucleotides 2011; 20:253-61. [PMID: 20977376 DOI: 10.1089/oli.2010.0229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study sought to determine if antisense oligodeoxynucleotides would inhibit E-selectin expression, which mediates leukocyte adhesion on endothelial cells, otherwise induced by in vivo endotoxin challenge. Six antisense phosphorothioate oligodeoxynucleotides calculated to bind porcine E-selectin mRNA were tested in porcine aortic endothelial cells. One, ISIS9481, exerted significant inhibition of E-selectin expression induced by tumor necrosis factor-α + endotoxin [lipopolysaccharide (LPS)]. Pigs were challenged with LPS (10 μg/kg) and treated with ISIS9481 (10 mg/kg) (n = 6). Two control groups were used, an antisense inactive in porcine aortic endothelial cells (n = 6) and saline (n = 5), and were combined as control (C = 11). Control pigs challenged with LPS expressed E-selectin in heart, lung, kidneys, and liver, whereas antisense-treated pigs expressed little E-selectin in these tissues. Cardiovascular data indicated that antisense treatment attenuated pathophysiological alterations induced by LPS. Specifically, in control pigs, LPS reduced cardiac output 32% from baseline, increased pulmonary (+116%) and systemic vascular resistances (+16%), and generated neutropenia (from 51,000 at basal to 18,000 polymorphonuclear neutrophils (PMN)/μL after LPS). In antisense-treated pigs, cardiac output decreased only 18%, pulmonary vascular resistance remained unchanged, whereas systemic vascular resistance decreased compared with basal values (-37%). PMN counts remained at 45,000-54,000/μL at 3-4 hours after LPS. These data demonstrate that antisense oligodeoxynucleotides, designed and tested in vitro to interact with 1 gene product, can be developed as either therapeutics or experimental tools in vivo.
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Affiliation(s)
- Roy D Goldfarb
- Department of Cardiology, Cooper University Hospital , Camden, NJ, USA.
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Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 2010; 5:e10433. [PMID: 20463976 PMCID: PMC2864759 DOI: 10.1371/journal.pone.0010433] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 03/29/2010] [Indexed: 11/21/2022] Open
Abstract
Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.
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Affiliation(s)
- Paul J Janssen
- Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium.
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