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Zahra I, DeVine L, Cole R, Malik HA, Wu J, Wen J, Hedfi A, Liaqat A, Ijaz R, Ramzan U, Shakoori AR, Shakoori FR, Betenbaugh MJ. Insights into the differential proteome landscape of a newly isolated Paramecium multimicronucleatum in response to cadmium stress. J Proteomics 2024; 300:105178. [PMID: 38636824 DOI: 10.1016/j.jprot.2024.105178] [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: 02/29/2024] [Revised: 04/01/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Employing microbial systems for the bioremediation of contaminated waters represent a potential option, however, limited understanding of the underlying mechanisms hampers the implication of microbial-mediated bioremediation. The omics tools offer a promising approach to explore the molecular basis of the bioremediation process. Here, a mass spectrometry-based quantitative proteome profiling approach was conducted to explore the differential protein levels in cadmium-treated Paramecium multimicronucleatum. The Proteome Discoverer software was used to identify and quantify differentially abundant proteins. The proteome profiling generated 7,416 peptide spectral matches, yielding 2824 total peptides, corresponding to 989 proteins. The analysis revealed that 29 proteins exhibited significant (p ≤ 0.05) differential levels, including a higher abundance of 6 proteins and reduced levels of 23 proteins in Cd2+ treated samples. These differentially abundant proteins were associated with stress response, energy metabolism, protein degradation, cell growth, and hormone processing. Briefly, a comprehensive proteome profile in response to cadmium stress of a newly isolated Paramecium has been established that will be useful in future studies identifying critical proteins involved in the bioremediation of metals in ciliates. SIGNIFICANCE: Ciliates are considered a good biological indicator of chemical pollution and relatively sensitive to heavy metal contamination. A prominent ciliate, Paramecium is a promising candidate for the bioremediation of polluted water. The proteins related to metal resistance in Paramecium species are still largely unknown and need further exploration. In order to identify and reveal the proteins related to metal resistance in Paramecia, we have reported differential protein abundance in Paramecium multimicronucleatum in response to cadmium stress. The proteins found in our study play essential roles during stress response, hormone processing, protein degradation, energy metabolism, and cell growth. It seems likely that Paramecia are not a simple sponge for metals but they could also transform them into less toxic derivatives or by detoxification by protein binding. This data will be helpful in future studies to identify critical proteins along with their detailed mechanisms involved in the bioremediation and detoxification of metal ions in Paramecium species.
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Affiliation(s)
- Itrat Zahra
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Lauren DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Robert Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Hafiza Aroosa Malik
- Bioenergy Research Center, Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan.
| | - Jinke Wu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Junneng Wen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Amor Hedfi
- Department of Biology, College of Sciences, Taif University, POBox 11099, Taif 21944, Saudi Arabia.
| | - Ayesha Liaqat
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Roohi Ijaz
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Uzma Ramzan
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Farah Rauf Shakoori
- Institute of Zoology, University of the Punjab, New Campus, Lahore 54590, Pakistan.
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
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Xu B, Chu T, Zhang R, Yang R, Zhu M, Guo F, Zan S. Earthworm gut bacteria facilitate cadmium immobilization through the formation of CdS nanoparticles. CHEMOSPHERE 2024; 361:142453. [PMID: 38821127 DOI: 10.1016/j.chemosphere.2024.142453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/17/2024] [Accepted: 05/25/2024] [Indexed: 06/02/2024]
Abstract
Gut bacteria of earthworm Amynthas hupeiensis exhibit significant potential for the in-situ remediation of cadmium (Cd)-contaminated soil. However, the mechanisms by which these gut bacteria immobilize and tolerate Cd remain elusive. The composition of the gut bacterial community was characterized by high-throughput sequencing. Cd-tolerant bacteria were isolated from the gut, and their roles in Cd immobilization, as well as their tolerance mechanisms, were explored through chemical characterization and transcriptome analysis. The predominant taxa in the gut bacterial community included unclassified Enterobacteriaceae, Citrobacter, and Bacillus, which were distinctly different from those in the surrounding soil. Notably, the most Cd-tolerant gut bacterium, Citrobacter freundii DS strain, immobilized 63.61% of Cd2+ within 96 h through extracellular biosorption and intracellular bioaccumulation of biosynthetic CdS nanoparticles, and modulation of solution pH and NH4+ concentration. Moreover, the characteristic signals of CdS were also observed in the gut content of A. hupeiensis when the sterilized Cd-contaminated soil was inoculated with C. freundii. The primary pathways involved in the response of C. freundii to Cd stress included the regulation of ABC transporters, bacterial chemotaxis, cell motility, oxidative phosphorylation, and two-component system. In conclusion, C. freundii facilitates Cd immobilization both in vitro and in vivo, thereby enhancing the host earthworm's adaptation to Cd-contaminated soil.
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Affiliation(s)
- Bo Xu
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Tingting Chu
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Ranran Zhang
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Ruyi Yang
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Meng Zhu
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Fuyu Guo
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
| | - Shuting Zan
- South Jiuhua Road No. 189, School of Ecology and Environment, Anhui Normal University, Wuhu, 241002, China.
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Kennedy V, Kaszecki E, Donaldson ME, Saville BJ. The impact of elevated sulfur and nitrogen levels on cadmium tolerance in Euglena species. Sci Rep 2024; 14:11734. [PMID: 38777815 PMCID: PMC11111685 DOI: 10.1038/s41598-024-61964-w] [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: 09/30/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Heavy metal (HM) pollution threatens human and ecosystem health. Current methods for remediating water contaminated with HMs are expensive and have limited effect. Therefore, bioremediation is being investigated as an environmentally and economically viable alternative. Freshwater protists Euglena gracilis and Euglena mutabilis were investigated for their tolerance to cadmium (Cd). A greater increase in cell numbers under Cd stress was noted for E. mutabilis but only E. gracilis showed an increase in Cd tolerance following pre-treatment with elevated concentrations of S or N. To gain insight regarding the nature of the increased tolerance RNA-sequencing was carried out on E. gracilis. This revealed transcript level changes among pretreated cells, and additional differences among cells exposed to CdCl2. Gene ontology (GO) enrichment analysis reflected changes in S and N metabolism, transmembrane transport, stress response, and physiological processes related to metal binding. Identifying these changes enhances our understanding of how these organisms adapt to HM polluted environments and allows us to target development of future pre-treatments to enhance the use of E. gracilis in bioremediation relating to heavy metals.
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Affiliation(s)
- Victoria Kennedy
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Emma Kaszecki
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Michael E Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
- Forensic Science Department, Trent University, Peterborough, ON, Canada
| | - Barry J Saville
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada.
- Forensic Science Department, Trent University, Peterborough, ON, Canada.
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Buda DM, Szekeres E, Tudoran LB, Esclapez J, Banciu HL. Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T. BMC Microbiol 2023; 23:381. [PMID: 38049746 PMCID: PMC10694973 DOI: 10.1186/s12866-023-03133-z] [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: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance. RESULTS The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data. CONCLUSIONS Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.
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Grants
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- PN-III-P4-ID-PCE-2020-1559 Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCD
- VIGRO-016 Vicerrectorado de Investigación y Transferencia de Conocimiento of the University of Alicante
- Ministry of Research, Innovation and Digitization, CNCS/CCCDI – UEFISCD
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Affiliation(s)
- Doriana Mădălina Buda
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
| | - Edina Szekeres
- Institute of Biological Research Cluj, NIRDBS, Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Lucian Barbu Tudoran
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania
- National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
| | - Julia Esclapez
- Biochemistry and Molecular Biology and Soil and Agricultural Chemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Alicante, Spain
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Babeș-Bolyai University, Cluj-Napoca, Romania.
- Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania.
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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [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: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
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6
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Zhang S, Ke C, Jiang M, Li Y, Huang W, Dang Z, Guo C. S(-II) reactivates Cd 2+-stressed Shewanella oneidensis via promoting low-molecular-weight thiols synthesis and activating antioxidant defense. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121516. [PMID: 36972810 DOI: 10.1016/j.envpol.2023.121516] [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: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Efficient remedies for living organisms including bacteria to counteract cadmium (Cd2+) toxicity are still highly needed. Plant toxicity studies have showed that exogenous S(-II) (including hydrogen sulfide and its ionic forms, i.e., H2S, HS-, and S2-) application can effectively alleviate adverse effects of Cd stress, but whether S(-II) could mitigate bacterial Cd toxicity remains unclear. In this study, S(-II) was applied exogenously to Cd-stressed Shewanella oneidensis MR-1 and the results showed that S(-II) can significantly reactivate impaired physiological processes including growth arrest and enzymatic ferric (Fe(III) reduction inhibition. The efficacy of S(-II) treatment is negatively correlated with the concentration and time length of Cd exposure. Energy-dispersive X-ray (EDX) analysis suggested the presence of cadmium sulfide inside cells treated with S(-II). Both compared proteomic analysis and RT-qPCR showed that enzymes associated with sulfate transport, sulfur assimilation, methionine, and glutathione biosynthesis were up-regulated in both mRNA and protein levels after the treatment, indicating S(-II) may induce the biosynthesis of functional low-molecular-weight (LMW) thiols to counteract Cd toxicity. Meanwhile, the antioxidant enzymes were positively modulated by S(-II) and thus the activity of intracellular reactive oxygen species was attenuated. The study demonstrated that exogenous S(-II) can effectively alleviate Cd stress for S. oneidensis likely through inducing intracellular trapping mechanisms and modulating cellular redox status. It suggested that S(-II) may be a highly effective remedy for bacteria such as S. oneidensis under Cd-polluted environments.
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Affiliation(s)
- Siyu Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Changdong Ke
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Mengge Jiang
- Guangzhou Metro Group Co., Ltd., Guangzhou, 510335, China
| | - Yuancheng Li
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou, 510006, China.
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7
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Synergy between microalgae and microbiome in polluted waters. Trends Microbiol 2023; 31:9-21. [PMID: 35985939 DOI: 10.1016/j.tim.2022.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.
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8
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Rogiers T, Van Houdt R, Williamson A, Leys N, Boon N, Mijnendonckx K. Molecular Mechanisms Underlying Bacterial Uranium Resistance. Front Microbiol 2022; 13:822197. [PMID: 35359714 PMCID: PMC8963506 DOI: 10.3389/fmicb.2022.822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.
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Affiliation(s)
- Tom Rogiers
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Adam Williamson
- Centre Etudes Nucléaires de Bordeaux Gradignan (CENBG), Bordeaux, France
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Kristel Mijnendonckx
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- *Correspondence: Kristel Mijnendonckx,
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9
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Gallois N, Alpha-Bazin B, Bremond N, Ortet P, Barakat M, Piette L, Mohamad Ali A, Lemaire D, Legrand P, Theodorakopoulos N, Floriani M, Février L, Den Auwer C, Arnoux P, Berthomieu C, Armengaud J, Chapon V. Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria. THE ISME JOURNAL 2022; 16:705-716. [PMID: 34556817 PMCID: PMC8857325 DOI: 10.1038/s41396-021-01113-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
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Affiliation(s)
- Nicolas Gallois
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Béatrice Alpha-Bazin
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Nicolas Bremond
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Philippe Ortet
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Laurie Piette
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Abbas Mohamad Ali
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - David Lemaire
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Pierre Legrand
- grid.426328.9Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192 Gif-sur-Yvette, France
| | - Nicolas Theodorakopoulos
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France ,grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Magali Floriani
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Laureline Février
- grid.418735.c0000 0001 1414 6236IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115 Saint Paul-lez-Durance, Cedex France
| | - Christophe Den Auwer
- grid.462124.70000 0004 0384 8488Université Côte d’Azur, CNRS, ICN, 06108 Nice, France
| | - Pascal Arnoux
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Catherine Berthomieu
- grid.5399.60000 0001 2176 4817Aix Marseille Université, CEA, CNRS, BIAM, 13108 Saint Paul-Lez-Durance, France
| | - Jean Armengaud
- grid.5583.b0000 0001 2299 8025Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France
| | - Virginie Chapon
- Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France.
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Tripathi AK, Saxena P, Thakur P, Rauniyar S, Samanta D, Gopalakrishnan V, Singh RN, Sani RK. Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. Int J Mol Sci 2022; 23:ijms23031396. [PMID: 35163324 PMCID: PMC8836040 DOI: 10.3390/ijms23031396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Composite and Nanocomposite Advanced Manufacturing Centre—Biomaterials, Rapid City, SD 57701, USA
- Correspondence:
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Maertens L, Cherry P, Tilquin F, Van Houdt R, Matroule JY. Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress. Microorganisms 2021; 9:1116. [PMID: 34064119 PMCID: PMC8224329 DOI: 10.3390/microorganisms9061116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
Bacteria encounter elevated copper (Cu) concentrations in multiple environments, varying from mining wastes to antimicrobial applications of copper. As the role of the environment in the bacterial response to Cu ion exposure remains elusive, we used a tagRNA-seq approach to elucidate the disparate responses of two morphotypes of Caulobacter crescentus NA1000 to moderate Cu stress in a complex rich (PYE) medium and a defined poor (M2G) medium. The transcriptome was more responsive in M2G, where we observed an extensive oxidative stress response and reconfiguration of the proteome, as well as the induction of metal resistance clusters. In PYE, little evidence was found for an oxidative stress response, but several transport systems were differentially expressed, and an increased need for histidine was apparent. These results show that the Cu stress response is strongly dependent on the cellular environment. In addition, induction of the extracytoplasmic function sigma factor SigF and its regulon was shared by the Cu stress responses in both media, and its central role was confirmed by the phenotypic screening of a sigF::Tn5 mutant. In both media, stalked cells were more responsive to Cu stress than swarmer cells, and a stronger basal expression of several cell protection systems was noted, indicating that the swarmer cell is inherently more Cu resistant. Our approach also allowed for detecting several new transcription start sites, putatively indicating small regulatory RNAs, and additional levels of Cu-responsive regulation.
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Affiliation(s)
- Laurens Maertens
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Pauline Cherry
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre (SCK CEN), 2400 Mol, Belgium; (L.M.); (R.V.H.)
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, University of Namur, 5000 Namur, Belgium; (P.C.); (F.T.)
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12
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You X, Xu N, Yang X, Sun W. Pollutants affect algae-bacteria interactions: A critical review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 276:116723. [PMID: 33611207 DOI: 10.1016/j.envpol.2021.116723] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
With increasing concerns on the ecological risks of pollutants, many efforts have been devoted to revealing the toxic effects of pollutants on algae or bacteria in their monocultures. However, how pollutants affect algae and bacteria in their cocultures is still elusive but crucial due to its more environmental relevance. The present review outlines the interactions between algae and bacteria, reveals the influential mechanisms of pollutants (including pesticides, metals, engineered nanomaterials, pharmaceutical and personal care products, and aromatic pollutants) to algae and bacteria in their coexisted systems, and puts forward prospects for further advancing toxic studies in algal-bacterial systems. Pollutants affect the physiological and ecological functions of bacteria and algae by interfering with their relationships. Cell-to-cell adhesion, substrate exchange and biodegradation of organic pollutants, enhancement of signal transduction, and horizontal transfer of tolerance genes are important defense strategies in algal-bacterial systems to cope with pollution stress. Developing suitable algal-bacterial models, identifying cross-kingdom signaling molecules, and deciphering the horizontal transfer of pollutant resistant genes between algae and bacteria under pollution stress are the way forward to fully exploit the risks of pollutants in natural aquatic environments.
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Affiliation(s)
- Xiuqi You
- College of Environmental Sciences and Engineering, Peking University, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing, 100871, China
| | - Nan Xu
- Shenzhen Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xi Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing, 100871, China.
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13
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Kolhe N, Kulkarni A, Zinjarde S, Acharya C. Transcriptome Response of the Tropical Marine Yeast Yarrowia lipolytica on Exposure to Uranium. Curr Microbiol 2021; 78:2033-2043. [PMID: 33772621 DOI: 10.1007/s00284-021-02459-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
In our earlier investigation, we reported the consequences of uranium (U)-induced oxidative stress and cellular defense mechanisms alleviating uranium toxicity in the marine yeast Yarrowia lipolytica NCIM 3589. However, there is lack of information on stress response towards uranium toxicity at molecular level in this organism. To gain an insight on this, transcriptional response of Y. lipolytica after exposure to 50 µM uranium was investigated by RNA sequencing at the global level in this study. The de novo transcriptome analysis (in triplicates) revealed 56 differentially expressed genes with significant up-regulation and down-regulation of 33 and 23 transcripts, respectively, in U-exposed yeast cells as compared to the control, U-unexposed cells. Highly up-regulated genes under U-treated condition were identified to be primarily involved in transport, DNA damage repair and oxidative stress. The major reaction of Y. lipolytica to uranium exposure was the activation of oxidative stress response mechanisms to protect the important biomolecules of the cells. On the other hand, genes involved in cell wall and cell cycle regulation were significantly down-regulated. Overall, the transcriptional profiling by RNA sequencing to stress-inducing concentration of uranium sheds light on the various responses of Y. lipolytica for coping with uranium toxicity, providing a foundation for understanding the molecular interactions between uranium and this marine yeast.
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Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.,Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India. .,Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai, 400094, India.
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14
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Pinel-Cabello M, Jroundi F, López-Fernández M, Geffers R, Jarek M, Jauregui R, Link A, Vílchez-Vargas R, Merroun ML. Multisystem combined uranium resistance mechanisms and bioremediation potential of Stenotrophomonas bentonitica BII-R7: Transcriptomics and microscopic study. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123858. [PMID: 33264934 DOI: 10.1016/j.jhazmat.2020.123858] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/18/2020] [Accepted: 08/24/2020] [Indexed: 06/12/2023]
Abstract
The potential use of microorganisms in the bioremediation of U pollution has been extensively described. However, a lack of knowledge on molecular resistance mechanisms has become a challenge for the use of these technologies. We reported on the transcriptomic and microscopic response of Stenotrophomonas bentonitica BII-R7 exposed to 100 and 250 μM of U. Results showed that exposure to 100 μM displayed up-regulation of 185 and 148 genes during the lag and exponential phases, respectively, whereas 143 and 194 were down-regulated, out of 3786 genes (>1.5-fold change). Exposure to 250 μM of U showed up-regulation of 68 genes and down-regulation of 290 during the lag phase. Genes involved in cell wall and membrane protein synthesis, efflux systems and phosphatases were up-regulated under all conditions tested. Microscopic observations evidenced the formation of U-phosphate minerals at membrane and extracellular levels. Thus, a biphasic process is likely to occur: the increased cell wall would promote the biosorption of U to the cell surface and its precipitation as U-phosphate minerals enhanced by phosphatases. Transport systems would prevent U accumulation in the cytoplasm. These findings contribute to an understanding of how microbes cope with U toxicity, thus allowing for the development of efficient bioremediation strategies.
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Affiliation(s)
- M Pinel-Cabello
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain.
| | - F Jroundi
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
| | - M López-Fernández
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - R Geffers
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - M Jarek
- Genome Analytics, Helmholtz Centre for Infection Research (HZI), 38124, Braunschweig, Germany
| | - R Jauregui
- AgResearch Grasslands Research Centre, Tennent drive, Palmerston North, New Zealand
| | - A Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44.39120, Magdeburg, Germany
| | - R Vílchez-Vargas
- Department of Gastroenterology, Hepatology and Infectious Diseases, University of Magdeburg, Leipziger Str. 44.39120, Magdeburg, Germany
| | - M L Merroun
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071, Granada, Spain
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Halim MA, Rahman MM, Megharaj M, Naidu R. Cadmium Immobilization in the Rhizosphere and Plant Cellular Detoxification: Role of Plant-Growth-Promoting Rhizobacteria as a Sustainable Solution. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13497-13529. [PMID: 33170689 DOI: 10.1021/acs.jafc.0c04579] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Food is the major cadmium (Cd)-exposure pathway from agricultural soils to humans and other living entities and must be reduced in an effective way. A plant can select beneficial microbes, like plant-growth-promoting rhizobacteria (PGPR), depending upon the nature of root exudates in the rhizosphere, for its own benefits, such as plant growth promotion as well as protection from metal toxicity. This review intends to seek out information on the rhizo-immobilization of Cd in polluted soils using the PGPR along with plant nutrient fertilizers. This review suggests that the rhizo-immobilization of Cd by a combination of PGPR and nanohybrid-based plant nutrient fertilizers would be a potential and sustainable technology for phytoavailable Cd immobilization in the rhizosphere and plant cellular detoxification, by keeping the plant nutrition flow and green dynamics of plant nutrition and boosting the plant growth and development under Cd stress.
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Affiliation(s)
- Md Abdul Halim
- Global Centre for Environmental Remediation (GCER), The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Department of Biotechnology, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), The University of Newcastle, Callaghan, New South Wales 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, Callaghan, New South Wales 2308, Australia
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16
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Liu H, Luo J, Shukla P. Effluents detoxification from pulp and paper industry using microbial engineering and advanced oxidation techniques. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122998. [PMID: 32502804 DOI: 10.1016/j.jhazmat.2020.122998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
Due to the high demand of paper and related items, pulp and paper industry is flourishing day by day. With increased production, come the hazards associated with the toxic elements present in the effluents. Various microorganisms are currently employed in the remediation of these toxic effluents. In addition, various techniques like ozonation, electrocoagulation, UV treatment, Fenton's reagent, and photo-Fenton based techniques are used in advanced oxidation processes to reduce these toxins from effluents. This review highlights various above mentioned advanced techniques and innovative processes along with the biological remediation of these toxic effluents with the help of some potential microbial consortia or their combinatory effects. Moreover, the present review will also disclose the ideas on utilizing the tools of metabolic engineering, systems biology, and artificial intelligence towards microbial engineering for relatively better bioremediation processes. In the future, these techniques might be helpful in increasing the capability of microbial consortia towards detoxification of effluents to make them environmentally safe. Finally, this review gives well-synchronized approaches to get more insights into these innovative methodologies and techniques and their use for various industrial applications.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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An X, Tian C, Xu J, Dong F, Liu X, Wu X, Zheng Y. Characterization of hexaconazole-degrading strain Sphingobacterium multivorum and analysis of transcriptome for biodegradation mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137171. [PMID: 32213434 DOI: 10.1016/j.scitotenv.2020.137171] [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: 12/11/2019] [Revised: 02/02/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Hexaconazole is a triazole fungicide, which is stable and difficult to degrade in the environment. The existence of hexaconazole could pose a certain risk to the environment and the health of living organisms. In this study, an efficient degradation strain B-3 (Sphingobacterium multivorum) of hexaconazole was isolated from sewage, activated sludge, and soil. The degradation efficiency of hexaconazole can reach 85.6% in 6 days at a temperature of 32.5 °C, pH of 6.31, initial inoculum of 0.4 g L-1 and initial concentration of hexaconazole of 50 mg L-1. During degradation, three metabolites (M1: 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol; M2: 2-(2, 4-dichlorophenyl) hexane-1, 2-diol; M3: 1H-1, 2, 4-triazole) were identified. Moreover, 45.6% hexaconazole can be degraded in 60 days in natural soil containing B-3. The results of the transcriptome sequencing indicated the presence of 864 differential genes, in which aldehyde dehydrogenase, monooxygenase, RND transporters, and ABC transporters were up-regulated. The generation of 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol may be due to the participation of monooxygenase.
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Affiliation(s)
- Xiaokang An
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyan Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fengshou Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohu Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongquan Zheng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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18
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Sanyal SK, Reith F, Shuster J. A genomic perspective of metal-resistant bacteria from gold particles: Possible survival mechanisms during gold biogeochemical cycling. FEMS Microbiol Ecol 2020; 96:5851273. [DOI: 10.1093/femsec/fiaa111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
A bacterial consortium was enriched from gold particles that ‘experienced’ ca. 80 years of biotransformation within waste-rock piles (Australia). This bacterial consortium was exposed to 10 µM AuCl3 to obtain Au-tolerant bacteria. From these isolates, Serratia sp. and Stenotrophomonas sp. were the most Au-tolerant and reduced soluble Au as pure gold nanoparticles, indicating that passive mineralisation is a mechanism for mediating the toxic effect of soluble Au produced during particle dissolution. Genome-wide analysis demonstrated that these isolates also possessed various genes that could provide cellular defence enabling survival under heavy-metal stressed condition by mediating the toxicity of heavy metals through active efflux/reduction. Diverse metal-resistant genes or genes clusters (cop, cus, czc, zntand ars) were detected, which could confer resistance to soluble Au. Comparative genome analysis revealed that the majority of detected heavy-metal resistant genes were similar (i.e. orthologous) to those genes of Cupriavidus metallidurans CH34. The detection of heavy-metal resistance, nutrient cycling and biofilm formation genes (pgaABCD, bsmAandhmpS) may have indirect yet important roles when dealing with soluble Au during particle dissolution. In conclusion, the physiological and genomic results suggest that bacteria living on gold particles would likely use various genes to ensure survival during Au-biogeochemical cycling.
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Affiliation(s)
- Santonu Kumar Sanyal
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
| | - Frank Reith
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
| | - Jeremiah Shuster
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
- CSIRO Land & Water, Environmental Contaminant Mitigation and Technologies, Gate 4 Waite Road, Glen Osmond, South Australia 5064, Australia
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Lin WH, Chen SC, Chien CC, Tsang DCW, Lo KH, Kao CM. Application of enhanced bioreduction for hexavalent chromium-polluted groundwater cleanup: Microcosm and microbial diversity studies. ENVIRONMENTAL RESEARCH 2020; 184:109296. [PMID: 32146214 DOI: 10.1016/j.envres.2020.109296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/19/2020] [Accepted: 02/23/2020] [Indexed: 06/10/2023]
Abstract
Hexavalent chromium (Cr6+) is a commonly found heavy metal at polluted groundwater sites. In this study, the effectiveness of Cr6+ bioreduction by the chromium-reducing bacteria was evaluated to remediate Cr6+-contaminated groundwater. Microcosms were constructed using indigenous microbial consortia from a Cr6+-contaminated aquifer as the inocula, and slow-releasing emulsified polycolloid-substrate (ES), cane molasses (CM), and nutrient broth (NB) as the primary substrates. The genes responsible for the bioreduction of Cr6+ and variations in bacterial diversity were evaluated using metagenomics assay. Complete Cr6+ reduction via the biological mechanism was observed within 80 days using CM as the carbon source under anaerobic processes with the increased trivalent chromium (Cr3+) concentrations. Cr6+ removal efficiencies were 83% and 59% in microcosms using ES and NB as the substrates, respectively. Increased bacterial communities associated with Cr6+ bioreduction was observed in microcosms treated with CM and ES. Decreased bacterial communities were observed in NB microcosms. Compared to ES, CM was more applicable by indigenous Cr6+ reduction bacteria and resulted in effective Cr6+ bioreduction, which was possibly due to the growth of Cr6+-reduction related bacteria including Sporolactobacillus, Clostridium, and Ensifer. While NB was applied for specific bacterial selection, it might not be appropriate for electron donor application. These results revealed that substrate addition had significant impact on microbial diversities, which affected Cr6+ bioreduction processes. Results are useful for designing a green and sustainable bioreduction system for Cr6+-polluted groundwater remediation.
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Affiliation(s)
- Wei-Han Lin
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, Chung-Li City, Taoyuan, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Chung-Li City, Taoyuan, Taiwan
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kai-Hung Lo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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20
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Wan W, Qin Y, Wu H, Zuo W, He H, Tan J, Wang Y, He D. Isolation and Characterization of Phosphorus Solubilizing Bacteria With Multiple Phosphorus Sources Utilizing Capability and Their Potential for Lead Immobilization in Soil. Front Microbiol 2020; 11:752. [PMID: 32390988 PMCID: PMC7190802 DOI: 10.3389/fmicb.2020.00752] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 11/13/2022] Open
Abstract
Phosphorus solubilizing bacteria (PSB) can promote the level of plant-absorbable phosphorus (P) in agro-ecosystems. However, little attention has been paid to PSB harboring abilities in utilizing multiple phosphorus sources and their potentials for heavy metal immobilization. In this study, we applied the strategy of stepwise acclimation by using Ca3(PO4)2, phytate, FePO4, and AlPO4 as sole P source. We gained 18 PSB possessing abilities of multiple P sources utilization, and these bacteria belonged to eight genera (Acinetobacter, Pseudomonas, Massilia, Bacillus, Arthrobacter, Stenotrophomonas, Ochrobactrum, and Cupriavidus), and clustered to two apparent parts: Gram-positive bacteria and Gram-negative bacteria. The isolate of Acinetobacter pittii gp-1 presented good performance for utilizing Ca3(PO4)2, FePO4, AlPO4, and phytate, with corresponding P solubilizing levels were 250.77, 46.10, 81.99, and 7.91 mg/L PO43–-P, respectively. The PSB A. pittii gp-1 exhibited good performance for solubilizing tricalcium phosphate in soil incubation experiments, with the highest values of water soluble P and available P were 0.80 and 1.64 mg/L, respectively. Additionally, the addition of A. pittii gp-1 could promote the immobilization of lead (Pb), and the highest Pb immobilization efficiency reached 23%. Simultaneously, we found the increases in abundances of both alkaline phosphatase gene (phoD) and β-propeller phytase gene (bpp) in strain gp-1 added soils. Besides, we observed the expression up-regulation of both pyrroloquinoline quinone gene (pqq) and polyphosphate kinases gene (ppk), with the highest relative expression levels of 18.18 and 5.23, respectively. We also found the polyphosphate particles using granule staining. To our knowledge, our findings first suggest that the solubilizing of tricalcium phosphate by phosphorus solubilizing bacterium belonging to Acinetobacter is coupled with the synthesis of polyphosphate. Taken together, A. pittii gp-1 could be a good candidate in improving soil fertility and quality.
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Affiliation(s)
- Wenjie Wan
- College of Life Science, South-Central University for Nationalities, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yin Qin
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Huiqin Wu
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Wenlong Zuo
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Huangmei He
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Jiadan Tan
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Yi Wang
- College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Donglan He
- College of Life Science, South-Central University for Nationalities, Wuhan, China
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21
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Abed RMM, Shanti M, Muthukrishnan T, Al-Riyami Z, Pracejus B, Moraetis D. The Role of Microbial Mats in the Removal of Hexavalent Chromium and Associated Shifts in Their Bacterial Community Composition. Front Microbiol 2020; 11:12. [PMID: 32082277 PMCID: PMC7001535 DOI: 10.3389/fmicb.2020.00012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 01/06/2020] [Indexed: 11/17/2022] Open
Abstract
Microbial mats are rarely reported for chromium-polluted ecosystems, hence information on their bacterial diversity and role in chromium removal are very scarce. We investigated the role of nine microbial mats, collected from three quarry sumps of chromium mining sites, in the removal of hexavalent chromium [Cr(VI)]. Bacterial diversity in these mats and community shifts after incubation with Cr(VI) have been investigated using MiSeq sequencing. In nature, a chromium content of 1,911 ± 100 mg kg–1 was measured in the microbial mats, constituting the third highest source of environmentally available chromium. The mats were able to remove 1 mg l–1 of Cr(VI) in 7 days under aerobic conditions. MiSeq sequencing of the original mats yielded 46–99% of the sequences affiliated to Proteobacteria, Firmicutes and Actinobacteria. When the mats were incubated with Cr(VI), the bacterial community shifted in the favor of Alphaproteobacteria and Verrucomicrobiae. We conclude that microbial mats in the quarry sumps harbor diverse microorganisms with the ability to remove toxic Cr(VI), hence these mats can be potentially used to remove chromium from polluted waters.
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Affiliation(s)
- Raeid M M Abed
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Mary Shanti
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | | | - Zayana Al-Riyami
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Bernhard Pracejus
- Earth Science Department, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Daniel Moraetis
- Department of Applied Physics and Astronomy, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
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22
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Kumar V, Dwivedi SK. Hexavalent chromium stress response, reduction capability and bioremediation potential of Trichoderma sp. isolated from electroplating wastewater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 185:109734. [PMID: 31574371 DOI: 10.1016/j.ecoenv.2019.109734] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
In the present study we are investigating the Cr(VI) reduction potential of a multi-metal tolerant fungus (isolate CR700); isolated from electroplating wastewater. Based on the ITS region sequencing, the isolate was identified as Trichoderma lixii isolate CR700 and able to tolerate As(2000 mg/L), Ni(1500 mg/L), Zn(1200 mg/L), Cu(1200 mg/L), Cr(1000 mg/L), and 100 mg/L of Pb and Cd evident from tolerance assay. Cr(VI) reduction experiment was conducted in Erlenmeyer flasks containing different concentration of Cr(VI) (0-200 mg/L) amended potato dextrose broth medium followed by inoculating with a disk (0.5 cm diameter) of 7 days grown isolate CR700, and achieved a maximum of 99.4% within 120 h at 50 mg/L of Cr(VI). However, the accumulation of total Cr by isolate CR700 was 2.12 ± 0.15 mg/g of dried biomass at the same concentration after 144 h of exposure. Isolate CR700 showed the capability to reduce Cr(VI) at different physicochemical stress conditions such as pH, temperature, heavy metals, metabolic inhibitor and also in tannery wastewater. Fungus exhibited multifarious morphological and biochemical response under the exposure of Cr(VI); the scanning electron microscopic analysis revealed that Cr(VI) treated mycelia of isolate CR700 comparatively irregular, aggregated and swelled than without treated mycelia which might be due to the tolerance mechanism and vacuolar compartmentation of chromium. Moreover, energy dispersive spectroscopy and x-ray photoelectron spectroscopic analysis exposed the Cr(III) precipitation on the mycelia surface of isolate CR700 and Fourier-transform infrared spectroscopic analysis suggested the contribution of the protein associated functional group in the complexation of Cr(VI). The phytotoxicity test of fungal treated 100 mg/L of Cr(VI) supernatant on Vigna radiata and Cicer arietinum revealed the successful detoxification/remediation of Cr(VI).
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Affiliation(s)
- Vinay Kumar
- Department of Environmental Science, Babasaheb Bhimarao Ambedkar University, Lucknow, 226025, India.
| | - S K Dwivedi
- Department of Environmental Science, Babasaheb Bhimarao Ambedkar University, Lucknow, 226025, India
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23
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Bonilla JO, Callegari EA, Estevéz MC, Villegas LB. Intracellular Proteomic Analysis of Streptomyces sp. MC1 When Exposed to Cr(VI) by Gel-Based and Gel-Free Methods. Curr Microbiol 2019; 77:62-70. [PMID: 31705393 DOI: 10.1007/s00284-019-01790-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The actinobacterium Streptomyces sp. MC1 has previously shown the capacity to resist and remove Cr(VI) from liquid culture media. The aim of this work is to analyze the differential expression pattern of intracellular proteins when Streptomyces sp. MC1 is exposed to Cr(VI) in order to explain the molecular mechanisms of resistance that this microorganism possesses. For this purpose, 2D-PAGE and shotgun proteomic analyses (2D-nanoUPLC-ESI-MS/MS) were applied. The presence of Cr(VI) induced the expression of proteins involved in molecular biosynthesis and energy generation, chaperones with a key role in the repair of misfolded proteins and stress response, transcription proteins, proteins of importance in the DNA supercoiling, repair and replication, and dehydrogenases involved in oxidation-reduction processes. These dehydrogenases can be associated with the reduction of Cr(VI) to Cr(III). The results of this study show that proteins from the groups mentioned before are important to face the stress caused by the Cr(VI) presence and help the microorganism to counteract the toxicity of the metal. The use of two proteomic approaches resulted in a larger number of peptides identified, which is also transduced in a significant number of protein ID. This decreased the potential complexity of the sample because of the protein dynamic range, as well as increased the recovery of peptides from the gel after digestion.
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Affiliation(s)
- José O Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina.,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María C Estevéz
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, Tucumán, Argentina
| | - Liliana B Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina. .,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina.
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24
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Zhang J, Li Q, Zeng Y, Zhang J, Lu G, Dang Z, Guo C. Bioaccumulation and distribution of cadmium by Burkholderia cepacia GYP1 under oligotrophic condition and mechanism analysis at proteome level. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:162-169. [PMID: 30927637 DOI: 10.1016/j.ecoenv.2019.03.091] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/17/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Bacteria have been applied for the bioremediation of cadmium-contaminated environment. Less is known about the bioaccumulation of high concentration of Cd over time under the oligotrophic environment. Burkholderia cepacia GYP1, which was isolated from multiple heavy metal contaminated farmland, was studied for its bioaccumulation mechanism of Cd under oligotrophic condition. GYP1 possessed highly accumulation capacity for cadmium reaching 116 mg Cd/g biomass (dry weight). ATR-FTIR, electron microscopy, flow cytometry along with subcellular fraction demonstrated that the uptake and distribution of cadmium varied with the increased amount of cadmium of GYP1 cell during the 7-day treatment time: the accumulation of cadmium was mainly on the outer membrane at the beginning (within 1 day), and the intracellular cadmium kept increased and held stable after 2 days, after that, the increased amount of cadmium mainly located extracellularly, related to the secreted EPS. Further mechanism analysis of bioaccumulation of Cd by GYP1 based on iTRAQ-based proteomics showed that Cd(II) could trigger the up-regulation of the Cd2+/Zn2+-exporting ATPase, type VI protein secretion systems, and glutathione-S-transferase that are related to cadmium response, which may contribute to maintain the intracellular cadmium homeostasis. In summary, the immobilization of Cd(II) by B. cepacia GYP1 contains three steps:(1) fast immobilization of Cd(II) on the cell surface coordinated with functional groups, (2) transport of Cd(II) to cells and accumulation in cytoplasm, and (3) efflux of intracellular Cd(II) depended on energy and the entrapped or adsorbed of extracellular Cd(II) by EPS. Our study provided the understanding of the cadmium accumulation process of B. cepacia GYP1 under oligotrophic condition, which would be helpful in bioremediation of natural cadmium contaminated environment.
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Affiliation(s)
- Junhui Zhang
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Qi Li
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Yufei Zeng
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Jian Zhang
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters (Ministry of Education), Guangzhou, Guangdong, 510006, PR China.
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25
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Nongkhlaw M, Joshi SR. Molecular insight into the expression of metal transporter genes in Chryseobacterium sp. PMSZPI isolated from uranium deposit. PLoS One 2019; 14:e0216995. [PMID: 31120947 PMCID: PMC6532875 DOI: 10.1371/journal.pone.0216995] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/02/2019] [Indexed: 11/18/2022] Open
Abstract
Metal tolerant bacterium Chryseobacterium sp. PMSZPI previously isolated and characterized from uranium ore deposit was studied for elucidating the role of metal transporter genes belonging to the Cation Diffusion Facilitator (CDF), Root-Nodulation-Division (RND) and PIB-type ATPase family in cadmium and uranium tolerance. The bacterium showed tolerance towards cadmium (MIC~6mM) and uranium (MIC~2mM) and was found to harbor metal transporter genes belonging to CDF, RND and PIB-type ATPase family of proteins. Expression studies by real-time PCR showed an upregulation of czcA(RND), czcD(CDF) and cadA(PIB-type ATPase) genes in presence of cadmium or uranium. Higher expression of czcA and czcD was found when the bacterium was treated with cadmium and uranium respectively. This study provides significant insight into the molecular mechanism that plays a role in cadmium and uranium tolerance in bacteria.
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Affiliation(s)
- Macmillan Nongkhlaw
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Mawlai, Umshing, Shillong, Meghalaya, India
| | - Santa Ram Joshi
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Mawlai, Umshing, Shillong, Meghalaya, India
- * E-mail:
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26
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Park DM, Taffet MJ. Combinatorial Sensor Design in Caulobacter crescentus for Selective Environmental Uranium Detection. ACS Synth Biol 2019; 8:807-817. [PMID: 30897331 DOI: 10.1021/acssynbio.8b00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to detect uranium (U) through environmental monitoring is of critical importance for informing water resource protection and nonproliferation efforts. While technologies exist for environmental U detection, wide-area environmental monitoring, i.e. sampling coverage over large areas not known to possess U contamination, remains a challenging prospect that necessitates the development of novel detection approaches. Herein, we describe the development of a whole-cell U sensor by integrating two functionally independent, native U-responsive two-component signaling systems (TCS), UzcRS and UrpRS, within an AND gate circuit in the bacterium Caulobacter crescentus. Through leverage of the distinct but imperfect selectivity profiles of both TCS, this combinatorial approach enabled greater selectivity relative to a prior biosensor developed with UzcRS alone; no cross-reactivity was observed with most common environmental metals (e.g, Fe, As, Cu, Ca, Mg, Cd, Cr, Al) or the U decay-chain product Th, and the selectivity against Zn and Pb was significantly improved. In addition, integration of the UzcRS signal amplifier protein UzcY within the AND gate circuit further enhanced overall sensitivity and selectivity for U. The functionality of the sensor in an environmental context was confirmed by detection of U concentrations as low as 1 μM in groundwater samples. The results highlight the value of a combinatorial approach for constructing whole-cell sensors for the selective detection of analytes for which there are no known evolved regulators.
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Affiliation(s)
- Dan M. Park
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Michael J. Taffet
- Environmental Restoration Department (ERD), Operations and Business Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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27
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OxyR and the hydrogen peroxide stress response in Caulobacter crescentus. Gene 2019; 700:70-84. [PMID: 30880241 DOI: 10.1016/j.gene.2019.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 11/22/2022]
Abstract
Oxidative stress generated by hydrogen peroxide is faced by bacteria when encountering hostile environments. In order to define the physiological and regulatory networks controlling the oxidative stress response in the free-living bacterium Caulobacter crescentus, a whole transcriptome analysis of wild type and ΔoxyR strains in the presence of hydrogen peroxide for two different exposure times was carried out. The C. crescentus response to H2O2 includes a decrease of the assimilative sulfate reduction and a shift in the amino acid synthesis pathways into favoring the synthesis of histidine. Moreover, the expression of genes encoding enzymes for the depolymerization of polyhydroxybutyrate was increased, and the RpoH-dependent genes were severely repressed. Based on the expression pattern and sequence analysis, we postulate that OxyR is probably directly required for the induction of three genes (katG, ahpCF). The putative binding of OxyR to the ahpC regulatory region could be responsible for the use of one of two alternative promoters in response to oxidative stress. Nevertheless, OxyR is required for the expression of 103 genes in response to H2O2. Fur and part of its regulon were differentially expressed in response to hydrogen peroxide independently of OxyR. The non-coding RNA OsrA was upregulated in both strains, and an in silico analysis indicated that it may have a regulatory role. This work characterizes the physiological response to H2O2 in C. crescentus, the regulatory networks and differentially regulated genes in oxidative stress and the participation of OxyR in this process. It is proposed that besides OxyR, a second layer of regulation may be achieved by a small regulatory RNA and other transcriptional regulators.
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28
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Agarwal M, Pathak A, Rathore RS, Prakash O, Singh R, Jaswal R, Seaman J, Chauhan A. Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress. Cells 2018; 7:cells7120269. [PMID: 30545132 PMCID: PMC6315756 DOI: 10.3390/cells7120269] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 01/15/2023] Open
Abstract
Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.
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Affiliation(s)
- Meenakshi Agarwal
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Ashish Pathak
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Rajesh Singh Rathore
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411007, India.
| | - Rakesh Singh
- Translational Science Lab, College of Medicine, Florida State University, Tallahassee, FL 32304, USA.
| | - Rajneesh Jaswal
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
| | - John Seaman
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA.
| | - Ashvini Chauhan
- Environmental Biotechnology Laboratory, School of the Environment, 1515 S. Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center, Florida A&M University, Tallahassee, FL 32307, USA.
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29
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Pereira EJ, Damare S, Furtado B, Ramaiah N. Response to chromate challenge by marine Staphylococcus sp. NIOMR8 evaluated by differential protein expression. 3 Biotech 2018; 8:500. [PMID: 30498673 DOI: 10.1007/s13205-018-1522-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/17/2018] [Indexed: 11/28/2022] Open
Abstract
Liquid Chromatography-Mass Spectrometry-Quadrupole Time of Flight (LC/MS QToF) protein profiling of marine-derived Staphyloccous gallinarum NIOMR8 was carried out to evaluate proteins conferring chromate (Cr6+) resistance and possible metabolic pathways that were altered as a result. Expressional (up or down-regulation) responses to varying Cr6+ (0, 50, 100, 150, and 200 µg mL- 1) concentrations varied, with as many as 346 proteins identified. Most number of proteins-their numbers in parentheses-were up-regulated when grown in medium with 50 µg mL- 1 (162) and, down-regulated in medium with 100 (281) or 200 µg mL- 1 Cr6+ (280). Among these, eight proteins were commonly up-regulated, while 58 were commonly down-regulated across all conditions of Cr6+. Expression of protein moieties in metabolic pathways like translation (38), transcription (14), replication (18) and repair (4), metabolism of carbohydrates (26), amino acids (27), nucleotides (17), and membrane transport (21) was evidenced. Up-regulation patterns suggest that reduction of molecular oxygen (5), DNA repair (4) and peptide misfolding (7) were the potential protective mechanisms employed to counter Cr6+ stress. Additionally, proteins associated with biofilm and cell wall biogenesis highlight their hypothetical involvement in toxicity tolerance. Results also indicate that at higher concentrations of Cr6+, down-regulation of functional proteins impedes normal cellular functions.
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Affiliation(s)
- Elroy Joe Pereira
- 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Samir Damare
- 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
| | - Bliss Furtado
- 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
- Present Address: Department of Microbiology, Copernicus University, Toruń, Poland
| | - Nagappa Ramaiah
- 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403004 India
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30
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Huang L, Zhou P, Quan X, Logan BE. Removal of binary Cr(VI) and Cd(II) from the catholyte of MFCs and determining their fate in EAB using fluorescence probes. Bioelectrochemistry 2018; 122:61-68. [DOI: 10.1016/j.bioelechem.2018.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/13/2018] [Accepted: 02/28/2018] [Indexed: 01/09/2023]
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31
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Ontañon OM, Landi C, Carleo A, Gagliardi A, Bianchi L, González PS, Agostini E, Bini L. What makes A. guillouiae SFC 500-1A able to co-metabolize phenol and Cr(VI)? A proteomic approach. JOURNAL OF HAZARDOUS MATERIALS 2018; 354:215-224. [PMID: 29753190 DOI: 10.1016/j.jhazmat.2018.04.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Acinetobacter guillouiae SFC 500-1A is an environmental bacterium able to efficiently co-remediate phenol and Cr(VI). To further understand the molecular mechanisms triggered in this strain during the bioremediation process, variations in the proteomic profile after treatment with phenol and phenol plus Cr(VI) were evaluated. The proteomic analysis revealed the induction of the β-ketoadipate pathway for phenol oxidation and the assimilation of degradation products through TCA cycle and glyoxylate shunt. Phenol exposure increased the abundance of proteins associated to energetic processes and ATP synthesis, but it also triggered cellular stress. The lipid bilayer was suggested as a target of phenol toxicity, and changing fatty acids composition seemed to be the bacterial response to protect the membrane integrity. The involvement of two flavoproteins in Cr(VI) reduction to Cr(III) was also proposed. The results suggested the important role of chaperones, antioxidant response and SOS-induced proteins in the ability of the strain to mitigate the damage generated by phenol and Cr(VI). This research contributes to elucidate the mechanisms involved in A. guillouiae SFC 500-1A tolerance and co-remediation of phenol and Cr(VI). Such information may result useful not only to improve its bioremediation efficiency but also to identify putative markers of resistance in environmental bacteria.
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Affiliation(s)
- Ornella Mailén Ontañon
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina.
| | - Claudia Landi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
| | - Alfonso Carleo
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy; Current address: Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - Assunta Gagliardi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy; Current address: Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Laura Bianchi
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
| | - Paola Solange González
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina
| | - Elizabeth Agostini
- Department of Molecular Biology, National University of Rio Cuarto, Córdoba, Argentina; National Council for Scientific and Technological Research (CONICET), Argentina
| | - Luca Bini
- Laboratory of Functional Proteomics, Department of Life Sciences, University of Siena, Siena, Italy
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Kolhe N, Zinjarde S, Acharya C. Responses exhibited by various microbial groups relevant to uranium exposure. Biotechnol Adv 2018; 36:1828-1846. [PMID: 30017503 DOI: 10.1016/j.biotechadv.2018.07.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/08/2018] [Accepted: 07/09/2018] [Indexed: 11/28/2022]
Abstract
There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.
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Affiliation(s)
- Nilesh Kolhe
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India; Department of Microbiology, Savitribai Phule Pune University, Pune 411007, India.
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Trombay, Mumbai 400094, India.
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Liao HY, Chien CC, Tang P, Chen CC, Chen CY, Chen SC. The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. JOURNAL OF HAZARDOUS MATERIALS 2018; 349:79-90. [PMID: 29414755 DOI: 10.1016/j.jhazmat.2018.01.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
Citrobacter sp. has been shown to degrade 2,4,6-trinitrotoluene (TNT). However, the mechanism of its TNT biodegradation is poorly understood. An integrated proteome and transcriptome analysis was performed for investigating the differential genes and differential proteins in bacterial growth at the onset of experiments and after 12 h treatment with TNT. With the RNA sequencing, we found a total of 3792 transcripts and 569 differentially expressed genes (≥2 fold, P < 0.05) by. Genes for amino acid transport, cellular metabolism and stress-shock proteins were up-regulated, while carbohydrate transport and metabolism were down-regulated. A total of 42 protein spots (≥1.5 fold, P < 0.05) showed differential expression on two-dimensional gel electrophoresis and these proteins were identified by mass spectrometry. The most prominent proteins up-regulated were involved in energy production and conversion, amino acid transport and metabolism, posttranslational modification, protein turnover and chaperones. Proteins involved in carbohydrate transport and metabolism were down-regulated. Most notably, we observed that nemA encoding N-ethylmaleimide reductase was the most up-regulated gene involved in TNT degradation, and further proved that it can transform TNT to 4-amino-2,6-dinitrotoluene (4-ADNT) and 2-amino-4,6-dinitrotoluene (2-ADNT). This study highlights the molecular mechanisms of Citrobacter sp. for TNT removal.
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Affiliation(s)
- Hung-Yu Liao
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135, Yuantung Rd., Jhongli City, Taoyuan, 32003, Taiwan
| | - Petrus Tang
- Department of Parasitology, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dis., Taoyuan City, 33302, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, No.116, Heping 1st Rd., Lingya District, Kaohsiung City, 80201, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan.
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Gallois N, Alpha-Bazin B, Ortet P, Barakat M, Piette L, Long J, Berthomieu C, Armengaud J, Chapon V. Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate. J Proteomics 2017; 177:148-157. [PMID: 29223802 DOI: 10.1016/j.jprot.2017.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. BIOLOGICAL SIGNIFICANCE Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.
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Affiliation(s)
- Nicolas Gallois
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Laurie Piette
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Justine Long
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France.
| | - Virginie Chapon
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
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Copper (II) binding of NAD(P)H- flavin oxidoreductase (NfoR) enhances its Cr (VI)-reducing ability. Sci Rep 2017; 7:15481. [PMID: 29133854 PMCID: PMC5684319 DOI: 10.1038/s41598-017-15588-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/23/2017] [Indexed: 12/16/2022] Open
Abstract
Microbes can reduce hexavalent chromium Cr (VI) to the less toxic and soluble trivalent Cr (III). Copper stimulates microbial reduction of Cr (VI) by the Bacillus, Ochrobactrum, and Gluconobacter species; however, the mechanism remains unclear. In our study, the rate of Cr (VI) reduction by Staphylococcus aureus LZ-01 was increased by 210 % when supplemented with 60 μM Cu (II). A putative NAD(P)H-flavin oxidoreductase gene (nfoR) was upregulated under Cr (VI) stress. NfoR-knockout mutant displayed impaired reduction of Cr (VI) and Cu (II)-enhanced Cr (VI) reduction by nfoR isogenic mutant was attenuated in the presence of Cu (II). In vitro tests showed an increased Vmax value of 25.22 μM min−1 mg−1 NfoR in the presence of Cu (II). Together, these results indicate that NfoR is responsible for Cu (II) enhancement. Isothermal titration calorimetry (ITC) assays confirmed the interaction of NfoR with Cu (II) at the dissociation constant of 85.5 μM. Site-directed mutagenesis indicates that His100, His128, and Met165 residues may be important for Cu (II) binding, while Cys163 is necessary for the FMN binding of NfoR. These findings show that Cu (II)-enhanced NfoR belongs to a new branch of Cr (VI) reductases and profoundly influences Cr (VI) reduction.
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Park DM, Overton KW, Liou MJ, Jiao Y. Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus. Mol Microbiol 2017; 104:46-64. [PMID: 28035693 DOI: 10.1111/mmi.13615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2016] [Indexed: 01/18/2023]
Abstract
Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA ) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, named UzcRS, which is responsible for U-dependent activation of PurcA . UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a noncanonical DNA-binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug-resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples the perception of U, Zn and Cu with a novel extracytoplasmic stress response.
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Affiliation(s)
- Dan M Park
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - K Wesley Overton
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan J Liou
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Yongqin Jiao
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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Wufuer R, Wei Y, Lin Q, Wang H, Song W, Liu W, Zhang D, Pan X, Gadd GM. Uranium Bioreduction and Biomineralization. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:137-168. [PMID: 29050665 DOI: 10.1016/bs.aambs.2017.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Following the development of nuclear science and technology, uranium contamination has been an ever increasing concern worldwide because of its potential for migration from the waste repositories and long-term contaminated environments. Physical and chemical techniques for uranium pollution are expensive and challenging. An alternative to these technologies is microbially mediated uranium bioremediation in contaminated water and soil environments due to its reduced cost and environmental friendliness. To date, four basic mechanisms of uranium bioremediation-uranium bioreduction, biosorption, biomineralization, and bioaccumulation-have been established, of which uranium bioreduction and biomineralization have been studied extensively. The objective of this review is to provide an understanding of recent developments in these two fields in relation to relevant microorganisms, mechanisms, influential factors, and obstacles.
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Panda B, Basu B, Acharya C, Rajaram H, Apte SK. Proteomic analysis reveals contrasting stress response to uranium in two nitrogen-fixing Anabaena strains, differentially tolerant to uranium. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 182:205-213. [PMID: 27940385 DOI: 10.1016/j.aquatox.2016.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD50 dose), following 3h exposure to 75μM and 200μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry. The two strains displayed significant differences in levels of proteins associated with photosynthesis, carbon metabolism, and oxidative stress alleviation, commensurate with their uranium tolerance. Higher uranium tolerance of Anabaena sp. strain L-31 could be attributed to sustained photosynthesis and carbon metabolism and superior oxidative stress defense, as compared to the uranium sensitive Anabaena sp. strain PCC 7120. SIGNIFICANCE Uranium responsive proteome modulations in two nitrogen-fixing strains of Anabaena, native to Indian paddy fields, revealed that rapid adaptation to better oxidative stress management, and maintenance of metabolic and energy homeostasis underlies superior uranium tolerance of Anabaena sp. strain L-31 compared to Anabaena sp. strain PCC 7120.
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Affiliation(s)
- Bandita Panda
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Shree Kumar Apte
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.
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Majumder ELW, Wall JD. Uranium Bio-Transformations: Chemical or Biological Processes? ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ojic.2017.72003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Two Outer Membrane Proteins Contribute to Caulobacter crescentus Cellular Fitness by Preventing Intracellular S-Layer Protein Accumulation. Appl Environ Microbiol 2016; 82:6961-6972. [PMID: 27663028 DOI: 10.1128/aem.02479-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/16/2016] [Indexed: 01/18/2023] Open
Abstract
Surface layers, or S-layers, are two-dimensional protein arrays that form the outermost layer of many bacteria and archaea. They serve several functions, including physical protection of the cell from environmental threats. The high abundance of S-layer proteins necessitates a highly efficient export mechanism to transport the S-layer protein from the cytoplasm to the cell exterior. Caulobacter crescentus is unique in that it has two homologous, seemingly redundant outer membrane proteins, RsaFa and RsaFb, which together with other components form a type I protein translocation pathway for S-layer export. These proteins have homology to Escherichia coli TolC, the outer membrane channel of multidrug efflux pumps. Here we provide evidence that, unlike TolC, RsaFa and RsaFb are not involved in either the maintenance of membrane stability or the active export of antimicrobial compounds. Rather, RsaFa and RsaFb are required to prevent intracellular accumulation and aggregation of the S-layer protein RsaA; deletion of RsaFa and RsaFb led to a general growth defect and lowered cellular fitness. Using Western blotting, transmission electron microscopy, and transcriptome sequencing (RNA-seq), we show that loss of both RsaFa and RsaFb led to accumulation of insoluble RsaA in the cytoplasm, which in turn caused upregulation of a number of genes involved in protein misfolding and degradation pathways. These findings provide new insight into the requirement for RsaFa and RsaFb in cellular fitness and tolerance to antimicrobial agents and further our understanding of the S-layer export mechanism on both the transcriptional and translational levels in C. crescentusIMPORTANCE Decreased growth rate and reduced cell fitness are common side effects of protein production in overexpression systems. Inclusion bodies typically form inside the cell, largely due to a lack of sufficient export machinery to transport the overexpressed proteins to the extracellular environment. This phenomenon can conceivably also occur in natural systems. As one example of a system evolved to prevent intracellular protein accumulation, our study demonstrates that Caulobacter crescentus has two homologous outer membrane transporter proteins that are involved in S-layer export. This is an interesting case study that demonstrates how bacteria can evolve redundancy to ensure adequate protein export functionality and maintain high cellular fitness. Moreover, we provide evidence that these two outer membrane proteins, although being the closest C. crescentus homologs to TolC in E. coli, do not process TolC functionality in C. crescentus.
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Synthesis of novel functional hydrothermal carbon spheres for removal of uranium from aqueous solution. J Radioanal Nucl Chem 2016. [DOI: 10.1007/s10967-016-5003-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Dekker L, Arsène-Ploetze F, Santini JM. Comparative proteomics of Acidithiobacillus ferrooxidans grown in the presence and absence of uranium. Res Microbiol 2016; 167:234-9. [DOI: 10.1016/j.resmic.2016.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/07/2015] [Indexed: 10/22/2022]
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Liang X, Csetenyi L, Gadd GM. Uranium bioprecipitation mediated by yeasts utilizing organic phosphorus substrates. Appl Microbiol Biotechnol 2016; 100:5141-51. [PMID: 26846744 DOI: 10.1007/s00253-016-7327-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/14/2023]
Abstract
In this research, we have demonstrated the ability of several yeast species to mediate U(VI) biomineralization through uranium phosphate biomineral formation when utilizing an organic source of phosphorus (glycerol 2-phosphate disodium salt hydrate (C3H7Na2O6P·xH2O (G2P)) or phytic acid sodium salt hydrate (C6H18O24P6·xNa(+)·yH2O (PyA))) in the presence of soluble UO2(NO3)2. The formation of meta-ankoleite (K2(UO2)2(PO4)2·6(H2O)), chernikovite ((H3O)2(UO2)2(PO4)2·6(H2O)), bassetite (Fe(++)(UO2)2(PO4)2·8(H2O)), and uramphite ((NH4)(UO2)(PO4)·3(H2O)) on cell surfaces was confirmed by X-ray diffraction in yeasts grown in a defined liquid medium amended with uranium and an organic phosphorus source, as well as in yeasts pre-grown in organic phosphorus-containing media and then subsequently exposed to UO2(NO3)2. The resulting minerals depended on the yeast species as well as physico-chemical conditions. The results obtained in this study demonstrate that phosphatase-mediated uranium biomineralization can occur in yeasts supplied with an organic phosphate substrate as sole source of phosphorus. Further understanding of yeast interactions with uranium may be relevant to development of potential treatment methods for uranium waste and utilization of organic phosphate sources and for prediction of microbial impacts on the fate of uranium in the environment.
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Affiliation(s)
- Xinjin Liang
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - Laszlo Csetenyi
- Concrete Technology Group, Department of Civil Engineering, University of Dundee, Dundee, Scotland, DD1 4HN, UK
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, DD1 5EH, UK.
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Acharya C, Blindauer CA. Unexpected Interactions of the Cyanobacterial Metallothionein SmtA with Uranium. Inorg Chem 2016; 55:1505-15. [DOI: 10.1021/acs.inorgchem.5b02327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Celin Acharya
- Molecular
Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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45
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Prabhakaran P, Ashraf MA, Aqma WS. Microbial stress response to heavy metals in the environment. RSC Adv 2016. [DOI: 10.1039/c6ra10966g] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Heavy metal contamination is a global environmental issue as it poses a significant threat to public health, and exposure to metals above a certain threshold level can cause deleterious effects in all living organisms including microbes.
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Affiliation(s)
- Pranesha Prabhakaran
- School of Biosciences and Biotechnology
- Faculty of Science and Technology
- Universiti Kebangsaan Malaysia
- 43600 Bangi
- Malaysia
| | - Muhammad Aqeel Ashraf
- Faculty of Science & Natural Resources
- Universiti Malaysia Sabah
- 88400 Kota Kinabalu
- Malaysia
- Department of Environmental Science and Engineering
| | - Wan Syaidatul Aqma
- School of Biosciences and Biotechnology
- Faculty of Science and Technology
- Universiti Kebangsaan Malaysia
- 43600 Bangi
- Malaysia
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Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance. J Bacteriol 2015. [PMID: 26195598 DOI: 10.1128/jb.00382-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED The ubiquitous aquatic bacterium Caulobacter crescentus is highly resistant to uranium (U) and facilitates U biomineralization and thus holds promise as an agent of U bioremediation. To gain an understanding of how C. crescentus tolerates U, we employed transposon (Tn) mutagenesis paired with deep sequencing (Tn-seq) in a global screen for genomic elements required for U resistance. Of the 3,879 annotated genes in the C. crescentus genome, 37 were found to be specifically associated with fitness under U stress, 15 of which were subsequently tested through mutational analysis. Systematic deletion analysis revealed that mutants lacking outer membrane transporters (rsaFa and rsaFb), a stress-responsive transcription factor (cztR), or a ppGpp synthetase/hydrolase (spoT) exhibited a significantly lower survival rate under U stress. RsaFa and RsaFb, which are homologues of TolC in Escherichia coli, have previously been shown to mediate S-layer export. Transcriptional analysis revealed upregulation of rsaFa and rsaFb by 4- and 10-fold, respectively, in the presence of U. We additionally show that rsaFa mutants accumulated higher levels of U than the wild type, with no significant increase in oxidative stress levels. Our results suggest a function for RsaFa and RsaFb in U efflux and/or maintenance of membrane integrity during U stress. In addition, we present data implicating CztR and SpoT in resistance to U stress. Together, our findings reveal novel gene targets that are key to understanding the molecular mechanisms of U resistance in C. crescentus. IMPORTANCE Caulobacter crescentus is an aerobic bacterium that is highly resistant to uranium (U) and has great potential to be used in U bioremediation, but its mechanisms of U resistance are poorly understood. We conducted a Tn-seq screen to identify genes specifically required for U resistance in C. crescentus. The genes that we identified have previously remained elusive using other omics approaches and thus provide significant insight into the mechanisms of U resistance by C. crescentus. In particular, we show that outer membrane transporters RsaFa and RsaFb, previously known as part of the S-layer export machinery, may confer U resistance by U efflux and/or by maintaining membrane integrity during U stress.
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Modulation of medium pH by Caulobacter crescentus facilitates recovery from uranium-induced growth arrest. Appl Environ Microbiol 2014; 80:5680-8. [PMID: 25002429 DOI: 10.1128/aem.01294-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments.
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Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus. Appl Environ Microbiol 2014; 80:4795-804. [PMID: 24878600 DOI: 10.1128/aem.01050-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus is known to tolerate high levels of uranium [U(VI)], but its detoxification mechanism is poorly understood. Here we show that C. crescentus is able to facilitate U(VI) biomineralization through the formation of U-Pi precipitates via its native alkaline phosphatase activity. The U-Pi precipitates, deposited on the cell surface in the form of meta-autunite structures, have a lower U/Pi ratio than do chemically produced precipitates. The enzyme that is responsible for the phosphatase activity and thus the biomineralization process is identified as PhoY, a periplasmic alkaline phosphatase with broad substrate specificity. Furthermore, PhoY is shown to confer a survival advantage on C. crescentus toward U(VI) under both growth and nongrowth conditions. Results obtained in this study thus highlight U(VI) biomineralization as a resistance mechanism in microbes, which not only improves our understanding of bacterium-mineral interactions but also aids in defining potential ecological niches for metal-resistant bacteria.
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