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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Functional response of Acinetobacter guillouiae SFC 500-1A to tannery wastewater as revealed by a complementary proteomic approach. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118333. [PMID: 37320920 DOI: 10.1016/j.jenvman.2023.118333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/22/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]
Abstract
Acinetobacter guillouiae SFC 500-1 A is a promising candidate for the bioremediation of tannery wastewater. In this study, we applied shotgun proteomic technology in conjunction with a gel-based assay (Gel-LC) to explore the strain's intracellular protein profile when grown in tannery wastewater as opposed to normal culture conditions. A total of 1775 proteins were identified, 52 of which were unique to the tannery wastewater treatment. Many of them were connected to the degradation of aromatic compounds and siderophore biosynthesis. On the other hand, 1598 proteins overlapped both conditions but were differentially expressed in each. Those that were upregulated in wastewater (109) were involved in the processes mentioned above, as well as in oxidative stress mitigation and intracellular redox state regulation. Particularly interesting were the downregulated proteins under the same treatment (318), which were diverse but mainly linked to the regulation of basic cellular functions (replication, transcription, translation, cell cycle, and wall biogenesis); metabolism (amino acids, lipids, sulphate, energetic processes); and other more complex responses (cell motility, exopolysaccharide production, biofilm formation, and quorum sensing). The findings suggest that SFC 500-1 A engages in survival and stress management strategies to cope with the toxic effects of tannery wastewater, and that such strategies may be mostly oriented at keeping metabolic processes to a minimum. Altogether, the results might be useful in the near future to improve the strain's effectiveness if it will be applied for bioremediation.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - María D Paez
- Division of Basic Biomedical Sciences, Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA.
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), 5800, Río Cuarto, Córdoba, Argentina; Instituto de Biotecnología Ambiental y Salud (INBIAS-CONICET), Río Cuarto, Córdoba, Argentina.
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2
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Li ZW, Wang JH. Analysis of the functional gene of degrading BDE-47 by Acinetobacter pittii GB-2 based on transcriptome sequencing. Gene 2022; 844:146826. [PMID: 35998843 DOI: 10.1016/j.gene.2022.146826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/06/2022] [Accepted: 08/16/2022] [Indexed: 11/19/2022]
Abstract
2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) is one of the most widely distributed PBDEs. BDE-47 is also the most abundant in organisms and the most toxic to humans and animals. Herein, we have studied the pathway of BDE-47 degradation and gene involvement in Acinetobacter pittii GB-2. This degradation is dominated by hydroxylation, resulting in hydroxylated products 6-OH-BDE-47, 5-OH-BDE-47 and 2'-OH-BDE-28, and bromophenol products 2,4-DBP and 4-BP. Transcriptome sequencing results showed 359 differentially expressed genes (DEGs) induced by BDE-47, of which 159 were up-regulated and 200 were down-regulated. The up-regulated ones were mainly related to substance transport, degradation and cell stress. From these results, we suggest that 1,2-dioxygenase, phenol hydroxylase and monooxygenase are involved in BDE-47 degradation. The function of AntA gene was identified by constructing a prokaryotic expression vector. Our study contributes to understanding how the metabolism of strain GB-2 changes under BDE-47 stress conditions, and sheds light on the mechanism of BDE-47 degradation.
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Affiliation(s)
- Zi-Wei Li
- School of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Ji-Hua Wang
- School of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
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3
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Role of Sulfate Transporters in Chromium Tolerance in Scenedesmus acutus M. (Sphaeropleales). PLANTS 2022; 11:plants11020223. [PMID: 35050111 PMCID: PMC8780407 DOI: 10.3390/plants11020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Sulfur (S) is essential for the synthesis of important defense compounds and in the scavenging potential of oxidative stress, conferring increased capacity to cope with biotic and abiotic stresses. Chromate can induce a sort of S-starvation by competing for uptake with SO42− and causing a depletion of cellular reduced compounds, thus emphasizing the role of S-transporters in heavy-metal tolerance. In this work we analyzed the sulfate transporter system in the freshwater green algae Scenedesmus acutus, that proved to possess both H+/SO42− (SULTRs) and Na+/SO42− (SLTs) plasma membrane sulfate transporters and a chloroplast-envelope localized ABC-type holocomplex. We discuss the sulfate uptake system of S. acutus in comparison with other taxa, enlightening differences among the clade Sphaeropleales and Volvocales/Chlamydomonadales. To define the role of S transporters in chromium tolerance, we analyzed the expression of SULTRs and SULPs components of the chloroplast ABC transporter in two strains of S. acutus with different Cr(VI) sensitivity. Their differential expression in response to Cr(VI) exposure and S availability seems directly linked to Cr(VI) tolerance, confirming the role of sulfate uptake/assimilation pathways in the metal stress response. The SULTRs up-regulation, observed in both strains after S-starvation, may directly contribute to enhancing Cr-tolerance by limiting Cr(VI) uptake and increasing sulfur availability for the synthesis of sulfur-containing defense molecules.
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Vieto S, Rojas-Gätjens D, Jiménez JI, Chavarría M. The potential of Pseudomonas for bioremediation of oxyanions. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:773-789. [PMID: 34369104 DOI: 10.1111/1758-2229.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Non-metal, metal and metalloid oxyanions occur naturally in minerals and rocks of the Earth's crust and are mostly found in low concentrations or confined in specific regions of the planet. However, anthropogenic activities including urban development, mining, agriculture, industrial activities and new technologies have increased the release of oxyanions to the environment, which threatens the sustainability of natural ecosystems, in turn affecting human development. For these reasons, the implementation of new methods that could allow not only the remediation of oxyanion contaminants but also the recovery of valuable elements from oxyanions of the environment is imperative. From this perspective, the use of microorganisms emerges as a strategy complementary to physical, mechanical and chemical methods. In this review, we discuss the opportunities that the Pseudomonas genus offers for the bioremediation of oxyanions, which is derived from its specialized central metabolism and the high number of oxidoreductases present in the genomes of these bacteria. Finally, we review the current knowledge on the transport and metabolism of specific oxyanions in Pseudomonas species. We consider that the Pseudomonas genus is an excellent starting point for the development of biotechnological approaches for the upcycling of oxyanions into added-value metal and metalloid byproducts.
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Affiliation(s)
- Sofía Vieto
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - José I Jiménez
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
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5
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Li SW, Wen Y, Leng Y. Transcriptome analysis provides new insights into the tolerance and reduction of Lysinibacillus fusiformis 15-4 to hexavalent chromium. Appl Microbiol Biotechnol 2021; 105:7841-7855. [PMID: 34546405 DOI: 10.1007/s00253-021-11586-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022]
Abstract
Microbial bioremediation of Cr(VI)-contaminated environments has drawn extensive concern. However, the molecular processes underlying the microbial Cr(VI) tolerance and reduction remain unclear. We isolated a Cr(VI)-reducing Lysinibacillus fusiformis strain 15-4 from soil on the Qinghai-Tibet Plateau. When grown in 1 mM and 2 mM Cr(VI)-containing medium, strain 15-4 could reduce 100% and 93.7% of Cr(VI) to Cr(III) after 36 h and 60 h of incubation, respectively. To know the molecular processes in response to Cr(VI), transcriptome sequencing was carried out using RNA-Seq technology. The results annotated a total of 3913 expressed genes in the strain. One thousand ninety-eight genes (28.1%) were significantly (fold change ≥ 2, false discovery rate ≤ 0.05) expressed in response to Cr(VI), of which 605 (55.1%) were upregulated and 493 (44.9%) were downregulated. The enrichment analysis showed that a total of 630 differentially expressed genes (DEGs) were enriched to 122 KEGG pathways, of which 8 pathways were significantly (p < 0.05) enriched in Cr(VI)-treated sample, including ATP-binding cassette (ABC) transporters (97 DEGs), ribosome (40), sulfur metabolism (16), aminoacyl-tRNA biosynthesis (19), porphyrin metabolism (20), quorum sensing (44), oxidative phosphorylation (17), and histidine metabolism (10), suggesting that these pathways play key roles to cope with Cr(VI) in the strain. The highly upregulated DEGs consisted of 29 oxidoreductase, 18 dehydrogenase, 14 cell redox homeostasis and stress response protein, and 10 DNA damage and repair protein genes. However, seven Na+:H+ antiporter complex-coding DEGs and most of transcriptional regulator-coding DEGs were significantly downregulated in the Cr-treated sample. Many of FMN/NAD(P)H-dependent reductase-encoding genes were greatly induced by Cr, suggesting the involvement of these genes in Cr(VI) reduction in strain 15-4. Sulfur and iron ions as well as the thiol-disulfide exchange reactions might play synergistic roles in Cr reduction.Key points• Lysinibacillus fusiformis 15-4 was able to tolerate and reduce Cr(VI) to Cr(III).• Transcriptome analysis revealed that 1098 DEGs and 8 key KEGG pathways significantly responded to Cr(VI).• Sulfur metabolism, protein biosynthesis, and porphyrin metabolism were the key pathways associated with the survival of strain 15-4 in response to Cr(VI).
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Affiliation(s)
- Shi-Weng Li
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, People's Republic of China. .,School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China. .,Key Laboratory of Extreme Environmental Microbial Resources and Engineering in Gansu Province, Lanzhou, 730000, People's Republic of China.
| | - Ya Wen
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China
| | - Yan Leng
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, People's Republic of China
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6
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Lara P, Vega-Alvarado L, Sahonero-Canavesi DX, Koenen M, Villanueva L, Riveros-Mckay F, Morett E, Juárez K. Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr. Front Microbiol 2021; 12:656589. [PMID: 34122372 PMCID: PMC8195247 DOI: 10.3389/fmicb.2021.656589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Klebsiella sp. strain AqSCr, isolated from Cr(VI)-polluted groundwater, reduces Cr(VI) both aerobically and anaerobically and resists up 34 mM Cr(VI); this resistance is independent of the ChrA efflux transporter. In this study, we report the whole genome sequence and the transcriptional profile by RNA-Seq of strain AqSCr under Cr(VI)-adapted conditions and found 255 upregulated and 240 downregulated genes compared to controls without Cr(VI) supplementation. Genes differentially transcribed were mostly associated with oxidative stress response, DNA repair and replication, sulfur starvation response, envelope-osmotic stress response, fatty acid (FA) metabolism, ribosomal subunits, and energy metabolism. Among them, genes not previously associated with chromium resistance, for example, cybB, encoding a putative superoxide oxidase (SOO), gltA2, encoding an alternative citrate synthase, and des, encoding a FA desaturase, were upregulated. The sodA gene encoding a manganese superoxide dismutase was upregulated in the presence of Cr(VI), whereas sodB encoding an iron superoxide dismutase was downregulated. Cr(VI) resistance mechanisms in strain AqSCr seem to be orchestrated by the alternative sigma factors fecl, rpoE, and rpoS (all of them upregulated). Membrane lipid analysis of the Cr(IV)-adapted strain showed a lower proportion of unsaturated lipids with respect to the control, which we hypothesized could result from unsaturated lipid peroxidation followed by degradation, together with de novo synthesis mediated by the upregulated FA desaturase-encoding gene, des. This report helps to elucidate both Cr(VI) toxicity targets and global bacterial response to Cr(VI).
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Affiliation(s)
- Paloma Lara
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leticia Vega-Alvarado
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, Texel, Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Fernando Riveros-Mckay
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Enrique Morett
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Katy Juárez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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7
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Xia X, Wu S, Zhou Z, Wang G. Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123685. [PMID: 33113721 DOI: 10.1016/j.jhazmat.2020.123685] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/16/2020] [Accepted: 08/05/2020] [Indexed: 05/21/2023]
Abstract
The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.
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Affiliation(s)
- Xian Xia
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China; Hubei Key Laboratory of Edible Wild Plants Conservation & Utilization, Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, National Experimental Teaching Demonstrating Center, College of Life Sciences, Hubei Normal University, Huangshi, 435002, PR China
| | - Shijuan Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zijie Zhou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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8
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Shi L, Dong P, Song W, Li C, Lu H, Wen Z, Wang C, Shen Z, Chen Y. Comparative transcriptomic analysis reveals novel insights into the response to Cr(VI) exposure in Cr(VI) tolerant ectomycorrhizal fungi Pisolithus sp. 1 LS-2017. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 188:109935. [PMID: 31740233 DOI: 10.1016/j.ecoenv.2019.109935] [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: 07/10/2019] [Revised: 10/21/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Chromium (Cr) is one of the most toxic heavy metals and a health hazard to millions of people worldwide. Ectomycorrhizal (ECM) fungi can assist plants in phytoremediation of heavy metal contaminated soil. Cr tolerance differs among ECM fungal varieties, but the underlying molecular mechanisms of Cr tolerance in ECM fungi are not clear. This study identified, analysed and compared the Cr(VI)-induced transcriptional changes between Cr(VI)-tolerant strain (Pisolithus sp. 1 LS-2017) and Cr(VI)-sensitive strain (Pisolithus sp. 2 LS-2017) by de novo transcriptomic analysis. The results showed that 93,642 assembled unique transcripts representing the 22,353 (46.76%) unigenes matched the proteins we have known in the Nr database and 47,801 unigenes were got from the Pisolithus spp. For DEGs between the control and 10 mg/L Cr(VI) treatment, cyanoamino acid metabolic, type I diabetes mellitus metabolism, nitrogen metabolism and beta-Alanine metabolism pathways were significantly enriched (p < 0.05) in Pisolithus sp. 1 LS-2017. Two nitrate reductase family genes (nidD, niiA) provide Cr(VI) tolerance for Pisolithus sp. 1 LS-2017 by regulating Cr(VI) reduction. In addition, NO produced by nidD, niiA regulated denitrification can alleviate Cr(VI) induced oxidative stress. In Pisolithus sp. 2 LS-2017, the alcC, aldA and lcf2 gene may alleviate Cr(VI) induced oxidative stress by protecting SH groups and increasing secondary metabolism, reducing detoxify aldehydes to carboxylic acids and producing LCPUFAs respectively; .T gene regulate Cr(VI) induced wound healing by pigmentation and stability of melanin in spore; MKP2 gene accelerate Cr(VI) induced cell death and gpmA gene regulated Cr(VI) induced energy emergency.
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Affiliation(s)
- Liang Shi
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Pengcheng Dong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Wuyu Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Chenxi Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Haining Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Zhugui Wen
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, Jiangsu, 224002, China.
| | - Chunchun Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China; The Collaborated Lab. of Plant Molecular Ecology (between College of Life Sciences of Nanjing Agricultural University and Asian Natural Environmental Science Center of the University of Tokyo), Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agiricultural University, Nanjing, Jiangsu, 210095, China; National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agiricultural University, Nanjing, Jiangsu, 210095, China.
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China; The Collaborated Lab. of Plant Molecular Ecology (between College of Life Sciences of Nanjing Agricultural University and Asian Natural Environmental Science Center of the University of Tokyo), Nanjing Agricultural University, Nanjing, 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, Nanjing Agiricultural University, Nanjing, Jiangsu, 210095, China; National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agiricultural University, Nanjing, Jiangsu, 210095, China.
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9
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Zhu Y, Yan J, Xia L, Zhang X, Luo L. Mechanisms of Cr(VI) reduction by Bacillus sp. CRB-1, a novel Cr(VI)-reducing bacterium isolated from tannery activated sludge. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 186:109792. [PMID: 31629191 DOI: 10.1016/j.ecoenv.2019.109792] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Cr(VI) reduction by microorganisms has been extensively reported, however, the mechanism of Cr(VI) reduction varies among different microorganisms. In this study, a Cr(VI)-reducing bacterium identified as Bacillus sp. was isolated from tannery activated sludge, strain CRB-1 was able to completely reduce 50 mg/L of Cr(VI) within 24 h under aerobic conditions and exhibited considerable Cr(VI) removal efficiency in the pH range from 7.0 to 9.0, temperature 24-42 °C. Cr(VI) reduction assays with resting cells, permeabilized cells, and subcellular fractions suggested that Cr(VI) reduction mainly occurred in the cytoplasm. According to qRT-PCR analysis, a chrA gene and a nitR2 gene were up-regulated under Cr(VI) stress. Heterologous expression of the chrA gene and the nitR2 gene indicated that ChrA was associated with Cr(VI) resistance, while NitR2 was responsible for Cr(VI) reduction. Furthermore, soluble end products were detected. On the basis of FTIR, it was speculated that the formation of soluble end products may be due to the complexation of EPS with Cr(III). Consequently, the Cr(VI)-reducing ability of strain CRB-1 and its chromate reductases enables CRB-1 a potential candidate for Cr(VI) bioremediation.
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Affiliation(s)
- Yunfei Zhu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Junwei Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Li Xia
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiang Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Lixin Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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10
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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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11
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Sardella A, Marieschi M, Mercatali I, Zanni C, Gorbi G, Torelli A. The relationship between sulfur metabolism and tolerance of hexavalent chromium in Scenedesmus acutus (Spheropleales): Role of ATP sulfurylase. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 216:105320. [PMID: 31590132 DOI: 10.1016/j.aquatox.2019.105320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/23/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Sulfur availability and the end products of its metabolism, cysteine, glutathione and phytochelatins, play an important role in heavy metal tolerance, chromium included. Sulfate and chromate not only compete for the transporters but also for assimilation enzymes and chromium tolerance in various organisms has been associated to differences in this pathway. We investigated the mechanisms of Cr(VI)-tolerance increase induced by S-starvation focusing on the role of ATP sulfurylase (ATS) in two strains of Scenedesmus acutus with different chromium sensitivity. S-starvation enhances the defence potential by increasing sulfate uptake/assimilation and decreasing chromium uptake, thus suggesting a change in the transport system. We isolated two isoforms of the enzyme, SaATS1 and SaATS2, with different sensitivity to sulfur availability, and analysed them in S-sufficient and S-replete condition both in standard and in chromium supplemented medium. SaATS2 expression is different in the two strains and presumably marks a different sulfur perception/exploitation in the Cr-tolerant. Its induction and silencing are compatible with a role in the transient tolerance increase induced by S-starvation. This enzyme can however hardly be responsible for the large cysteine production of the Cr-tolerant strain after starvation, suggesting that cytosolic rather than chloroplastic cysteine production is differently regulated in the two strains.
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Affiliation(s)
- Alessio Sardella
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11A I-43124, Parma, Italy.
| | - Matteo Marieschi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11A I-43124, Parma, Italy.
| | - Isabel Mercatali
- ISPRA - Italian National Institute for Environmental Protection and Research, Via di Castel Romano 100-00128, Rome, Italy.
| | - Corrado Zanni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11A I-43124, Parma, Italy.
| | - Gessica Gorbi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11A I-43124, Parma, Italy.
| | - Anna Torelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11A I-43124, Parma, Italy.
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12
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Hoyos-Hernandez C, Courbert C, Simonucci C, David S, Vogel TM, Larose C. Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima. FEMS Microbiol Lett 2019; 366:5556529. [DOI: 10.1093/femsle/fnz180] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 08/26/2019] [Indexed: 12/19/2022] Open
Abstract
ABSTRACT
Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.
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Affiliation(s)
- Carolina Hoyos-Hernandez
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
| | - Christelle Courbert
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
| | - Caroline Simonucci
- Laboratoire sur le devenir des pollutions de sites radioactifs, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320, Fontenay-aux-Roses Cedex, France
- Laboratoire d'expertise et d'intervention en radioprotection Nord, Institut de Radioprotection et de Sûreté Nucléaire, 31 avenue de la Division Leclerc, 92320 Fontenay aux Roses, France
| | - Sebastien David
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampere, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue 69134, Ecully, France
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13
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Shah S, Damare S. Proteomic response of marine-derived Staphylococcus cohnii #NIOSBK35 to varying Cr(vi) concentrations. Metallomics 2019; 11:1465-1471. [PMID: 31237606 DOI: 10.1039/c9mt00089e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chromium in its hexavalent state is a water-soluble and toxic element to living organisms present in the environment. However, some organisms are resistant and reduce the toxic forms of Cr(vi) to less toxic or non-toxic forms. A global proteomic analysis of Staphylococcus sp. #NIOSBK35 under different chromate concentrations (0, 100, 200 and 300 mg L-1) at different time points in its growth stages (6, 9, 12, 18, 24 and 36 h) resulted in the identification of 878 proteins. Of all the proteins expressed, 13 proteins [23 rDNA (uracil-5-) methyltransferase RumA, multidrug ABC transporter ATP binding protein, dihydroxy acid dehydratase, polysaccharide biosynthesis protein, etc.] were expressed only in the presence of chromium. 14 proteins were up-regulated in response to chromium(vi), namely, alkyl hydroperoxide reductase, ATP-dependent Zn metallopeptidase, hsp90- like protein, NAD (P)-dependent oxidoreductase, etc. Most of the proteins involved in normal cell functioning like 1-pyrroline-5-carboxylate dehydrogenase, ribosomal proteins (30S ribosomal protein S11, 30S ribosomal protein S2, and 50S ribosomal protein L32), aconitate hydratase, DNA primase, serine-tRNA ligase, phosphoenolpyruvate-protein phosphotransferase, enolase, sulfur transferase FdhD, etc. were found to be down-regulated. On grouping these proteins into their COG (cluster of orthologous groups) functional categories, they were found to be involved in translation, carbohydrate metabolism, stress proteins, amino acid transport and membrane transport mechanisms. The proteomic response given by Staphylococcus sp. #NIOSBK35 did not show expression of Cr-specific proteins, indicating a different mechanism of Cr-tolerance as the organism was able to survive and grow at high concentrations of Cr(vi).
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Affiliation(s)
- Shruti Shah
- Biological Oceanography Division, CSIR - National Institute of Oceanography, Dona Paula, Goa 403004, India.
| | - Samir Damare
- Biological Oceanography Division, CSIR - National Institute of Oceanography, Dona Paula, Goa 403004, India.
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14
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Chai L, Ding C, Li J, Yang Z, Shi Y. Multi-omics response of Pannonibacter phragmitetus BB to hexavalent chromium. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:63-73. [PMID: 30878863 DOI: 10.1016/j.envpol.2019.03.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/25/2019] [Accepted: 03/03/2019] [Indexed: 05/27/2023]
Abstract
The release of hexavalent chromium [Cr(VI)] into water bodies poses a major threat to the environment and human health. However, studies of the biological response to Cr(VI) are limited. In this study, a toxic bacterial mechanism of Cr(VI) was investigated using Pannonibacter phragmitetus BB (hereafter BB), which was isolated from chromate slag. The maximum Cr(VI) concentrations with respect to the resistance and reduction by BB are 4000 mg L-1 and 2500 mg L-1, respectively. In the BB genome, more genes responsible for Cr(VI) resistance and reduction are observed compared with other P. phragmitetus strains. A total of 361 proteins were upregulated to respond to Cr(VI) exposure, including enzymes for Cr(VI) uptake, intracellular reduction, ROS detoxification, DNA repair, and Cr(VI) efflux and proteins associated with novel mechanisms involving extracellular reduction mediated by electron transfer, quorum sensing, and chemotaxis. Based on metabolomic analysis, 174 metabolites were identified. Most of the upregulated metabolites are involved in amino acid, glucose, lipid, and energy metabolisms. The results show that Cr(VI) induces metabolite production, while metabolites promote Cr(VI) reduction. Overall, multi-enzyme expression and metabolite production by BB contribute to its high ability to resist/reduce Cr(VI). This study provides details supporting the theory of Cr(VI) reduction and a theoretical basis for the efficient bioremoval of Cr(VI) from the environment.
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Affiliation(s)
- Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China
| | - Chunlian Ding
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China
| | - Jiawei Li
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China
| | - Zhihui Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China
| | - Yan Shi
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083, Changsha, China; National Engineering Research Center for Heavy Metals Pollution Control and Treatment, 410083, Changsha, China.
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15
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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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16
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Chowdhury MDEK, Bae H. Bacterial endophytes isolated from mountain-cultivated ginseng (Panax ginseng Mayer) have biocontrol potential against ginseng pathogens. BIOLOGICAL CONTROL 2018; 126:97-108. [DOI: 10.1016/j.biocontrol.2018.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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17
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Chai L, Ding C, Tang C, Yang W, Yang Z, Wang Y, Liao Q, Li J. Discerning three novel chromate reduce and transport genes of highly efficient Pannonibacter phragmitetus BB: From genome to gene and protein. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 162:139-146. [PMID: 29990725 DOI: 10.1016/j.ecoenv.2018.06.090] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Here, Pannonibacter phragmitetus BB was investigated at genomic, genetic and protein levels to explore molecular mechanisms of chromium biotransformation, respectively. The results of Miseq sequencing uncovered that a high-qualified bacterial genome draft was achieved with 5.07 Mb in length. Three novel genes involved in chromate reduce and transport, named nitR, chrA1 and chrA2, were identified by alignment, annotation and phylogenetic tree analyses, which encode a chromate reductase (NitR) and two chromate transporters (ChrA1 and ChrA2). Reverse transcription real-time polymerase chain reaction (RT-qPCR) analyses showed that the relative quantitative transcription of the three genes as the maximum reduction rate of Cr(VI) were significantly up-regulated with the increasing initial Cr(VI) concentrations. However, at the maximum cell growth points nitR was in a low transcription level, while the transcription of chrA1 and chrA2 were hold at a relatively high level and decreased with the increasing initial Cr(VI) concentrations. The ex-situ chromate reducing activity of NitR was revealed a Vmax of 34.46 µmol/min/mg enzyme and Km of 14.55 µmol/L, suggesting feasibility of the reaction with Cr(VI) as substrate. The multiple alignment demonstrates that NitR is potentially a nicotinamide adenine dinucleotide phosphate (NADPH) dependent flavin mononucleotide (FMN) reductase of Class I chromate reductases. Our results will prompt a large-scaled bioremediation on the contaminated soils and water by Pannonibacter phragmitetus BB, taking advantage of uncovering its molecular mechanisms of chromium biotransformation.
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Affiliation(s)
- Liyuan Chai
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Chunlian Ding
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China
| | - Chongjian Tang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Weichun Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Zhihui Yang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China
| | - Yangyang Wang
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; College of Environment and Planning, Henan University, 475004 Kaifeng, China
| | - Qi Liao
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, 410083 Changsha, China.
| | - Jiawei Li
- Institute of Environmental Science and Engineering, School of Metallurgy and Environment, Central South University, 410083 Changsha, China
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18
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Löwe H, Sinner P, Kremling A, Pflüger-Grau K. Engineering sucrose metabolism in Pseudomonas putida highlights the importance of porins. Microb Biotechnol 2018; 13:97-106. [PMID: 29808622 PMCID: PMC6922520 DOI: 10.1111/1751-7915.13283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
Using agricultural wastes as a substrate for biotechnological processes is of great interest in industrial biotechnology. A prerequisite for using these wastes is the ability of the industrially relevant microorganisms to metabolize the sugars present therein. Therefore, many metabolic engineering approaches are directed towards widening the substrate spectrum of the workhorses of industrial biotechnology like Escherichia coli, yeast or Pseudomonas putida. For instance, neither xylose or arabinose from cellulosic residues, nor sucrose, the main sugar in waste molasses, can be metabolized by most E. coli and P. putida wild types. We evaluated a new, so far uncharacterized gene cluster for sucrose metabolism from Pseudomonas protegens Pf‐5 and showed that it enables P. putida to grow on sucrose as the sole carbon and energy source. Even when integrated into the genome of P. putida, the resulting strain grew on sucrose at rates similar to the rate of the wild type on glucose – making it the fastest growing, plasmid‐free P. putida strain known so far using sucrose as substrate. Next, we elucidated the role of the porin, an orthologue of the sucrose porin ScrY, in the gene cluster and found that in P. putida, a porin is needed for sucrose transport across the outer membrane. Consequently, native porins were not sufficient to allow unlimited growth on sucrose. Therefore, we concluded that the outer membrane can be a considerable barrier for substrate transport, depending on strain, genotype and culture conditions, all of which should be taken into account in metabolic engineering approaches. We additionally showed the potential of the engineered P. putida strains by growing them on molasses with efficiencies twice as high as obtained with the wild‐type P. putida. This can be seen as a further step towards the production of low‐value chemicals and biofuels with P. putida from alternative and more affordable substrates in the future.
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Affiliation(s)
- Hannes Löwe
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Peter Sinner
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
| | - Andreas Kremling
- Systems Biotechnology, Technical University of Munich, 85748, Garching, Germany
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19
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Izrael-Živković L, Rikalović M, Gojgić-Cvijović G, Kazazić S, Vrvić M, Brčeski I, Beškoski V, Lončarević B, Gopčević K, Karadžić I. Cadmium specific proteomic responses of a highly resistantPseudomonas aeruginosasan ai. RSC Adv 2018; 8:10549-10560. [PMID: 35540485 PMCID: PMC9078880 DOI: 10.1039/c8ra00371h] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/07/2018] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas aeruginosa san ai is a promising candidate for bioremediation of cadmium pollution, as it resists a high concentration of up to 7.2 mM of cadmium. Leaving biomass of P. aeruginosa san ai exposed to cadmium has a large biosorption potential, implying its capacity to extract heavy metal from contaminated medium. In the present study, we investigated tolerance and accumulation of cadmium on protein level by shotgun proteomics approach based on liquid chromatography and tandem mass spectrometry coupled with bioinformatics to identify proteins. Size exclusion chromatography was used for protein prefractionation to preserve native forms of metalloproteins and protein complexes. Using this approach a total of 60 proteins were observed as up-regulated in cadmium-amended culture. Almost a third of the total numbers of up-regulated were metalloproteins. Particularly interesting are denitrification proteins which are over expressed but not active, suggesting their protective role in conditions of heavy metal exposure. P. aeruginosa san ai developed a complex mechanism to adapt to cadmium, based on: extracellular biosorption, bioaccumulation, the formation of biofilm, controlled siderophore production, enhanced respiration and modified protein profile. An increased abundance of proteins involved in: cell energy metabolism, including denitrification proteins; amino acid metabolism; cell motility and posttranslational modifications, primarily based on thiol-disulfide exchange, were observed. Enhanced oxygen consumption of biomass in cadmium-amended culture versus control was found. Our results signify that P. aeruginosa san ai is naturally well equipped to overcome and survive high doses of cadmium and, as such, has a great potential for application in bioremediation of cadmium polluted sites. When exposed to cadmium a highly resistant strain P. aeruginosa san ai responds by an increased metalloprotein expression (particularly denitrification proteins), an enhanced respiration, and a pronounced thiol-disulfide protein modifications.![]()
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Affiliation(s)
| | - Milena Rikalović
- Faculty of Applied Ecology Futura
- University of Singidunum
- Belgrade
- Serbia
| | - Gordana Gojgić-Cvijović
- Institute of Chemistry
- Technology and Metallurgy
- Department of Chemistry
- University of Belgrade
- Belgrade
| | | | - Miroslav Vrvić
- Faculty of Chemistry
- University of Belgrade
- Belgrade
- Serbia
| | - Ilija Brčeski
- Faculty of Chemistry
- University of Belgrade
- Belgrade
- Serbia
| | | | - Branka Lončarević
- Institute of Chemistry
- Technology and Metallurgy
- Department of Chemistry
- University of Belgrade
- Belgrade
| | - Kristina Gopčević
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- Belgrade
- Serbia
| | - Ivanka Karadžić
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- Belgrade
- Serbia
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20
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Xu J, Zhang L, Hou J, Wang X, Liu H, Zheng D, Liang R. iTRAQ-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain Pseudomonas putida SJTE-1. Sci Rep 2017; 7:41682. [PMID: 28155874 PMCID: PMC5290480 DOI: 10.1038/srep41682] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 12/23/2016] [Indexed: 11/28/2022] Open
Abstract
Microorganism degradation is efficient to remove the steroid hormones like 17β-estradiol (E2); but their degradation mechanism and metabolic network to these chemicals are still not very clear. Here the global responses of the estrogen-degradation strain Pseudomonas putida SJTE-1 to 17β-estradiol and glucose were analyzed and compared using the iTRAQ (isobaric tags for relative and absolute quantization) strategy combined with LC-MS/MS (liquid chromatography-tandem mass spectrometry). 78 proteins were identified with significant changes in expression; 45 proteins and 33 proteins were up-regulated and down-regulated, respectively. These proteins were mainly involved in the processes of stress response, energy metabolism, transportation, chemotaxis and cell motility, and carbon metabolism, considered probably responding to 17β-estradiol and playing a role in its metabolism. The up-regulated proteins in electron transfer, energy generation and transport systems were thought crucial for efficient uptake, translocation and transformation of 17β-estradiol. The over-expression of carbon metabolism proteins indicated cells may activate related pathway members to utilize 17β-estradiol. Meanwhile, proteins functioning in glucose capture and metabolism were mostly down-regulated. These findings provide important clues to reveal the 17β-estradiol degradation mechanism in P. putida and promote its bioremediation applications.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lei Zhang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jingli Hou
- Instrumental Analysis Center of Shanghai Jiaotong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Huan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Daning Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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Thatoi HN, Pradhan SK. Detoxification and Bioremediation of Hexavalent Chromium Using Microbes and Their Genes: An Insight into Genomic, Proteomic and Bioinformatics Studies. Microb Biotechnol 2017. [DOI: 10.1007/978-981-10-6847-8_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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22
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Teng L, Wang X, Wang X, Gou H, Ren L, Wang T, Wang Y, Ji Y, Huang WE, Xu J. Label-free, rapid and quantitative phenotyping of stress response in E. coli via ramanome. Sci Rep 2016; 6:34359. [PMID: 27756907 PMCID: PMC5069462 DOI: 10.1038/srep34359] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/13/2016] [Indexed: 12/12/2022] Open
Abstract
Rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. We propose a single-cell-level biochemical fingerprinting approach named “ramanome”, which is the collection of Single-cell Raman Spectra (SCRS) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population. SCRS of Escherichia coli cells are sensitive to both exposure time (eight time points) and dosage (six doses) of ethanol, with detection time as early as 5 min and discrimination rate of either factor over 80%. Moreover, the ramanomes upon six chemical compounds from three categories, including antibiotics of ampicillin and kanamycin, alcohols of ethanol and n-butanol and heavy metals of Cu2+ and Cr6+, were analyzed and 31 marker Raman bands were revealed which distinguish stress-responses via cytotoxicity mechanism and variation of inter-cellular heterogeneity. Furthermore, specificity, reproducibility and mechanistic basis of ramanome were validated by tracking stress-induced dynamics of metabolites and by contrasting between cells with and without genes that convey stress resistance. Thus ramanome enables rapid prediction and mechanism-based screening of cytotoxicity and stress-response programs at single-cell resolution.
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Affiliation(s)
- Lin Teng
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojun Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honglei Gou
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Lihui Ren
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Tingting Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yun Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Wei E Huang
- Department of Engineering, University of Oxford, Oxford, Parks Road, OX1 3PJ, UK
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
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23
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Branco R, Morais PV. Two superoxide dismutases from TnOtchr are involved in detoxification of reactive oxygen species induced by chromate. BMC Microbiol 2016; 16:27. [PMID: 26944876 PMCID: PMC4779226 DOI: 10.1186/s12866-016-0648-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background Superoxide dismutases (SOD) have been reported as the most relevant bacterial enzymes involved in cells protection from reactive oxygen species (ROS). These toxic species are often the product of heavy metal stress. Results Two genes, chrC and chrF, from TnOtchr genetic determinant of strain Ochrobactrum tritici 5bvl1 were cloned in Escherichia coli in order to overexpress the respective proteins. Both proteins were purified and characterized as superoxide dismutases. ChrC was confirmed as being a Fe-SOD, and the enzymatic activity of the ChrF, not inhibited by hydrogen peroxide or potassium cyanide, suggested its inclusion in the Mn-SOD family. This identification was supported by chemical quantification of total metal content in purified enzyme. Both enzymes showed a maximum activity between pH 7.2-7.5. ChrF retained nearly full activity over a broader range of pH and was slightly more thermostable than ChrC. The genes encoding these enzymes in strain O. tritici 5bvl1 were inactivated, developing single and double mutants, to understand the contribution of these enzymes in detoxification mechanism of reactive oxygen species induced by chromate. During chromate stress, assays using fluorescent dyes indicated an increase of these toxic compounds in chrC, chrF and chrC/chrF mutant cells. Conclusions In spite of the multiple genes coding for putative superoxide dismutase enzymes detected in the genome of O. tritici 5bvl1, the ChrC and ChrF might help the strain to decrease the levels of reactive oxygen species in cells.
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Affiliation(s)
- Rita Branco
- CEMUC-Department of Mechanical Engineering, University of Coimbra, 3030-788, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, 3001-401, Coimbra, Portugal.
| | - Paula V Morais
- CEMUC-Department of Mechanical Engineering, University of Coimbra, 3030-788, Coimbra, Portugal. .,Department of Life Sciences, University of Coimbra, 3001-401, Coimbra, Portugal.
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24
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Herbst FA, Danielsen HN, Wimmer R, Nielsen PH, Dueholm MS. Label-free quantification reveals major proteomic changes in Pseudomonas putida F1 during the exponential growth phase. Proteomics 2015; 15:3244-52. [PMID: 26122999 DOI: 10.1002/pmic.201400482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 04/30/2015] [Accepted: 06/26/2015] [Indexed: 01/12/2023]
Abstract
The physiological adaptation to stationary growth by Pseudomonas putida F1, a model organism for the degradation of aromatic compounds, was investigated by proteome-wide label-free quantification.The data unveiled that entrance to the stationary phase did not involve an abrupt switch within the P. putida F1 proteome, but rather an ongoing adaptation that started already during the mid-exponential growth phase. The proteomic adaptations involved a clear increase in amino acid degradation capabilities and a loss of transcriptional as well as translational capacity. The final entrance to the stationary phase was accompanied by increased oxidative stress protection, although the stress and stationary sigma factor RpoS increased in abundance already during mid-exponential growth. The results show that it is important to consider significant sample variations when exponentially growing cultures are studied alone or compared across proteomic or transcriptomic literature. All MS data have been deposited in the ProteomeXchange with identifier PXD001219 (http://proteomecentral.proteomexchange.org/dataset/PXD001219).
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Affiliation(s)
- Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Heidi Nolsøe Danielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Reinhard Wimmer
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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25
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Chua SL, Sivakumar K, Rybtke M, Yuan M, Andersen JB, Nielsen TE, Givskov M, Tolker-Nielsen T, Cao B, Kjelleberg S, Yang L. C-di-GMP regulates Pseudomonas aeruginosa stress response to tellurite during both planktonic and biofilm modes of growth. Sci Rep 2015; 5:10052. [PMID: 25992876 PMCID: PMC4438720 DOI: 10.1038/srep10052] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/20/2015] [Indexed: 11/09/2022] Open
Abstract
Stress response plays an important role on microbial adaptation under hostile environmental conditions. It is generally unclear how the signaling transduction pathway mediates a stress response in planktonic and biofilm modes of microbial communities simultaneously. Here, we showed that metalloid tellurite (TeO3(2-)) exposure induced the intracellular content of the secondary messenger cyclic di-GMP (c-di-GMP) of Pseudomonas aeruginosa. Two diguanylate cyclases (DGCs), SadC and SiaD, were responsible for the increased intracellular content of c-di-GMP. Enhanced c-di-GMP levels by TeO3(2-) further increased P. aeruginosa biofilm formation and resistance to TeO3(2-). P. aeruginosa ΔsadCΔsiaD and PAO1/p(lac)-yhjH mutants with low intracellular c-di-GMP content were more sensitive to TeO3(2-) exposure and had low relative fitness compared to the wild-type PAO1 planktonic and biofilm cultures exposed to TeO3(2-). Our study provided evidence that c-di-GMP level can play an important role in mediating stress response in microbial communities during both planktonic and biofilm modes of growth.
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Affiliation(s)
- Song Lin Chua
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore 117543
| | - Krishnakumar Sivakumar
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551
| | - Morten Rybtke
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Mingjun Yuan
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Jens Bo Andersen
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Thomas E Nielsen
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551
| | - Michael Givskov
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, 2200 København N, Denmark
| | - Bin Cao
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Staffan Kjelleberg
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] Center for Marine Bio-Innovation and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Liang Yang
- 1] Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637551 [2] School of Biological Sciences, Nanyang Technological University, Singapore 637551
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26
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Comparative proteomics reveal the impact of OmcA/MtrC deletion on Shewanella oneidensis MR-1 in response to hexavalent chromium exposure. Appl Microbiol Biotechnol 2014; 98:9735-47. [PMID: 25341401 DOI: 10.1007/s00253-014-6143-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 09/29/2014] [Accepted: 10/04/2014] [Indexed: 10/24/2022]
Abstract
Hexavalent chromium [Cr(VI)] is a priority pollutant causing serious environmental issues. Microbial reduction provides an alternative strategy for Cr(VI) remediation. The dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, was employed to study Cr(VI) reduction and toxicity in this work. To understand the effect of membrane cytochromes on Cr(VI) response, a comparative protein profile analysis from S. oneidensis MR-1 wild type and its mutant of deleting OmcA and MtrC (△omcA/mtrC) was conducted using two-dimensional electrophoresis (2-DE) technology. The 2-DE patterns were compared, and the proteins with abundant changes of up to twofold in the Cr(VI) treatment were detected. Using mass spectrometry, 38 and 45 differentially abundant proteins were identified in the wild type and the mutant, respectively. Among them, 25 proteins were shared by the two strains. The biological functions of these identified proteins were analyzed. Results showed that Cr(VI) exposure decreased the abundance of proteins involved in transcription, translation, pyruvate metabolism, energy production, and function of cellular membrane in both strains. There were also significant differences in protein expressions between the two strains under Cr(VI) treatment. Our results suggest that OmcA/MtrC deletion might result in the Cr(VI) toxicity to outer membrane and decrease assimilation of lactate, vitamin B12, and cystine. When carbohydrate metabolism was inhibited by Cr(VI), leucine and sulfur metabolism may act as the important compensatory mechanisms in the mutant. Furthermore, the mutant may regulate electron transfer in the inner membrane and periplasm to compensate for the deletion of OmcA and MtrC in Cr(VI) reduction.
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27
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Yung MC, Ma J, Salemi MR, Phinney BS, Bowman GR, Jiao Y. Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium. J Proteome Res 2014; 13:1833-47. [PMID: 24555639 DOI: 10.1021/pr400880s] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ubiquitous bacterium Caulobacter crescentus holds promise to be used in bioremediation applications due to its ability to mineralize U(VI) under aerobic conditions. Here, cell free extracts of C. crescentus grown in the presence of uranyl nitrate [U(VI)], potassium chromate [Cr(VI)], or cadmium sulfate [Cd(II)] were used for label-free proteomic analysis. Proteins involved in two-component signaling and amino acid metabolism were up-regulated in response to all three metals, and proteins involved in aerobic oxidative phosphorylation and chemotaxis were down-regulated under these conditions. Clustering analysis of proteomic enrichment revealed that the three metals also induce distinct patterns of up- or down-regulated expression among different functional classes of proteins. Under U(VI) exposure, a phytase enzyme and an ABC transporter were up-regulated. Heat shock and outer membrane responses were found associated with Cr(VI), while efflux pumps and oxidative stress proteins were up-regulated with Cd(II). Experimental validations were performed on select proteins. We found that a phytase plays a role in U(VI) and Cr(VI) resistance and detoxification and that a Cd(II)-specific transporter confers Cd(II) resistance. Interestingly, analysis of promoter regions in genes associated with differentially expressed proteins suggests that U(VI) exposure affects cell cycle progression.
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Affiliation(s)
- Mimi C Yung
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
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28
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Codreanu SG, Ullery JC, Zhu J, Tallman KA, Beavers WN, Porter NA, Marnett LJ, Zhang B, Liebler DC. Alkylation damage by lipid electrophiles targets functional protein systems. Mol Cell Proteomics 2014; 13:849-59. [PMID: 24429493 PMCID: PMC3945913 DOI: 10.1074/mcp.m113.032953] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein alkylation by reactive electrophiles contributes to chemical toxicities and oxidative stress, but the functional impact of alkylation damage across proteomes is poorly understood. We used Click chemistry and shotgun proteomics to profile the accumulation of proteome damage in human cells treated with lipid electrophile probes. Protein target profiles revealed three damage susceptibility classes, as well as proteins that were highly resistant to alkylation. Damage occurred selectively across functional protein interaction networks, with the most highly alkylation-susceptible proteins mapping to networks involved in cytoskeletal regulation. Proteins with lower damage susceptibility mapped to networks involved in protein synthesis and turnover and were alkylated only at electrophile concentrations that caused significant toxicity. Hierarchical susceptibility of proteome systems to alkylation may allow cells to survive sublethal damage while protecting critical cell functions.
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Affiliation(s)
- Simona G Codreanu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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29
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Viti C, Marchi E, Decorosi F, Giovannetti L. Molecular mechanisms of Cr(VI) resistance in bacteria and fungi. FEMS Microbiol Rev 2013; 38:633-59. [PMID: 24188101 DOI: 10.1111/1574-6976.12051] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/13/2013] [Accepted: 10/28/2013] [Indexed: 11/28/2022] Open
Abstract
Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.
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Affiliation(s)
- Carlo Viti
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente - sezione di Microbiologia, Università degli Studi di Firenze, Florence, Italy
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Mandalakis M, Panikov N, Dai S, Ray S, Karger BL. Comparative proteomic analysis reveals mechanistic insights into Pseudomonas putida F1 growth on benzoate and citrate. AMB Express 2013; 3:64. [PMID: 24156539 PMCID: PMC3827995 DOI: 10.1186/2191-0855-3-64] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022] Open
Abstract
Pseudomonas species are capable to proliferate under diverse environmental conditions and thus have a significant bioremediation potential. To enhance our understanding of their metabolic versatility, this study explores the changes in the proteome and physiology of Pseudomonas putida F1 resulting from its growth on benzoate, a moderate toxic compound that can be catabolized, and citrate, a carbon source that is assimilated through central metabolic pathways. A series of repetitive batch cultivations were performed to ensure a complete adaptation of the bacteria to each of these contrasting carbon sources. After several growth cycles, cell growth stabilized at the maximum level and exhibited a reproducible growth profile. The specific growth rates measured for benzoate (1.01 ± 0.11 h-1) and citrate (1.11 ± 0.12 h-1) were similar, while a higher yield was observed for benzoate (0.6 and 0.3 g cell mass per g of benzoate and citrate, respectively), reflecting the different degrees of carbon reduction in the two substrates. Comparative proteomic analysis revealed an enrichment of several oxygenases/dehydrogenases in benzoate-grown cells, indicative of the higher carbon reduction of benzoate. Moreover, the upregulation of all 14 proteins implicated in benzoate degradation via the catechol ortho-cleavage pathway was observed, while several stress-response proteins were increased to aid cells to cope with benzoate toxicity. Unexpectedly, citrate posed more challenges than benzoate in the maintenance of pH homeostasis, as indicated by the enhancement of the Na+/H+ antiporter and carbonic anhydrase. The study provides important mechanistic insights into Pseudomonas adaptation to varying carbon sources that are of great relevance to bioremediation efforts.
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31
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Gene expression profiling of Pseudomonas putida F1 after exposure to aromatic hydrocarbon in soil by using proteome analysis. Arch Microbiol 2013; 195:805-13. [DOI: 10.1007/s00203-013-0932-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/27/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
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32
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Moreno R, Rojo F. The contribution of proteomics to the unveiling of the survival strategies used by Pseudomonas putida
in changing and hostile environments. Proteomics 2013; 13:2822-30. [DOI: 10.1002/pmic.201200503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/26/2013] [Accepted: 03/28/2013] [Indexed: 01/14/2023]
Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología; CSIC Madrid Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología; CSIC Madrid Spain
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33
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Comparative c-type cytochrome expression analysis in Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C grown with soluble and insoluble oxidized metal electron acceptors. Biochem Soc Trans 2013; 40:1204-10. [PMID: 23176455 DOI: 10.1042/bst20120182] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The genomes of Shewanella oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C encode 40 and 69 putative c-type cytochrome genes respectively. Deletion mutant and biochemical studies have assigned specific functions to a few c-type cytochromes involved in electron transfer to oxidized metals in S. oneidensis strain MR-1. Although promising, the genetic approach is limited to gene deletions that produce a distinct phenotype and to an organism for which a genetic system is available. To investigate and compare c-type cytochrome expression in S. oneidensis strain MR-1 and Anaeromyxobacter dehalogenans strain 2CP-C more comprehensively, proteomic measurements were used to characterize lysates of cells grown with soluble Fe(III) (as ferric citrate) and insoluble Mn(IV) (as MnO2) as electron acceptors. Strain MR-1 expressed 19 and 20, and strain 2CP-C expressed 27 and 25, c-type cytochromes when grown with Fe(III) and Mn(IV) respectively. The majority of c-type cytochromes (77% for strain MR-1 and 63% for strain 2CP-C) were expressed under both growth conditions; however, the analysis also revealed unique c-type cytochromes that were specifically expressed in cells grown with soluble Fe(III) or insoluble Mn(IV). Proteomic characterization proved to be a promising approach for determining the c-type cytochrome complement expressed under different growth conditions, and will help to elucidate the specific functions of more c-type cytochromes that are the basis for Shewanella and Anaeromyxobacter respiratory versatility.
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Poirier I, Hammann P, Kuhn L, Bertrand M. Strategies developed by the marine bacterium Pseudomonas fluorescens BA3SM1 to resist metals: A proteome analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2013; 128-129:215-32. [PMID: 23314334 DOI: 10.1016/j.aquatox.2012.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 12/05/2012] [Accepted: 12/09/2012] [Indexed: 05/17/2023]
Abstract
A global proteomic evaluation of the response of the marine bacterium Pseudomonas fluorescens BA3SM1 to Cd, Zn and Cu was performed by two dimensional gel electrophoresis followed by mass spectrometry. When stressed with Cd, the most toxic metal for P. fluorescens BA3SM1, cell growth is rapidly affected and the number of proteins up-regulated (sixteen for 0.4 mM Cd) remains low in comparison with results obtained for Zn and Cu (twenty eight for 1.5mM Zn and forty four for 1.5 mM Cu). The changes in protein expression indicate that the cell adapts to metals by inducing essentially seven defense mechanisms: cell aggregation/biofilm formation (Zn=Cu>Cd); modification of envelope properties to increase the extracellular metal biosorption and/or control the uptake of metal (Cu>Zn); metal export (Cd=Zn and probably Cu); responses to oxidative stress (Cu>Zn>Cd); intracellular metal sequestration (Zn=Cu and probably Cd); hydrolysis of abnormally folded proteins (Cd=Cu), and the over-synthesis of proteins inhibited by metal (Cd>Cu>Zn). To the best of our knowledge, this is the first report showing that a marine P. fluorescens is able to acquire a metal-resistant phenotype, making the strain BA3SM1 a promising agent for bioremediation processes.
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Affiliation(s)
- Isabelle Poirier
- Microorganismes Métaux et Toxicité, Institut National des Sciences et Techniques de la Mer, Conservatoire National des Arts et Métiers, Cherbourg-Octeville, France.
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Kohler C, Lourenço RF, Avelar GM, Gomes SL. Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress. BMC Microbiol 2012; 12:210. [PMID: 22985357 PMCID: PMC3511200 DOI: 10.1186/1471-2180-12-210] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/10/2012] [Indexed: 11/26/2022] Open
Abstract
Background The α-proteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metals in these sites. It has been reported that C. crescentus responds to exposure to various heavy metals by altering the expression of a large number of genes. Results In this work, we show that the ECF sigma factor σF is one of the regulatory proteins involved in the control of the transcriptional response to chromium and cadmium. Microarray experiments indicate that σF controls eight genes during chromium stress, most of which were previously described as induced by heavy metals. Surprisingly, σF itself is not strongly auto-regulated under metal stress conditions. Interestingly, σF-dependent genes are not induced in the presence of agents that generate reactive oxygen species. Promoter analyses revealed that a conserved σF-dependent sequence is located upstream of all genes of the σF regulon. In addition, we show that the second gene in the sigF operon acts as a negative regulator of σF function, and the encoded protein has been named NrsF (Negative regulator of sigma F). Substitution of two conserved cysteine residues (C131 and C181) in NrsF affects its ability to maintain the expression of σF-dependent genes at basal levels. Furthermore, we show that σF is released into the cytoplasm during chromium stress and in cells carrying point mutations in both conserved cysteines of the protein NrsF. Conclusion A possible mechanism for induction of the σF-dependent genes by chromium and cadmium is the inactivation of the putative anti-sigma factor NrsF, leading to the release of σF to bind RNA polymerase core and drive transcription of its regulon.
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Affiliation(s)
- Christian Kohler
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av, Prof, Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
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Manara A, DalCorso G, Baliardini C, Farinati S, Cecconi D, Furini A. Pseudomonas putida Response to Cadmium: Changes in Membrane and Cytosolic Proteomes. J Proteome Res 2012; 11:4169-79. [DOI: 10.1021/pr300281f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Manara
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Giovanni DalCorso
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Cecilia Baliardini
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Silvia Farinati
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Daniela Cecconi
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Antonella Furini
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134 Verona, Italy
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Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, VerBerkmoes NC. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One 2012; 7:e38077. [PMID: 22666452 PMCID: PMC3364186 DOI: 10.1371/journal.pone.0038077] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/30/2012] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response in S. thermophilus DGCC7710 infected with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectrometry. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance following infection, including the signature Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.
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Affiliation(s)
- Jacque C. Young
- Graduate School for Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Brian D. Dill
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Manesh Shah
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | - Rodolphe Barrangou
- DuPont Nutrition and Health, Madison, Wisconsin, United States of America
| | - Nathan C. VerBerkmoes
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Li Z, Adams RM, Chourey K, Hurst GB, Hettich RL, Pan C. Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos. J Proteome Res 2012; 11:1582-90. [PMID: 22188275 DOI: 10.1021/pr200748h] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these methods were compared in terms of the depth of proteome coverage, quantification accuracy, precision, and reproducibility using a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) the spectral counting method provides the deepest proteome coverage for identification, but its quantification performance is worse than labeling-based approaches, especially the quantification reproducibility; (2) metabolic labeling and isobaric chemical labeling are capable of accurate, precise, and reproducible quantification and provide deep proteome coverage for quantification; isobaric chemical labeling surpasses metabolic labeling in terms of quantification precision and reproducibility; and (3) iTRAQ and TMT perform similarly in all aspects compared in the current study using a CID-HCD dual scan configuration. On the basis of the unique advantages of each method, we provide guidance for selection of the appropriate method for a quantitative proteomics study.
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Affiliation(s)
- Zhou Li
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory , Knoxville, Tennessee 37996, United States
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Sulpizio M, Falone S, Amicarelli F, Marchisio M, Di Giuseppe F, Eleuterio E, Di Ilio C, Angelucci S. Molecular basis underlying the biological effects elicited by extremely low-frequency magnetic field (ELF-MF) on neuroblastoma cells. J Cell Biochem 2011; 112:3797-806. [DOI: 10.1002/jcb.23310] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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40
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Braconi D, Bernardini G, Santucci A. Linking protein oxidation to environmental pollutants: redox proteomic approaches. J Proteomics 2011; 74:2324-37. [PMID: 21767673 DOI: 10.1016/j.jprot.2011.06.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 06/17/2011] [Accepted: 06/28/2011] [Indexed: 12/11/2022]
Abstract
Environmental pollutants, such as compounds used in agriculture or deriving from vehicles, industries and human activities, can represent major concern for human health since they are considered to contribute significantly to many diseased states with major public health significance. Besides considerable epidemiological evidence linking environmental pollutants with adverse health effects, little information is provided on the effects of these compounds at the cellular and molecular level. Though oxidative stress is generally acknowledged as one of the most important mechanisms of action for pollutant-induced toxicity, redox proteomics, the elective tool to identify post-translationally oxidized proteins, is still in its very infancy in this field of investigation. This review will provide the readers with an outline of the use of redox proteomics in evaluating pollutant-induced oxidative damage to proteins in various biological systems. Future potential applications of redox proteomic approaches from an environmental point of view will be discussed as well.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Università degli Studi di Siena, SI, Italy
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41
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Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, Tom LM, Brodie EL, Hettich RL. Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res 2010; 9:6615-22. [PMID: 20954746 DOI: 10.1021/pr100787q] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a novel direct protocol for deep proteome characterization of microorganisms in soil. The method employs thermally assisted detergent-based cellular lysis (SDS) of soil samples, followed by TCA precipitation for proteome extraction/cleanup prior to liquid chromatography-mass spectrometric characterization. This approach was developed and optimized using different soils inoculated with genome-sequenced bacteria (Gram-negative Pseudomonas putida or Gram-positive Arthrobacter chlorophenolicus). Direct soil protein extraction was compared to protein extraction from cells isolated from the soil matrix prior to lysis (indirect method). Each approach resulted in identification of greater than 500 unique proteins, with a wide range in molecular mass and functional categories. To our knowledge, this SDS-TCA approach enables the deepest proteome characterizations of microbes in soil to date, without significant biases in protein size, localization, or functional category compared to pure cultures. This protocol should provide a powerful tool for ecological studies of soil microbial communities.
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Affiliation(s)
- Karuna Chourey
- Oak Ridge National Laboratory, Tennessee 37831-6131, United States
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