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Fernandez M, Callegari EA, Paez MD, González PS, Agostini E. Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress. Biometals 2023; 36:1081-1108. [PMID: 37209221 DOI: 10.1007/s10534-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/24/2023] [Indexed: 05/22/2023]
Abstract
Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.
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Affiliation(s)
- Marilina Fernandez
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina.
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina.
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María D Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Paola S González
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
| | - Elizabeth Agostini
- Departamento de Biología Molecular, FCEFQyN, Universidad Nacional de Río Cuarto (UNRC), Ruta 36 Km 601, CP 5800, Río Cuarto, Córdoba, Argentina
- CONICET, Instituto de Biotecnología Ambiental y Salud (INBIAS), Río Cuarto, Córdoba, Argentina
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Sahoo H, Kumari S, Naik UC. Characterization of multi-metal-resistant Serratia sp. GP01 for treatment of effluent from fertilizer industries. Arch Microbiol 2021; 203:5425-5435. [PMID: 34405261 DOI: 10.1007/s00203-021-02523-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 12/29/2022]
Abstract
The effluent generated from fertilizer plants in Paradeep in the coast of the Bay of Bengal is the major pollutant causing health hazard in the vicinity of the area with respect to plants, animals and microbes. Samples of effluent were found to contain heavy metals (mg L-1): Cr (100), Ni (36.975), Mn (68.673), Pb (20.133), Cu (74.44), Zn (176.716), Hg (5.358) and As (24.287) as analyzed by XRF. Indigenous bacterial strains were screened for chromate and multi-metal resistance to remediate the toxic pollutants. The isolated strain G1 was identified as Serratia sp. through 16S-rDNA sequence homology. The potent strain Serratia sp. GP01 treated with 100 mg L-1 of K2Cr2O7 has shown the efficacy of reducing 69.05 mg L-1 of Cr over 48 h of incubation. Further, presence of chromate reductase gene (ChR) in Serratia sp. confirmed the enzymatic reduction of Cr(VI). SEM-EDX and SEM mapping analysis revealed substantial biosorption of Cr and other heavy metals present in effluent by Serratia sp. GP01. Antioxidant enzymes such as catalase (72.15 U mL-1), SOD (57.14 U mL-1) and peroxidase (62.49 U mL-1) were found to be higher as compared to the control condition. FTIR study also revealed the role of N-H, O-H, C = C, C-H, C-O, C-N, and C = O functional groups of the cell surface of Serratia sp. treated with K2Cr2O7 and effluent from the fertilizer industry. Isolated strain Serratia sp. could be used for the detoxification of Cr(VI) and other heavy metals in fertilizer plant effluent.
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Affiliation(s)
- Hrudananda Sahoo
- Environmental Microbiology Laboratory, Department of Botany, Ravenshaw University, Cuttack, 753003, India
| | - Sushama Kumari
- Environmental Microbiology Laboratory, Department of Botany, Ravenshaw University, Cuttack, 753003, India
| | - Umesh Chandra Naik
- Environmental Microbiology Laboratory, Department of Botany, Ravenshaw University, Cuttack, 753003, India. .,Centre of Excellence in Environment and Public Health, Ravenshaw University, Cuttack, 753003, India.
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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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You X, Xu N, Yang X, Sun W. Pollutants affect algae-bacteria interactions: A critical review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 276:116723. [PMID: 33611207 DOI: 10.1016/j.envpol.2021.116723] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
With increasing concerns on the ecological risks of pollutants, many efforts have been devoted to revealing the toxic effects of pollutants on algae or bacteria in their monocultures. However, how pollutants affect algae and bacteria in their cocultures is still elusive but crucial due to its more environmental relevance. The present review outlines the interactions between algae and bacteria, reveals the influential mechanisms of pollutants (including pesticides, metals, engineered nanomaterials, pharmaceutical and personal care products, and aromatic pollutants) to algae and bacteria in their coexisted systems, and puts forward prospects for further advancing toxic studies in algal-bacterial systems. Pollutants affect the physiological and ecological functions of bacteria and algae by interfering with their relationships. Cell-to-cell adhesion, substrate exchange and biodegradation of organic pollutants, enhancement of signal transduction, and horizontal transfer of tolerance genes are important defense strategies in algal-bacterial systems to cope with pollution stress. Developing suitable algal-bacterial models, identifying cross-kingdom signaling molecules, and deciphering the horizontal transfer of pollutant resistant genes between algae and bacteria under pollution stress are the way forward to fully exploit the risks of pollutants in natural aquatic environments.
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Affiliation(s)
- Xiuqi You
- College of Environmental Sciences and Engineering, Peking University, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing, 100871, China
| | - Nan Xu
- Shenzhen Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xi Yang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing, 100871, China.
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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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Orellana LH, Hatt JK, Iyer R, Chourey K, Hettich RL, Spain JC, Yang WH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. Sci Rep 2019; 9:17630. [PMID: 31772206 PMCID: PMC6879594 DOI: 10.1038/s41598-019-53679-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/14/2019] [Indexed: 01/29/2023] Open
Abstract
To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.
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Affiliation(s)
- Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Laboratorio de Enteropatogenos, Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida, USA
| | - Wendy H Yang
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joanne C Chee-Sanford
- U.S. Department of Agriculture, Agricultural Research Service, Urbana, Illinois, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, and Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Gang H, Xiao C, Xiao Y, Yan W, Bai R, Ding R, Yang Z, Zhao F. Proteomic analysis of the reduction and resistance mechanisms of Shewanella oneidensis MR-1 under long-term hexavalent chromium stress. ENVIRONMENT INTERNATIONAL 2019; 127:94-102. [PMID: 30909098 DOI: 10.1016/j.envint.2019.03.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/25/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Hexavalent chromium [Cr(VI)] is a priority heavy metal pollutant causing a series of environmental issues, and bio-reduction of Cr(VI) to trivalent chromium can remarkably decrease the environmental risk of Cr(VI). The reduction and resistance abilities of microorganisms to Cr(VI) can be dramatically improved by acclimatization. In the present study, we collected Shewanella oneidensis MR-1 from a 120-day acclimatization by increasing Cr(VI) concentration in the culture media to investigate its adaptation mechanisms under long-term Cr(VI) stress at the proteome level. Tandem mass tag-based quantitative proteomic analysis was performed to study the differences between 9 collected samples. A total of 2500 proteins were quantified from 2723 identified protein groups. Bioinformatics analysis showed that the differentially expressed proteins after the 120-day Cr(VI) acclimatization were mostly related to flagellar assembly, ribosomes, transport, sulfur metabolism, and energy metabolism. The findings of this study present novel insights into the molecular mechanisms for the reduction and resistance of S. oneidensis MR-1 responding to long-term Cr(VI) stress at the proteome level.
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Affiliation(s)
- Haiyin Gang
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Changye Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weifu Yan
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Rui Bai
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Ding
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaohui Yang
- Key Laboratory of Environmental Biology and Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Hunan University, Changsha 410082, China.
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Suzuki H. Remarkable diversification of bacterial azoreductases: primary sequences, structures, substrates, physiological roles, and biotechnological applications. Appl Microbiol Biotechnol 2019; 103:3965-3978. [PMID: 30941462 DOI: 10.1007/s00253-019-09775-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022]
Abstract
Azoreductases reductively cleave azo linkages by using NAD(P)H as an electron donor. The enzymes are widely found in bacteria and act on numerous azo dyes, which allow various unique applications. This review describes primary amino acid sequences, structures, substrates, physiological roles, and biotechnological applications of bacterial azoreductases to discuss their remarkable diversification. According to primary sequences, azoreductases were classified phylogenetically into four main clades. Most members of clades I-III are flavoproteins, whereas clade IV members include flavin-free azoreductases. Clades I and II prefer NADPH and NADH, respectively, as electron donors, whereas other members generally use both. Several enzymes formed no clades; moreover, some bacteria produce azoreductases with longer primary structures than those hitherto identified, which implies further diversification of bacterial azoreductases. The crystal structures commonly reveal the Rossmann folds; however, ternary structures are moderately varied with different quaternary conformation. Although physiological roles are obscure, several azoreductases have been shown to act on metabolites such as flavins, quinones, and metal ions more efficiently than on azo dyes. Considering that many homologs exclusively act on these metabolites, it is possible that azoreductases are actually side activities of versatile reductases that act on various substrates with different specificities. In parallel, this idea raises the possibility that homologous enzymes, even if these are already defined as other types of reductases, widely harbor azoreductase activities. Although azoreductases for which their genes have been identified are not abundant, it may be simple to identify azoreductases of biotechnological importance that have novel substrate specificities.
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Affiliation(s)
- Hirokazu Suzuki
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan. .,Center for Research on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.
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Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism. Appl Environ Microbiol 2019; 85:AEM.02768-18. [PMID: 30658979 DOI: 10.1128/aem.02768-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/08/2019] [Indexed: 11/20/2022] Open
Abstract
Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCE Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium Dehalobacterium formicoaceticum and "Candidatus Dichloromethanomonas elyunquensis" strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.
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Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ. Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. Front Microbiol 2018; 9:2917. [PMID: 30559729 PMCID: PMC6286981 DOI: 10.3389/fmicb.2018.02917] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/13/2018] [Indexed: 01/17/2023] Open
Abstract
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.
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Affiliation(s)
- Hang Yu
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States.,Ronald and Maxine Linde Center for Global Environmental Science, California Institute of Technology, Pasadena, CA, United States
| | - Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Connor T Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Silvan Scheller
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, United States
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11
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Estenson K, Hurst GB, Standaert RF, Bible AN, Garcia D, Chourey K, Doktycz MJ, Morrell-Falvey JL. Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343. J Proteome Res 2018; 17:1361-1374. [PMID: 29464956 DOI: 10.1021/acs.jproteome.7b00708] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indole-3-acetic acid (IAA) plays a central role in plant growth and development, and many plant-associated microbes produce IAA using tryptophan as the precursor. Using genomic analyses, we predicted that Pantoea sp. YR343, a microbe isolated from Populus deltoides, synthesizes IAA using the indole-3-pyruvate (IPA) pathway. To better understand IAA biosynthesis and the effects of IAA exposure on cell physiology, we characterized proteomes of Pantoea sp. YR343 grown in the presence of tryptophan or IAA. Exposure to IAA resulted in upregulation of proteins predicted to function in carbohydrate and amino acid transport and exopolysaccharide (EPS) biosynthesis. Metabolite profiles of wild-type cells showed the production of IPA, IAA, and tryptophol, consistent with an active IPA pathway. Finally, we constructed an Δ ipdC mutant that showed the elimination of tryptophol, consistent with a loss of IpdC activity, but was still able to produce IAA (20% of wild-type levels). Although we failed to detect intermediates from other known IAA biosynthetic pathways, this result suggests the possibility of an alternate pathway or the production of IAA by a nonenzymatic route in Pantoea sp. YR343. The Δ ipdC mutant was able to efficiently colonize poplar, suggesting that an active IPA pathway is not required for plant association.
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Affiliation(s)
- Kasey Estenson
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | | | - Robert F Standaert
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Shull Wollan Center - a Joint Institute for Neutron Sciences , Oak Ridge , Tennessee 37831 , United States
| | - Amber N Bible
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - David Garcia
- Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | | | - Mitchel J Doktycz
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Bredesen Center , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Jennifer L Morrell-Falvey
- UT-ORNL Graduate School of Genome Science and Technology , University of Tennessee , Knoxville , Tennessee 37996 , United States.,Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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12
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Raymond-Bouchard I, Chourey K, Altshuler I, Iyer R, Hettich RL, Whyte LG. Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis. Environ Microbiol 2017; 19:4460-4479. [PMID: 28834033 DOI: 10.1111/1462-2920.13893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/13/2017] [Indexed: 01/22/2023]
Abstract
The eurypsychrophilic bacterium Planococcus halocryophilus is capable of growth down to -15°C, making it ideal for studying adaptations to subzero growth. To increase our understanding of the mechanisms and pathways important for subzero growth, we performed proteomics on P. halocryophilus grown at 23°C, 23°C with 12% w/v NaCl and -10°C with 12% w/v NaCl. Many proteins with increased abundances at -10°C versus 23°C also increased at 23C-salt versus 23°C, indicating a closely tied relationship between salt and cold stress adaptation. Processes which displayed the largest changes in protein abundance were peptidoglycan and fatty acid (FA) synthesis, translation processes, methylglyoxal metabolism, DNA repair and recombination, and protein and nucleotide turnover. We identified intriguing targets for further research at -10°C, including PlsX and KASII (FA metabolism), DD-transpeptidase and MurB (peptidoglycan synthesis), glyoxalase family proteins (reactive electrophile response) and ribosome modifying enzymes (translation turnover). PemK/MazF may have a crucial role in translational reprogramming under cold conditions. At -10°C P. halocryophilus induces stress responses, uses resources efficiently, and carefully controls its growth and metabolism to maximize subzero survival. The present study identifies several mechanisms involved in subzero growth and enhances our understanding of cold adaptation.
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Affiliation(s)
- Isabelle Raymond-Bouchard
- Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
| | - Ianina Altshuler
- Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA
| | - Lyle G Whyte
- Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
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13
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Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea. mBio 2017; 8:mBio.00530-17. [PMID: 28765215 PMCID: PMC5539420 DOI: 10.1128/mbio.00530-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors. Some archaea, known as anaerobic methanotrophs, are capable of converting methane into carbon dioxide when they are growing syntopically with sulfate-reducing bacteria. This partnership is the primary mechanism for methane removal in ocean sediments; however, there is still much to learn about how this syntrophy works. Previous studies have failed to identify the metabolic intermediate, such as hydrogen or formate, that is passed between partners. However, recent analysis of methanotrophic archaea has suggested that the syntrophy is formed through direct electron transfer. In this research, we analyzed the genomes of multiple partner bacteria and showed that they also contain the genes necessary to perform extracellular electron transfer, which are absent in related bacteria that do not form syntrophic partnerships with anaerobic methanotrophs. This genomic evidence shows a possible mechanism for direct electron transfer from methanotrophic archaea into the metabolism of the partner bacteria.
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14
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Meyers A, Chourey K, Weiskittel TM, Pfiffner S, Dunlap JR, Hettich RL, Dalhaimer P. The protein and neutral lipid composition of lipid droplets isolated from the fission yeast, Schizosaccharomyces pombe. J Microbiol 2017; 55:112-122. [PMID: 28120187 DOI: 10.1007/s12275-017-6205-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/04/2016] [Accepted: 10/20/2016] [Indexed: 12/17/2022]
Abstract
Lipid droplets consist of a core of neutral lipids surrounded by a phospholipid monolayer with bound proteins. Much of the information on lipid droplet function comes from proteomic and lipodomic studies that identify the components of droplets isolated from organisms throughout the phylogenetic tree. Here, we add to that important inventory by reporting lipid droplet factors from the fission yeast, Schizosaccharomyces pombe. Unique to this study was the fact that cells were cultured in three different environments: 1) late log growth phase in glucose-based media, 2) stationary phase in glucosebased media, and 3) late log growth phase in media containing oleic acid. We confirmed colocalization of major factors with lipid droplets using live-cell fluorescent microscopy. We also analyzed droplets from each of the three conditions for sterol ester (SE) and triacylglycerol (TAG) content, along with their respective fatty acid compositions. We identified a previously undiscovered lipid droplet protein, Vip1p, which affects droplet size distribution. The results provide further insight into the workings of these ubiquitous organelles.
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Affiliation(s)
- Alex Meyers
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996-2200, USA
| | - Karuna Chourey
- Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Taylor M Weiskittel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996-2200, USA
| | - Susan Pfiffner
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - John R Dunlap
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.,Advanced Microscopy and Imaging Center, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Paul Dalhaimer
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996-2200, USA. .,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA. .,Institute of Biomedical Engineering, University of Tennessee, Knoxville, TN, 37996, USA.
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15
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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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16
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Fowler GJS, Pereira-Medrano AG, Jaffe S, Pasternak G, Pham TK, Ledezma P, Hall STE, Ieropoulos IA, Wright PC. An iTRAQ characterisation of the role of TolC during electron transfer from Shewanella oneidensis MR-1. Proteomics 2016; 16:2764-2775. [PMID: 27599463 DOI: 10.1002/pmic.201500538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 07/20/2016] [Accepted: 09/02/2016] [Indexed: 02/04/2023]
Abstract
Anodophilic bacteria have the ability to generate electricity in microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigated the anode-specific responses of Shewanella oneidensis MR-1, an exoelectroactive Gammaproteobacterium, using for the first time iTRAQ and 2D-LC MS/MS driven membrane proteomics to compare protein abundances in S. oneidensis when generating power in MFCs, and growing in a continuous culture. The regulated dataset produced was enriched in membrane proteins. Proteins shown to be more abundant in anaerobic electroactive anodic cells included efflux pump TolC and an uncharacterised tetratricopeptide repeat (TPR) protein, whilst the TonB2 system and associated uncharacterised proteins such as TtpC2 and DUF3450 were more abundant in microaerobic planktonic cells. In order to validate the iTRAQ data, the functional role for TolC was examined using a δTolC knockout mutant of S. oneidensis. Possible roles for the uncharacterised proteins were identified using comparative bioinformatics. We demonstrate that employing an insoluble extracellular electron acceptor requires multiple proteins involved in cell surface properties. All MS and processed data are available via ProteomeXchange with identifier PXD004090.
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Affiliation(s)
- Gregory J S Fowler
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ana G Pereira-Medrano
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Stephen Jaffe
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Grzegorz Pasternak
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Trong Khoa Pham
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Pablo Ledezma
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Simon T E Hall
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Ioannis A Ieropoulos
- Bristol Robotics Laboratory, Universities of Bristol and of the West of England, , Frenchay Campus, Bristol, UK
| | - Phillip C Wright
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK. .,Faculty of Science, Agriculture & Engineering, Newcastle University, Devonshire Building, Newcastle upon Tyne, UK.
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17
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Xu J, He W, Li Y, Zhang D, Zhou J, Zhang C, Li Y, Wang R, Su X. Selective colonization mechanism of Shewanella putrefaciens in dyeing wastewater outlets. RSC Adv 2016. [DOI: 10.1039/c6ra18576b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The responses ofS. putrefaciensto dyeing wastewater have been investigated using differential proteomics, metabolomics, and real-time fluorescent quantitative PCR techniques.
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Affiliation(s)
- Jiajie Xu
- School of Marine Science
- Ningbo University
- People's Republic China
- College of Engineering
- China Agricultural University
| | - Weina He
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Yanyan Li
- School of Marine Science
- Ningbo University
- People's Republic China
- Department of Food Science
- Cornell University
| | - DiJun Zhang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Jun Zhou
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Chundan Zhang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Ye Li
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Rixin Wang
- School of Marine Science
- Ningbo University
- People's Republic China
| | - Xiurong Su
- School of Marine Science
- Ningbo University
- People's Republic China
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18
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Lau MCY, Stackhouse BT, Layton AC, Chauhan A, Vishnivetskaya TA, Chourey K, Ronholm J, Mykytczuk NCS, Bennett PC, Lamarche-Gagnon G, Burton N, Pollard WH, Omelon CR, Medvigy DM, Hettich RL, Pfiffner SM, Whyte LG, Onstott TC. An active atmospheric methane sink in high Arctic mineral cryosols. ISME JOURNAL 2015; 9:1880-91. [PMID: 25871932 DOI: 10.1038/ismej.2015.13] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/21/2014] [Accepted: 01/05/2015] [Indexed: 11/09/2022]
Abstract
Methane (CH4) emission by carbon-rich cryosols at the high latitudes in Northern Hemisphere has been studied extensively. In contrast, data on the CH4 emission potential of carbon-poor cryosols is limited, despite their spatial predominance. This work employs CH4 flux measurements in the field and under laboratory conditions to show that the mineral cryosols at Axel Heiberg Island in the Canadian high Arctic consistently consume atmospheric CH4. Omics analyses present the first molecular evidence of active atmospheric CH4-oxidizing bacteria (atmMOB) in permafrost-affected cryosols, with the prevalent atmMOB genotype in our acidic mineral cryosols being closely related to Upland Soil Cluster α. The atmospheric (atm) CH4 uptake at the study site increases with ground temperature between 0 °C and 18 °C. Consequently, the atm CH4 sink strength is predicted to increase by a factor of 5-30 as the Arctic warms by 5-15 °C over a century. We demonstrate that acidic mineral cryosols are a previously unrecognized potential of CH4 sink that requires further investigation to determine its potential impact on larger scales. This study also calls attention to the poleward distribution of atmMOB, as well as to the potential influence of microbial atm CH4 oxidation, in the context of regional CH4 flux models and global warming.
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Affiliation(s)
- M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - B T Stackhouse
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - A C Layton
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - A Chauhan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - T A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - K Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - J Ronholm
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - N C S Mykytczuk
- 1] Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada [2] Vale Living with Lakes Centre, Laurentian University, Sudbury, Ontario, Canada
| | - P C Bennett
- Department of Geological Sciences, The University of Texas at Austin, Austin, TX, USA
| | - G Lamarche-Gagnon
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - N Burton
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - W H Pollard
- Department of Geography, McGill University, Montreal, Quebec, Canada
| | - C R Omelon
- Department of Geological Sciences, The University of Texas at Austin, Austin, TX, USA
| | - D M Medvigy
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - R L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - S M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - L G Whyte
- Department of Natural Resource Sciences, McGill University, Ste. Anna de Bellevue, Quebec, Canada
| | - T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, USA
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19
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Buttiglieri G, Collado N, Casas N, Comas J, Rodriguez-Roda I. Proteomics reliability for micropollutants degradation insight into activated sludge systems. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2015; 72:882-888. [PMID: 26360747 DOI: 10.2166/wst.2015.286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Little information is available on pharmaceutical trace compounds degradation pathways in wastewater. The potential of the proteomics approach has been evaluated to extract information on activated sludge microbial metabolism in degrading a trace concentration of a pharmaceutical compound (ibuprofen). Ibuprofen is one of the most consumed pharmaceuticals, measured in wastewater at very high concentrations and, despite its high removal rates, found in different environmental compartments. Aerated and completely mixed activated sludge batch tests were spiked with ibuprofen at 10 and 1,000 μg L(-1). Ibuprofen concentrations were determined in the liquid phase: 100% removal was observed and the kinetics were estimated. The solid phase was sampled for proteomics purposes. The first objective was to apply proteomics to evaluate protein profile variations in a complex matrix such as activated sludge. The second objective was to determine, at different ibuprofen concentrations, which proteins followed pre-defined trends. No newly expressed proteins were found. Nonetheless, the obtained results suggest that proteomics itself is a promising methodology to be applied in this field. Statistical and comparative studies analyses provided, in fact, useful information on biological reproducibility and permitted us to detect 62 proteins following coherent and plausible expected trends in terms of presence and intensity change.
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Affiliation(s)
- Gianluigi Buttiglieri
- ICRA, Catalan Institute for Water Research, Parc Científic Tecnològic de la UdG, Girona 17003, Spain E-mail:
| | - Neus Collado
- LEQUiA, Institute of the Environment, University of Girona, Girona, Catalonia E-17071, Spain
| | - Nuria Casas
- Desarrollos Ecológicos Industriales S.A. (DEISA), José Agustín Goytisolo 30-32, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Joaquim Comas
- LEQUiA, Institute of the Environment, University of Girona, Girona, Catalonia E-17071, Spain
| | - Ignasi Rodriguez-Roda
- ICRA, Catalan Institute for Water Research, Parc Científic Tecnològic de la UdG, Girona 17003, Spain E-mail: ; LEQUiA, Institute of the Environment, University of Girona, Girona, Catalonia E-17071, Spain
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20
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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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21
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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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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: 155] [Impact Index Per Article: 14.1] [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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Glass JB, Yu H, Steele JA, Dawson KS, Sun S, Chourey K, Pan C, Hettich RL, Orphan VJ. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments. Environ Microbiol 2013; 16:1592-611. [DOI: 10.1111/1462-2920.12314] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/13/2013] [Indexed: 01/17/2023]
Affiliation(s)
- Jennifer B. Glass
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Hang Yu
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Joshua A. Steele
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Katherine S. Dawson
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Shulei Sun
- The CAMERA Project; University of California San Diego; San Diego CA 92093 USA
| | - Karuna Chourey
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Chongle Pan
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Robert L. Hettich
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
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Chourey K, Nissen S, Vishnivetskaya T, Shah M, Pfiffner S, Hettich RL, Löffler FE. Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site. Proteomics 2013; 13:2921-30. [DOI: 10.1002/pmic.201300155] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Karuna Chourey
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN USA
| | - Silke Nissen
- Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN USA
- Department of Microbiology; University of Tennessee; Knoxville TN USA
| | | | - Manesh Shah
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN USA
| | - Susan Pfiffner
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN USA
| | - Robert L. Hettich
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN USA
- Department of Microbiology; University of Tennessee; Knoxville TN USA
| | - Frank E. Löffler
- Biosciences Division; Oak Ridge National Laboratory; Oak Ridge TN USA
- Department of Microbiology; University of Tennessee; Knoxville TN USA
- Center for Environmental Biotechnology; University of Tennessee; Knoxville TN USA
- Department of Civil and Environmental Engineering; University of Tennessee; Knoxville TN USA
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Hettich RL, Pan C, Chourey K, Giannone RJ. Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Anal Chem 2013; 85:4203-14. [PMID: 23469896 PMCID: PMC3696428 DOI: 10.1021/ac303053e] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The availability of extensive genome information for many different microbes, including unculturable species in mixed communities from environmental samples, has enabled systems-biology interrogation by providing a means to access genomic, transcriptomic, and proteomic information. To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample.
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Insights into the structure and metabolic function of microbes that shape pelagic iron-rich aggregates ("iron snow"). Appl Environ Microbiol 2013; 79:4272-81. [PMID: 23645202 DOI: 10.1128/aem.00467-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Microbial ferrous iron [Fe(II)] oxidation leads to the formation of iron-rich macroscopic aggregates ("iron snow") at the redoxcline in a stratified lignite mine lake in east-central Germany. We aimed to identify the abundant Fe-oxidizing and Fe-reducing microorganisms likely to be involved in the formation and transformation of iron snow present in the redoxcline in two basins of the lake that differ in their pH values. Nucleic acid- and lipid-stained microbial cells of various morphologies detected by confocal laser scanning microscopy were homogeneously distributed in all iron snow samples. The dominant iron mineral appeared to be schwertmannite, with shorter needles in the northern than in the central basin samples. Total bacterial 16S rRNA gene copies ranged from 5.0 × 10(8) copies g (dry weight)(-1) in the acidic central lake basin (pH 3.3) to 4.0 × 10(10) copies g (dry weight)(-1) in the less acidic (pH 5.9) northern basin. Total RNA-based quantitative PCR assigned up to 61% of metabolically active microbial communities to Fe-oxidizing- and Fe-reducing-related bacteria, indicating that iron metabolism was an important metabolic strategy. Molecular identification of abundant groups suggested that iron snow surfaces were formed by chemoautotrophic iron oxidizers, such as Acidimicrobium, Ferrovum, Acidithiobacillus, Thiobacillus, and Chlorobium, in the redoxcline and were rapidly colonized by heterotrophic iron reducers, such as Acidiphilium, Albidiferax-like, and Geobacter-like groups. Metaproteomics yielded 283 different proteins from northern basin iron snow samples, and protein identification provided a glimpse into some of their in situ metabolic processes, such as primary production (CO2 fixation), respiration, motility, and survival strategies.
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Ravindranath SP, Kadam US, Thompson DK, Irudayaraj J. Intracellularly grown gold nanoislands as SERS substrates for monitoring chromate, sulfate and nitrate localization sites in remediating bacteria biofilms by Raman chemical imaging. Anal Chim Acta 2012; 745:1-9. [PMID: 22938600 DOI: 10.1016/j.aca.2012.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 07/23/2012] [Accepted: 07/26/2012] [Indexed: 11/25/2022]
Abstract
Understanding the chemical composition of biofilm matrices is vital in different fields of biology such as surgery, dental medicine, synthetic grafts and bioremediation. The knowledge of biofilm development, composition, active reduction sites and remediation efficacy will help in the development of effective solutions and evaluation of remediating approaches prior to implementation. Surface-enhanced Raman spectroscopy (SERS) based imaging is an invaluable tool to obtain an understanding of the remediating efficacy of microorganisms and its role in the formation of organic and inorganic compounds in biofilms. We demonstrate for the first time, the presence of chromate, sulfate, nitrate and reduced trivalent chromium in soil biofilms. In addition, we demonstrate that SERS imaging was able to validate two observations made by previous studies on chromate/sulfate and chromate/nitrate interactions in Shewanella oneidensis MR-1 biofilms. Additionally, we show a detailed Raman mapping based evidence of the existence of chromate-sulfate competition for cellular entry. Subsequently, we use Raman mapping to study the effect of nitrate on chromate reduction. The findings presented in this paper are among the first to report - detection of multiple metallic ions in bacterial biofilms using intracellular SERS substrates. Such a detailed characterization of biofilms using gold nanoislands based SERS mapping substrate can be extended to study cellular localization of other metallic ions and chemical species of biological and toxicological significance and their effect on reduction reactions in bacterial biofilms.
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Affiliation(s)
- Sandeep P Ravindranath
- Bindley Bioscience Centre, Department of Agricultural & Biological Engineering, United States.
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Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D. Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis. Nucleic Acids Res 2012; 40:7132-49. [PMID: 22638572 PMCID: PMC3424579 DOI: 10.1093/nar/gks467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
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Affiliation(s)
- Qasim K Beg
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
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Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl Environ Microbiol 2011; 78:1424-36. [PMID: 22179257 DOI: 10.1128/aem.06792-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.
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Parker DL, Borer P, Bernier-Latmani R. The Response of Shewanella oneidensis MR-1 to Cr(III) Toxicity Differs from that to Cr(VI). Front Microbiol 2011; 2:223. [PMID: 22125549 PMCID: PMC3221395 DOI: 10.3389/fmicb.2011.00223] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 10/20/2011] [Indexed: 11/18/2022] Open
Abstract
Chromium is a contaminant of concern that is found in drinking water in its soluble, hexavalent form [Cr(VI)] and that is known to be toxic to eukaryotes and prokaryotes. Trivalent chromium [Cr(III)] is thought to be largely harmless due to its low solubility and inability to enter cells. Previous work has suggested that Cr(III) may also be toxic to microorganisms but the mechanism remained elusive. In this work, we probe the toxicity of Cr(III) to Shewanella oneidensis MR-1, a bacterium able to reduce Cr(VI) to Cr(III) and compare it to Cr(VI) toxicity. We found evidence for Cr(III) toxicity both under Cr(VI) reducing conditions, during which Cr(III) was generated by the reduction process, and under non-reducing conditions, when Cr(III) was amended exogenously. Interestingly, cells exposed to Cr(III) (200 μM) experienced rapid viability loss as measured by colony forming units on Luria–Bertani (LB) agar plates. In contrast, they maintained some enzymatic activity and cellular integrity. Cr(VI)-exposed cells exhibited loss of enzymatic activity and cell lysis. The loss of viability of Cr(III)-exposed cells was not due to membrane damage or to enzymatic inhibition but rather appeared to be associated with an abnormal morphology that consisted of chains of membrane-enclosed units of irregular size. Exposure of abnormal cells to growth conditions resulted in membrane damage and cell death, which is consistent with the observed viability loss on LB plates. While Cr(VI) was taken up intracellularly and caused cell lysis, the toxic effect of Cr(III) appeared to be associated with extracellular interactions leading to an ultimately lethal cell morphology.
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Affiliation(s)
- Dorothy L Parker
- Environmental Microbiology Laboratory, Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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Schmitz-Spanke S, Rettenmeier AW. Protein expression profiling in chemical carcinogenesis: A proteomic-based approach. Proteomics 2011; 11:644-56. [DOI: 10.1002/pmic.201000403] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/12/2010] [Accepted: 10/15/2010] [Indexed: 11/11/2022]
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Henne KL, Wan XF, Wei W, Thompson DK. SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1. BMC Microbiol 2011; 11:125. [PMID: 21624143 PMCID: PMC3127752 DOI: 10.1186/1471-2180-11-125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 05/31/2011] [Indexed: 11/14/2022] Open
Abstract
Background The Shewanella oneidensis MR-1 genome encodes a predicted orphan DNA-binding response regulator, SO2426. Previous studies with a SO2426-deficient MR-1 strain suggested a putative functional role for SO2426 in the regulation of iron acquisition genes, in particular, the siderophore (hydroxamate) biosynthesis operon so3030-3031-3032. To further investigate the functional role of SO2426 in iron homeostasis, we employed computational strategies to identify putative gene targets of SO2426 regulation and biochemical approaches to validate the participation of SO2426 in the control of siderophore biosynthesis in S. oneidensis MR-1. Results In silico prediction analyses revealed a single 14-bp consensus motif consisting of two tandem conserved pentamers (5'-CAAAA-3') in the upstream regulatory regions of 46 genes, which were shown previously to be significantly down-regulated in a so2426 deletion mutant. These genes included so3030 and so3032, members of an annotated siderophore biosynthetic operon in MR-1. Electrophoretic mobility shift assays demonstrated that the SO2426 protein binds to its motif in the operator region of so3030. A "short" form of SO2426, beginning with a methionine at position 11 (M11) of the originally annotated coding sequence for SO2426, was also functional in binding to its consensus motif, confirming previous 5' RACE results that suggested that amino acid M11 is the actual translation start codon for SO2426. Alignment of SO2426 orthologs from all sequenced Shewanella spp. showed a high degree of sequence conservation beginning at M11, in addition to conservation of a putative aspartyl phosphorylation residue and the helix-turn-helix (HTH) DNA-binding domain. Finally, the so2426 deletion mutant was unable to synthesize siderophores at wild-type rates upon exposure to the iron chelator 2,2'-dipyridyl. Conclusions Collectively, these data support the functional characterization of SO2426 as a positive regulator of siderophore-mediated iron acquisition and provide the first insight into a coordinate program of multiple regulatory schemes controlling iron homeostasis in S. oneidensis MR-1.
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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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He M, Li X, Guo L, Miller SJ, Rensing C, Wang G. Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BMC Microbiol 2010; 10:221. [PMID: 20723231 PMCID: PMC2936356 DOI: 10.1186/1471-2180-10-221] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 08/19/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by Bacillus cereus SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence. RESULTS Bacillus cereus SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, chrIA1, and two additional chrA genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene azoR and four nitroreductase genes nitR possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes chrA1 and chrI was induced in response to Cr(VI) but expression of the other two chromate transporter genes chrA2 and chrA3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of chrIA1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of chrIA1 in B. cereus SJ1 implied the possibility of recent horizontal gene transfer. CONCLUSION Our results indicate that expression of the chromate transporter gene chrA1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the chrIA1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of B. cereus SJ1.
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Affiliation(s)
- Minyan He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Thompson DK, Chourey K, Wickham GS, Thieman SB, VerBerkmoes NC, Zhang B, McCarthy AT, Rudisill MA, Shah M, Hettich RL. Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge. BMC Genomics 2010; 11:311. [PMID: 20482812 PMCID: PMC2996968 DOI: 10.1186/1471-2164-11-311] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 05/19/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudomonas putida is a model organism for bioremediation because of its remarkable metabolic versatility, extensive biodegradative functions, and ubiquity in contaminated soil environments. To further the understanding of molecular pathways responding to the heavy metal chromium(VI) [Cr(VI)], the proteome of aerobically grown, Cr(VI)-stressed P. putida strain F1 was characterized within the context of two disparate nutritional environments: rich (LB) media and minimal (M9L) media containing lactate as the sole carbon source. RESULTS Growth studies demonstrated that F1 sensitivity to Cr(VI) was impacted substantially by nutrient conditions, with a carbon-source-dependent hierarchy (lactate > glucose >> acetate) observed in minimal media. Two-dimensional HPLC-MS/MS was employed to identify differential proteome profiles generated in response to 1 mM chromate under LB and M9L growth conditions. The immediate response to Cr(VI) in LB-grown cells was up-regulation of proteins involved in inorganic ion transport, secondary metabolite biosynthesis and catabolism, and amino acid metabolism. By contrast, the chromate-responsive proteome derived under defined minimal growth conditions was characterized predominantly by up-regulated proteins related to cell envelope biogenesis, inorganic ion transport, and motility. TonB-dependent siderophore receptors involved in ferric iron acquisition and amino acid adenylation domains characterized up-regulated systems under LB-Cr(VI) conditions, while DNA repair proteins and systems scavenging sulfur from alternative sources (e.g., aliphatic sulfonates) tended to predominate the up-regulated proteome profile obtained under M9L-Cr(VI) conditions. CONCLUSIONS Comparative analysis indicated that the core molecular response to chromate, irrespective of the nutritional conditions tested, comprised seven up-regulated proteins belonging to six different functional categories including transcription, inorganic ion transport/metabolism, and amino acid transport/metabolism. These proteins might potentially serve as indicators of chromate stress in natural microbial communities.
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Affiliation(s)
- Dorothea K Thompson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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Thompson MR, Chourey K, Froelich JM, Erickson BK, VerBerkmoes NC, Hettich RL. Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Anal Chem 2009; 80:9517-25. [PMID: 19072265 DOI: 10.1021/ac801707s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many methods of microbial proteome characterizations require large quantities of cellular biomass (>1-2 g) for sample preparation and protein identification. Our experimental approach differs from traditional techniques by providing the ability to identify the proteomic state of a microbe from a few milligrams of starting cellular material. The small-scale, guanidine lysis method minimizes sample loss by achieving cellular lysis and protein digestion in a single-tube experiment. For this experimental approach, the freshwater microbe Shewanella oneidensis MR-1 and the purple non-sulfur bacterium Rhodopseudomonas palustris CGA0010 were used as model organisms for technology development and evaluation. A 2-D LC-MS/MS comparison between a standard sonication lysis method and the small-scale guanidine lysis techniques demonstrates that the guanidine lysis method is more efficient with smaller sample amounts of cell pellet (i.e., down to 1 mg). The described methodology enables deeper proteome measurements from a few milliliters of confluent bacterial cultures. We also report a new protocol for efficient lysis from small amounts of natural biofilm samples for deep proteome measurements, which should greatly enhance the emerging field of environmental microbial community proteomics. This straightforward sample boiling protocol is complementary to the small-scale guanidine lysis technique, is amenable for small sample quantities, and requires no special reagents that might complicate the MS measurements.
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Affiliation(s)
- Melissa R Thompson
- Graduate School of Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee, Knoxville, Tennessee 37830, USA
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Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol Mol Biol Rev 2009; 73:62-70. [PMID: 19258533 DOI: 10.1128/mmbr.00028-08] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.
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Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:75-87. [PMID: 19279070 DOI: 10.1093/bfgp/elp005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.
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Affiliation(s)
- Carla M R Lacerda
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
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VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol 2009; 7:196-205. [DOI: 10.1038/nrmicro2080] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Mugerfeld I, Law BA, Wickham GS, Thompson DK. A putative azoreductase gene is involved in the Shewanella oneidensis response to heavy metal stress. Appl Microbiol Biotechnol 2009; 82:1131-41. [PMID: 19238379 DOI: 10.1007/s00253-009-1911-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/03/2009] [Accepted: 02/05/2009] [Indexed: 11/24/2022]
Abstract
The Shewanella oneidensis MR-1 gene SO3585, which is annotated as a putative flavin mononucleotide-dependent azoreductase, shares 28% sequence identity with Bacillus subtilis azoreductase and Pseudomonas putida ChrR, a soluble flavoprotein exhibiting chromate reductase activity. Reverse transcription polymerase chain reaction demonstrated that the SO3585 gene is co-transcribed with two downstream open reading frames: SO3586 (a glyoxalase family protein) and SO3587 (a predicted membrane-associated hypothetical protein). The transcriptional start site of the so3585 transcript was localized using 5' rapid amplification of complementary DNA ends analysis. To investigate the cellular function of SO3585, an in-frame deletion of the so3585 locus was generated in MR-1, and the phenotype of the resulting mutant was characterized. The so3585 deletion mutant was comparable to the parental strain in its ability to decolorize two sulfonated azo dyes (Orange II, Direct Blue 15) under aerobic conditions. By contrast, growth of the so3585 deletion mutant was sensitive to different exogenous transition heavy metals [Cr(VI), Cd(II), Cu(II), and Zn(II)], while the most severe growth deficiencies were observed in the presence of Cd(II) and Cu(II). In addition, the rate of extracellular chromate disappearance by the deletion strain was initially impaired, although both the so3585 mutant and MR-1 wild type reduced Cr(VI) within the same time period.
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Affiliation(s)
- Irina Mugerfeld
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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Henne KL, Turse JE, Nicora CD, Lipton MS, Tollaksen SL, Lindberg C, Babnigg G, Giometti CS, Nakatsu CH, Thompson DK, Konopka AE. Global Proteomic Analysis of the Chromate Response in Arthrobacter sp. Strain FB24. J Proteome Res 2009; 8:1704-16. [DOI: 10.1021/pr800705f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kristene L. Henne
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Joshua E. Turse
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carrie D. Nicora
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Mary S. Lipton
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Sandra L. Tollaksen
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carl Lindberg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Gyorgy Babnigg
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Carol S. Giometti
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Cindy H. Nakatsu
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Dorothea K. Thompson
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Allan E. Konopka
- Departments of Biological Sciences and Agronomy, Purdue University, West Lafayette, Indiana 47907, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, and Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
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Chourey K, Thompson MR, Shah M, Zhang B, VerBerkmoes NC, Thompson DK, Hettich RL. Comparative Temporal Proteomics of a Response Regulator (SO2426)-Deficient Strain and Wild-Type Shewanella oneidensis MR-1 During Chromate Transformation. J Proteome Res 2009; 8:59-71. [DOI: 10.1021/pr800776d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karuna Chourey
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Melissa R. Thompson
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Manesh Shah
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Bing Zhang
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Nathan C. VerBerkmoes
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Dorothea K. Thompson
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Robert L. Hettich
- Environmental Sciences Division, Graduate School of Genome Science and Technology, ORNL-UTK, Chemical Sciences Division, Biosciences Division, Oak Ridge National Laboratory, Tennessee 37831, Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
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Viti C, Decorosi F, Mini A, Tatti E, Giovannetti L. Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28. Microbiology (Reading) 2009; 155:95-105. [DOI: 10.1099/mic.0.021873-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas corrugata28 is a Cr(VI)-hyper-resistant bacterium. A Cr(VI)-sensitive mutant was obtained by insertional mutagenesis using EZ-Tn5<R6Kγori/KAN-2>Tnp. The mutant strain was impaired in a gene, here namedoscA(organosulphurcompounds), which encoded a hypothetical small protein of unknown function. The gene was located upstream of a gene cluster that encodes the components of the sulphate ABC transporter, and it formed a transcriptional unit withsbp, which encoded the periplasmic binding protein of the transporter. TheoscA–sbptranscriptional unit was strongly and quickly overexpressed after chromate exposure, suggesting the involvement ofoscAin chromate resistance, which was further confirmed by means of a complementation experiment. Phenotype MicroArray (PM) analysis made it possible to assay 1536 phenotypes and also indicated that theoscAgene was involved in the utilization of organosulphur compounds as a sole source of sulphur. This is believed to be the first evidence thatoscAplays a role in activating a sulphur starvation response, which is required to cope with oxidative stress induced by chromate.
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Affiliation(s)
- Carlo Viti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Annalisa Mini
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Enrico Tatti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
| | - Luciana Giovannetti
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Piazzale delle Cascine 24, 50144 Firenze, Italy
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Chourey K, Wei W, Wan XF, Thompson DK. Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge. BMC Genomics 2008; 9:395. [PMID: 18718017 PMCID: PMC2535785 DOI: 10.1186/1471-2164-9-395] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 08/21/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shewanella oneidensis MR-1 exhibits diverse metal ion-reducing capabilities and thus is of potential utility as a bioremediation agent. Knowledge of the molecular components and regulatory mechanisms dictating cellular responses to heavy metal stress, however, remains incomplete. In a previous work, the S. oneidensis so2426 gene, annotated as a DNA-binding response regulator, was demonstrated to be specifically responsive at both the transcript and protein levels to acute chromate [Cr(VI)] challenge. To delineate the cellular function of SO2426 and its contribution to metal stress response, we integrated genetic and physiological approaches with a genome-wide screen for target gene candidates comprising the SO2426 regulon. RESULTS Inactivation of so2426 by an in-frame deletion resulted in enhanced chromate sensitivity and a reduced capacity to remove extracellular Cr(VI) relative to the parental strain. Time-resolved microarray analysis was used to compare transcriptomic profiles of wild-type and SO2426-deficient mutant S. oneidensis under conditions of chromate exposure. In total, 841 genes (18% of the arrayed genome) were up- or downregulated at least twofold in the Deltaso2426 mutant for at least one of six time-point conditions. Hierarchical cluster analysis of temporal transcriptional profiles identified a distinct cluster (n = 46) comprised of co-ordinately regulated genes exhibiting significant downregulated expression (p < 0.05) over time. Thirteen of these genes encoded proteins associated with transport and binding functions, particularly those involved in Fe transport and homeostasis (e.g., siderophore biosynthetic enzymes, TonB-dependent receptors, and the iron-storage protein ferritin). A conserved hypothetical operon (so1188-so1189-so1190), previously identified as a potential target of Fur-mediated repression, as well as a putative bicyclomycin resistance gene (so2280) and cation efflux family protein gene (so2045) also were repressed in the so2426 deletion mutant. Furthermore, the temporal expression profiles of four regulatory genes including a cpxR homolog were perturbed in the chromate-challenged mutant. CONCLUSION Our findings suggest a previously unrecognized functional role for the response regulator SO2426 in the activation of genes required for siderophore-mediated Fe acquisition, Fe storage, and other cation transport mechanisms. SO2426 regulatory function is involved at a fundamental molecular level in the linkage between Fe homeostasis and the cellular response to chromate-induced stress in S. oneidensis.
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Affiliation(s)
- Karuna Chourey
- Department of Biological Sciences, Purdue University, 915 W, State Street, West Lafayette, IN 47907, USA.
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Holland S, Lodwig E, Sideri T, Reader T, Clarke I, Gkargkas K, Hoyle DC, Delneri D, Oliver SG, Avery SV. Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity. Genome Biol 2008; 8:R268. [PMID: 18088421 PMCID: PMC2246270 DOI: 10.1186/gb-2007-8-12-r268] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/18/2007] [Accepted: 12/18/2007] [Indexed: 11/14/2022] Open
Abstract
Competitive growth between over 6,000 heterozygous yeast mutants in the presence of chromium together with microarray-based screens showed that proteasomal activity is crucial for cellular chromium resistance. Background The serious biological consequences of metal toxicity are well documented, but the key modes of action of most metals are unknown. To help unravel molecular mechanisms underlying the action of chromium, a metal of major toxicological importance, we grew over 6,000 heterozygous yeast mutants in competition in the presence of chromium. Microarray-based screens of these heterozygotes are truly genome-wide as they include both essential and non-essential genes. Results The screening data indicated that proteasomal (protein degradation) activity is crucial for cellular chromium (Cr) resistance. Further investigations showed that Cr causes the accumulation of insoluble and toxic protein aggregates, which predominantly arise from proteins synthesised during Cr exposure. A protein-synthesis defect provoked by Cr was identified as mRNA mistranslation, which was oxygen-dependent. Moreover, Cr exhibited synergistic toxicity with a ribosome-targeting drug (paromomycin) that is known to act via mistranslation, while manipulation of translational accuracy modulated Cr toxicity. Conclusion The datasets from the heterozygote screen represent an important public resource that may be exploited to discover the toxic mechanisms of chromium. That potential was validated here with the demonstration that mRNA mistranslation is a primary cause of cellular Cr toxicity.
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Affiliation(s)
- Sara Holland
- School of Biology, Institute of Genetics, The University of Nottingham, University Park, Nottingham NG7 2RD, UK
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