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Su Y, Liu S, Dong Q, Zeng Y, Yang Y, Gao Q. Tracking virulence genes and their interaction with antibiotic resistome during manure fertilization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119736. [PMID: 35810986 DOI: 10.1016/j.envpol.2022.119736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/08/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance genes, collectively termed as antibiotic resistome, are regarded as emerging contaminants. Antibiotics resistome can be highly variable in different environments, imposing environmental safety concern and public health risk when it is in conjunction with pathogenic bacteria. However, it remains elusive how pathogenic bacteria interact with antibiotic resistome, making it challenging to assess microbial risk. Here, we examined the presence and relative abundance of bacterial virulence genes representing potential pathogens in swine manure, compost, compost-amended soil, and unamended agricultural soil in five suburban areas of Beijing, China. The absolute abundances of virulence genes were marginally significantly (p < 0.100) increased in compost-amended soils than unamended soil, revealing potential health risks in manure fertilization. The composition of potential pathogens differed by sample types and was linked to temperature, antibiotics, and heavy metals. As antibiotics can confer pathogens the resistance to clinic treatment, it was alarming to note that virulence genes tended to co-exist with antibiotic resistance genes, as shown by prevalently positive links among them. Collectively, our results demonstrate that manure fertilization in agriculture might give rise to the development of potentially antibiotic-resistant pathogens, unveiling an environmental health risk that has been frequently overlooked.
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Affiliation(s)
- Yifan Su
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Suo Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing, 102205, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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Dai Q, Zhang T, Zhao Y, Li Q, Dong F, Jiang C. Potentiality of living Bacillus pumilus SWU7-1 in biosorption of strontium radionuclide. CHEMOSPHERE 2020; 260:127559. [PMID: 32673872 DOI: 10.1016/j.chemosphere.2020.127559] [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: 04/23/2020] [Revised: 06/21/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Bacillus pumilus SWU7-1 was isolated from strontium ion (Sr(II))-uncontaminated soil, its biosorption potential was evaluated, and the effect of γ-ray radiation treatment on its biosorption was discussed. Domesticated under Sr(II) stress promoted the biosorption ability of B. pumilus to Sr(II), and the biosorption efficiency increased from 46.09% to 94.69%. At a lower initial concentration, the living bacteria had the ability to resist the biosorption of Sr(II). The optimal initial concentration range was 54-130 mg/L. The biosorption profile was better matched by Langmuir than Freundlich model, showing that the biosorption process of Sr(II) by the experimental strain was closer to the surface adsorption. According to Langmuir model, the maximum biosorption capacity of B. pumilus on Sr (II) was 299.4 mg/g. During the bacterial growth in the biosorption process, the changes in biosorption capacity and efficiency can be divided into two phases, and a pseudo-second-order model is followed in each phase. There was no significant difference in the biosorption efficiency of bacteria with different culture time after γ-ray radiation, and all of them were above 90%, which showed that B. pumilus had significant radiation resistance under experimental conditions. This study emphasized the potential application of B. pumilus in the treatment of radioactive Sr(II) pollution by biosorption.
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Affiliation(s)
- Qunwei Dai
- Fundamental Science on Nuclear Waste and Environmental Safety Laboratory (SWUST), Mianyang City, Sichuan, 621010, China; Key Laboratory of Solid Waste Treatment and Resource Recycle (SWUST, Ministry of Education), Mianyang City, Sichuan, 621010, China.
| | - Ting Zhang
- Key Laboratory of Solid Waste Treatment and Resource Recycle (SWUST, Ministry of Education), Mianyang City, Sichuan, 621010, China
| | - Yulian Zhao
- Key Laboratory of Solid Waste Treatment and Resource Recycle (SWUST, Ministry of Education), Mianyang City, Sichuan, 621010, China
| | - Qiongfang Li
- Key Laboratory of Solid Waste Treatment and Resource Recycle (SWUST, Ministry of Education), Mianyang City, Sichuan, 621010, China
| | - Faqin Dong
- Key Laboratory of Solid Waste Treatment and Resource Recycle (SWUST, Ministry of Education), Mianyang City, Sichuan, 621010, China
| | - Chunqi Jiang
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA
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Zinicovscaia I, Yushin N, Grozdov D, Vergel K, Popova N, Artemiev G, Safonov A. Metal Removal from Nickel-Containing Effluents Using Mineral-Organic Hybrid Adsorbent. MATERIALS 2020; 13:ma13194462. [PMID: 33050087 PMCID: PMC7578995 DOI: 10.3390/ma13194462] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 11/17/2022]
Abstract
Nickel is one of the most dangerous environmental pollutants and its removal from wastewater is an important task. The capacity of a mineral–organic hybrid adsorbent, consisting of Shewanella xiamenensis biofilm and zeolite (clinoptilolite of the Chola deposit), to remove metal ions from nickel-containing batch systems under different experimental conditions was tested. The obtained biosorbent was characterized using neutron activation, SEM, and FTIR techniques. It was established that maximum removal of cations, up to 100%, was achieved at pH 6.0. Several mathematical models were applied to describe the equilibrium and kinetics data. The maximum adsorption capacity of the hybrid biosorbent, calculated using the Langmuir model, varied from 3.6 to 3.9 mg/g. Negative Gibbs energy values and positive ∆H° values indicate the spontaneous and endothermic character of the biosorption process. The effects of several parameters (pH and biosorbent dosage) on Ni(II) removal from real effluent, containing nickel with a concentration of 125 mg/L, were investigated. The optimal pH for Ni(II) removal was 5.0–6.0 and an increase of sorbent dosage from 0.5 to 2.0 led to an increase in Ni(II) removal from 17% to 27%. At two times effluent dilution, maximum Ni(II) removal of 26% was attained at pH 6.0 and sorbent dosage of 1.0 g. A 12-fold effluent dilution resulted in the removal of 72% of Ni(II) at the same pH and sorbent dosage values. The obtained hybrid biosorbent can be used for Ni(II) removal from industrial effluents with low Ni(II) concentrations.
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Affiliation(s)
- Inga Zinicovscaia
- Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 1419890 Dubna, Russia; (N.Y.); (D.G.); (K.V.)
- Horia Hulubei National Institute for R&D in Physics and Nuclear Engineering, 30 Reactorului, MG-6 Bucharest-Magurele, Romania
- Correspondence: ; Tel.: +7-49621-65609
| | - Nikita Yushin
- Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 1419890 Dubna, Russia; (N.Y.); (D.G.); (K.V.)
| | - Dmitrii Grozdov
- Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 1419890 Dubna, Russia; (N.Y.); (D.G.); (K.V.)
| | - Konstantin Vergel
- Joint Institute for Nuclear Research, Joliot-Curie Str. 6, 1419890 Dubna, Russia; (N.Y.); (D.G.); (K.V.)
| | - Nadezhda Popova
- Frumkin Institute of Physical Chemistry, Russian Academy of Science, 31 Leninsky Prospect, GSP-1, 119071 Moscow, Russia; (N.P.); (G.A.); (A.S.)
| | - Grigoriy Artemiev
- Frumkin Institute of Physical Chemistry, Russian Academy of Science, 31 Leninsky Prospect, GSP-1, 119071 Moscow, Russia; (N.P.); (G.A.); (A.S.)
| | - Alexey Safonov
- Frumkin Institute of Physical Chemistry, Russian Academy of Science, 31 Leninsky Prospect, GSP-1, 119071 Moscow, Russia; (N.P.); (G.A.); (A.S.)
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Evaluation of mtr cluster expression in Shewanella RCRI7 during uranium removal. Arch Microbiol 2020; 202:2711-2726. [DOI: 10.1007/s00203-020-01981-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 07/03/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
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Yan X, Song M, Zhou M, Ding C, Wang Z, Wang Y, Yang W, Yang Z, Liao Q, Shi Y. Response of Cupriavidus basilensis B-8 to CuO nanoparticles enhances Cr(VI) reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:46-55. [PMID: 31229827 DOI: 10.1016/j.scitotenv.2019.05.438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
CuO nanoparticles (NPs) released into aqueous environments induce metal toxicity, which generally exerts negative effects on various organisms and leads to great challenge for wastewater biotreatment. In this study, a promotion effect of CuO NPs on biological process was first found. Cr(VI) reduction by Cupriavidus basilensis B-8 (hereafter B-8) was enhanced in the presence of CuO NPs. The efficiency of Cr(VI) bioreduction was much higher with B-8 and CuO NPs (approximately 100%) than with B-8 (approximately 37.6%) and CuO NPs (39.9-44.7%) alone, indicating a stimulatory effect of CuO NPs on Cr(VI) reduction by B-8. Our material analyses revealed different response mechanisms of B-8 to Cr(VI), with and without CuO NPs. The addition of CuO NPs influenced the interaction of Cr(VI) with the N-, P-, S-, and C-related functional groups of B-8. Transcriptomic analysis indicated that multiple mechanisms, including Cr(VI) uptake and reactive oxygen species detoxification, were induced by Cr(VI). Many genes involved in various metabolic processes were significantly upregulated by the addition of CuO NPs. To a certain extent, the pressure of DNA repairment by B-8 induced by Cr(VI) was also alleviated by the presence of CuO NPs. They contributed to facilitate B-8 growth and enhance Cr(VI) reduction, even with 50 mg/L Cr(VI). This study not only elaborated the mechanisms of bacterial Cr(VI) reduction when enhanced by CuO NPs, but also provided a novel perspective for wastewater biotreatment.
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Affiliation(s)
- Xu Yan
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Mengmeng Song
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Mo Zhou
- Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Chunlian Ding
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Zhongren Wang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Yunyan Wang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Weichun Yang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Zhihui Yang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Qi Liao
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China
| | - Yan Shi
- School of Metallurgy and Environment, Central South University, Changsha 410083, China; Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, Changsha 410083, China.
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Kargozar S, Montazerian M, Fiume E, Baino F. Multiple and Promising Applications of Strontium (Sr)-Containing Bioactive Glasses in Bone Tissue Engineering. Front Bioeng Biotechnol 2019; 7:161. [PMID: 31334228 PMCID: PMC6625228 DOI: 10.3389/fbioe.2019.00161] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/20/2019] [Indexed: 12/22/2022] Open
Abstract
Improving and accelerating bone repair still are partially unmet needs in bone regenerative therapies. In this regard, strontium (Sr)-containing bioactive glasses (BGs) are highly-promising materials to tackle this challenge. The positive impacts of Sr on the osteogenesis makes it routinely used in the form of strontium ranelate (SR) in the clinical setting, especially for patients suffering from osteoporosis. Therefore, a large number of silicate-, borate-, and phosphate-based BGs doped with Sr and produced in different shapes have been developed and characterized, in order to be used in the most advanced therapeutic strategies designed for the management of bone defects and injuries. Although the influence of Sr incorporation in the glass is debated regarding the obtained physicochemical and mechanical properties, the biological improvements have been found to be substantial both in vitro and in vivo. In the present study, we provide a comprehensive overview of Sr-containing glasses along with the current state of their clinical use. For this purpose, different types of Sr-doped BG systems are described, including composites, coatings and porous scaffolds, and their applications are discussed in the light of existing experimental data along with the significant challenges ahead.
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Affiliation(s)
- Saeid Kargozar
- Tissue Engineering Research Group (TERG), Department of Anatomy and Cell Biology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maziar Montazerian
- Center for Research, Technology and Education in Vitreous Materials, Federal University of São Carlos, São Carlos, Brazil
| | - Elisa Fiume
- Department of Applied Science and Technology, Institute of Materials Physics and Engineering, Politecnico di Torino, Turin, Italy
| | - Francesco Baino
- Department of Applied Science and Technology, Institute of Materials Physics and Engineering, Politecnico di Torino, Turin, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research, Italy
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7
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Bennett BD, Redford KE, Gralnick JA. MgtE Homolog FicI Acts as a Secondary Ferrous Iron Importer in Shewanella oneidensis Strain MR-1. Appl Environ Microbiol 2018; 84:e01245-17. [PMID: 29330185 PMCID: PMC5835737 DOI: 10.1128/aem.01245-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 01/05/2018] [Indexed: 01/28/2023] Open
Abstract
The transport of metals into and out of cells is necessary for the maintenance of appropriate intracellular concentrations. Metals are needed for incorporation into metalloproteins but become toxic at higher concentrations. Many metal transport proteins have been discovered in bacteria, including the Mg2+ transporter E (MgtE) family of passive Mg2+/Co2+ cation-selective channels. Low sequence identity exists between members of the MgtE family, indicating that substrate specificity may differ among MgtE transporters. Under anoxic conditions, dissimilatory metal-reducing bacteria, such as Shewanella and Geobacter species, are exposed to high levels of soluble metals, including Fe2+ and Mn2+ Here we characterize SO_3966, which encodes an MgtE homolog in Shewanella oneidensis that we name FicI (ferrous iron and cobalt importer) based on its role in maintaining metal homeostasis. A SO_3966 deletion mutant exhibits enhanced growth over that of the wild type under conditions with high Fe2+ or Co2+ concentrations but exhibits wild-type Mg2+ transport and retention phenotypes. Conversely, deletion of feoB, which encodes an energy-dependent Fe2+ importer, causes a growth defect under conditions of low Fe2+ concentrations but not high Fe2+ concentrations. We propose that FicI represents a secondary, less energy-dependent mechanism for iron uptake by S. oneidensis under high Fe2+ concentrations.IMPORTANCEShewanella oneidensis MR-1 is a target of microbial engineering for potential uses in biotechnology and the bioremediation of heavy-metal-contaminated environments. A full understanding of the ways in which S. oneidensis interacts with metals, including the means by which it transports metal ions, is important for optimal genetic engineering of this and other organisms for biotechnology purposes such as biosorption. The MgtE family of metal importers has been described previously as Mg2+ and Co2+ transporters. This work broadens that designation with the discovery of an MgtE homolog in S. oneidensis that imports Fe2+ but not Mg2+ The research presented here also expands our knowledge of the means by which microorganisms have adapted to take up essential nutrients such as iron under various conditions.
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Affiliation(s)
- Brittany D Bennett
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Kaitlyn E Redford
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
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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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Dai J, Wei H, Tian C, Damron FH, Zhou J, Qiu D. An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis. BMC Microbiol 2015; 15:34. [PMID: 25887418 PMCID: PMC4336711 DOI: 10.1186/s12866-015-0357-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
Background Bacteria use alternative sigma factors (σs) to regulate condition-specific gene expression for survival and Shewanella harbors multiple ECF (extracytoplasmic function) σ genes and cognate anti-sigma factor genes. Here we comparatively analyzed two of the rpoE-like operons in the strain MR-1: rpoE-rseA-rseB-rseC and rpoE2-chrR. Results RpoE was important for bacterial growth at low and high temperatures, in the minimal medium, and high salinity. The degP/htrA orthologue, required for growth of Escherichia coli and Pseudomonas aeruginosa at high temperature, is absent in Shewanella, while the degQ gene is RpoE-regulated and is required for bacterial growth at high temperature. RpoE2 was essential for the optimal growth in oxidative stress conditions because the rpoE2 mutant was sensitive to hydrogen peroxide and paraquat. The operon encoding a ferrochelatase paralogue (HemH2) and a periplasmic glutathione peroxidase (PgpD) was identified as RpoE2-dependent. PgpD exhibited higher activities and played a more important role in the oxidative stress responses than the cytoplasmic glutathione peroxidase CgpD under tested conditions. The rpoE2-chrR operon and the identified regulon genes, including pgpD and hemH2, are coincidently absent in several psychrophilic and/or deep-sea Shewanella strains. Conclusion In S. oneidensis MR-1, the RpoE-dependent degQ gene is required for optimal growth under high temperature. The rpoE2 and RpoE2-dependent pgpD gene encoding a periplasmic glutathione peroxidase are involved in oxidative stress responses. But rpoE2 is not required for bacterial growth at low temperature and it even affected bacterial growth under salt stress, indicating that there is a tradeoff between the salt resistance and RpoE2-mediated oxidative stress responses. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0357-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingcheng Dai
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hehong Wei
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Chunyuan Tian
- School of Life Sciences and Technology, Hubei University of Engineering, 272 Jiaotong Avenue, Xiaogan, 432000, China.
| | - Fredrick Heath Damron
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, 22908, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Stephenson Research and Technology Center, 101 David L. Boren Blvd, Norman, OK 73019, USA.
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose. Appl Environ Microbiol 2014; 80:5001-11. [PMID: 24907337 DOI: 10.1128/aem.00998-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermoanaerobacterium saccharolyticum, a Gram-positive thermophilic anaerobic bacterium, grows robustly on insoluble hemicellulose, which requires a specialized suite of secreted and transmembrane proteins. We report here the characterization of proteins secreted by this organism. Cultures were grown on hemicellulose, glucose, xylose, starch, and xylan in pH-controlled bioreactors, and samples were analyzed via spotted microarrays and liquid chromatography-mass spectrometry. Key hydrolases and transporters employed by T. saccharolyticum for growth on hemicellulose were, for the most part, hitherto uncharacterized and existed in two clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 through Tsac_1349 for starch). A phosphotransferase system subunit, Tsac_0032, also appeared to be exclusive to growth on glucose. Previously identified hydrolases that showed strong conditional expression changes included XynA (Tsac_1459), XynC (Tsac_0897), and a pullulanase, Apu (Tsac_1342). An omnipresent transcript and protein making up a large percentage of the overall secretome, Tsac_0361, was tentatively identified as the primary S-layer component in T. saccharolyticum, and deletion of the Tsac_0361 gene resulted in gross morphological changes to the cells. The view of hemicellulose degradation revealed here will be enabling for metabolic engineering efforts in biofuel-producing organisms that degrade cellulose well but lack the ability to catabolize C5 sugars.
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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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Strontium-induced genomic responses of Cupriavidus metallidurans and strontium bioprecipitation as strontium carbonate. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0462-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Moberly JG, Miller CL, Brown SD, Biswas A, Brandt CC, Palumbo AV, Elias DA. Role of morphological growth state and gene expression in Desulfovibrio africanus strain Walvis Bay mercury methylation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4926-4932. [PMID: 22500779 DOI: 10.1021/es3000933] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The biogeochemical transformations of mercury are a complex process, with the production of methylmercury, a potent human neurotoxin, repeatedly demonstrated in sulfate- and Fe(III)-reducing as well as methanogenic bacteria. However, little is known regarding the morphology, genes, or proteins involved in methylmercury generation. Desulfovibrio africanus strain Walvis Bay is a Hg-methylating δ-proteobacterium with a sequenced genome and has unusual pleomorphic forms. In this study, a relationship between the pleomorphism and Hg methylation was investigated. Proportional increases in the sigmoidal (regular) cell form corresponded with increased net MeHg production but decreased when the pinched cocci (persister) form became the major morphotype. D. africanus microarrays indicated that the ferrous iron transport genes (feoAB), as well as ribosomal genes and several genes whose products are predicted to have metal binding domains (CxxC), were up-regulated during exposure to Hg in the exponential phase. Whereas no specific methylation pathways were identified, the finding that Hg may interfere with iron transport and the correlation of growth-phase-dependent morphology with MeHg production are notable. The identification of these relationships between differential gene expression, morphology, and the growth-phase dependence of Hg transformations suggests that actively growing cells are primarily responsible for methylation, and so areas with ample carbon and electron-acceptor concentrations may also generate a higher proportion of methylmercury than more oligotrophic environments. The observation of increased iron transporter expression also suggests that Hg methylation may interfere with iron biogeochemical cycles.
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Affiliation(s)
- James G Moberly
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Abstract
The shewanellae are ubiquitous in aquatic and sedimentary systems that are chemically stratified on a permanent or seasonal basis. In addition to their ability to utilize a diverse array of terminal electron acceptors, the microorganisms have evolved both common and unique responding mechanisms to cope with various stresses. This paper focuses on the response and adaptive mechanism of the shewanellae, largely based on transcriptional data.
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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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Physiological roles of ArcA, Crp, and EtrA and their interactive control on aerobic and anaerobic respiration in Shewanella oneidensis. PLoS One 2010; 5:e15295. [PMID: 21203399 PMCID: PMC3011009 DOI: 10.1371/journal.pone.0015295] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 11/05/2010] [Indexed: 12/31/2022] Open
Abstract
In the genome of Shewanella oneidensis, genes encoding the global regulators ArcA, Crp, and EtrA have been identified. All these proteins deviate from their counterparts in E. coli significantly in terms of functionality and regulon. It is worth investigating the involvement and relationship of these global regulators in aerobic and anaerobic respiration in S. oneidensis. In this study, the impact of the transcriptional factors ArcA, Crp, and EtrA on aerobic and anaerobic respiration in S. oneidensis were assessed. While all these proteins appeared to be functional in vivo, the importance of individual proteins in these two major biological processes differed. The ArcA transcriptional factor was critical in aerobic respiration while the Crp protein was indispensible in anaerobic respiration. Using a newly developed reporter system, it was found that expression of arcA and etrA was not influenced by growth conditions but transcription of crp was induced by removal of oxygen. An analysis of the impact of each protein on transcription of the others revealed that Crp expression was independent of the other factors whereas ArcA repressed both etrA and its own transcription while EtrA also repressed arcA transcription. Transcriptional levels of arcA in the wild type, crp, and etrA strains under either aerobic or anaerobic conditions were further validated by quantitative immunoblotting with a polyclonal antibody against ArcA. This extensive survey demonstrated that all these three global regulators are functional in S. oneidensis. In addition, the reporter system constructed in this study will facilitate in vivo transcriptional analysis of targeted promoters.
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Pelletier DA, Suresh AK, Holton GA, McKeown CK, Wang W, Gu B, Mortensen NP, Allison DP, Joy DC, Allison MR, Brown SD, Phelps TJ, Doktycz MJ. Effects of engineered cerium oxide nanoparticles on bacterial growth and viability. Appl Environ Microbiol 2010; 76:7981-9. [PMID: 20952651 PMCID: PMC3008265 DOI: 10.1128/aem.00650-10] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 10/05/2010] [Indexed: 11/20/2022] Open
Abstract
Interest in engineered nanostructures has risen in recent years due to their use in energy conservation strategies and biomedicine. To ensure prudent development and use of nanomaterials, the fate and effects of such engineered structures on the environment should be understood. Interactions of nanomaterials with environmental microorganisms are inevitable, but the general consequences of such interactions remain unclear, due to a lack of standard methods for assessing such interactions. Therefore, we have initiated a multianalytical approach to understand the interactions of synthesized nanoparticles with bacterial systems. These efforts are focused initially on cerium oxide nanoparticles and model bacteria in order to evaluate characterization procedures and the possible fate of such materials in the environment. The growth and viability of the Gram-negative species Escherichia coli and Shewanella oneidensis, a metal-reducing bacterium, and the Gram-positive species Bacillus subtilis were examined relative to cerium oxide particle size, growth media, pH, and dosage. A hydrothermal synthesis approach was used to prepare cerium oxide nanoparticles of defined sizes in order to eliminate complications originating from the use of organic solvents and surfactants. Bactericidal effects were determined from MIC and CFU measurements, disk diffusion tests, and live/dead assays. For E. coli and B. subtilis, clear strain- and size-dependent inhibition was observed, whereas S. oneidensis appeared to be unaffected by the particles. Transmission electron microscopy along with microarray-based transcriptional profiling was used to understand the response mechanism of the bacteria. Use of multiple analytical approaches adds confidence to toxicity assessments, while the use of different bacterial systems highlights the potential wide-ranging effects of nanomaterial interactions in the environment.
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Affiliation(s)
- Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Anil K. Suresh
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Gregory A. Holton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Catherine K. McKeown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Wei Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Baohua Gu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Ninell P. Mortensen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - David P. Allison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - David C. Joy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Martin R. Allison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Tommy J. Phelps
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6445, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, Department of Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6488
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Yang S, Pelletier DA, Lu TYS, Brown SD. The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. BMC Microbiol 2010; 10:135. [PMID: 20459639 PMCID: PMC2877685 DOI: 10.1186/1471-2180-10-135] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 05/07/2010] [Indexed: 11/29/2022] Open
Abstract
Background Zymomonas mobilis produces near theoretical yields of ethanol and recombinant strains are candidate industrial microorganisms. To date, few studies have examined its responses to various stresses at the gene level. Hfq is a conserved bacterial member of the Sm-like family of RNA-binding proteins, coordinating a broad array of responses including multiple stress responses. In a previous study, we observed Z. mobilis ZM4 gene ZMO0347 showed higher expression under anaerobic, stationary phase compared to that of aerobic, stationary conditions. Results We generated a Z. mobilis hfq insertion mutant AcRIM0347 in an acetate tolerant strain (AcR) background and investigated its role in model lignocellulosic pretreatment inhibitors including acetate, vanillin, furfural and hydroxymethylfurfural (HMF). Saccharomyces cerevisiae Lsm protein (Hfq homologue) mutants and Lsm protein overexpression strains were also assayed for their inhibitor phenotypes. Our results indicated that all the pretreatment inhibitors tested in this study had a detrimental effect on both Z. mobilis and S. cerevisiae, and vanillin had the most inhibitory effect followed by furfural and then HMF for both Z. mobilis and S. cerevisiae. AcRIM0347 was more sensitive than the parental strain to the inhibitors and had an increased lag phase duration and/or slower growth depending upon the conditions. The hfq mutation in AcRIM0347 was complemented partially by trans-acting hfq gene expression. We also assayed growth phenotypes for S. cerevisiae Lsm protein mutant and overexpression phenotypes. Lsm1, 6, and 7 mutants showed reduced tolerance to acetate and other pretreatment inhibitors. S. cerevisiae Lsm protein overexpression strains showed increased acetate and HMF resistance as compared to the wild-type, while the overexpression strains showed greater inhibition under vanillin stress conditions. Conclusions We have shown the utility of the pKNOCK suicide plasmid for mutant construction in Z. mobilis, and constructed a Gateway compatible expression plasmid for use in Z. mobilis for the first time. We have also used genetics to show Z. mobilis Hfq and S. cerevisiae Lsm proteins play important roles in resisting multiple, important industrially relevant inhibitors. The conserved nature of this global regulator offers the potential to apply insights from these fundamental studies for further industrial strain development.
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Affiliation(s)
- Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Comparative analysis of membranous proteomics of Shewanella decolorationis S12 grown with azo compound or Fe (III) citrate as sole terminal electron acceptor. Appl Microbiol Biotechnol 2010; 86:1513-23. [DOI: 10.1007/s00253-010-2475-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/23/2010] [Accepted: 01/25/2010] [Indexed: 02/06/2023]
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Yang Y, Harris DP, Luo F, Xiong W, Joachimiak M, Wu L, Dehal P, Jacobsen J, Yang Z, Palumbo AV, Arkin AP, Zhou J. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics 2009; 10:131. [PMID: 19321007 PMCID: PMC2667191 DOI: 10.1186/1471-2164-10-131] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 03/25/2009] [Indexed: 01/08/2023] Open
Abstract
Background Iron homeostasis of Shewanella oneidensis, a γ-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis. Results We show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator (SO2426) involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein (SO3032) and a gene previously implicated in protein degradation (SO2017) led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor (SO1415) caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways. Conclusion Using a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor (SO1415) with a role in anaerobic energy metabolism.
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Affiliation(s)
- Yunfeng Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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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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Involvement of Shewanella oneidensis MR-1 LuxS in biofilm development and sulfur metabolism. Appl Environ Microbiol 2009; 75:1301-7. [PMID: 19124589 DOI: 10.1128/aem.01393-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The role of LuxS in Shewanella oneidensis MR-1 has been examined by transcriptomic profiling, biochemical, and physiological experiments. The results indicate that a mutation in luxS alters biofilm development, not by altering quorum-sensing abilities but by disrupting the activated methyl cycle (AMC). The S. oneidensis wild type can produce a luminescence response in the AI-2 reporter strain Vibrio harveyi MM32. This luminescence response is abolished upon the deletion of luxS. The deletion of luxS also alters biofilm formations in static and flowthrough conditions. Genetic complementation restores the mutant biofilm defect, but the addition of synthetic AI-2 has no effect. These results suggest that AI-2 is not used as a quorum-sensing signal to regulate biofilm development in S. oneidensis. Growth on various sulfur sources was examined because of the involvement of LuxS in the AMC. A mutation in luxS produced a reduced ability to grow with methionine as the sole sulfur source. Methionine is a key metabolite used in the AMC to produce a methyl source in the cell and to recycle homocysteine. These data suggest that LuxS is important to metabolizing methionine and the AMC in S. oneidensis.
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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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Eicosapentaenoic acid plays a beneficial role in membrane organization and cell division of a cold-adapted bacterium, Shewanella livingstonensis Ac10. J Bacteriol 2008; 191:632-40. [PMID: 19011019 DOI: 10.1128/jb.00881-08] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Shewanella livingstonensis Ac10, a psychrotrophic gram-negative bacterium isolated from Antarctic seawater, produces eicosapentaenoic acid (EPA) as a component of phospholipids at low temperatures. EPA constitutes about 5% of the total fatty acids of cells grown at 4 degrees C. We found that five genes, termed orf2, orf5, orf6, orf7, and orf8, are specifically required for the synthesis of EPA by targeted disruption of the respective genes. The mutants lacking EPA showed significant growth retardation at 4 degrees C but not at 18 degrees C. Supplementation of a synthetic phosphatidylethanolamine that contained EPA at the sn-2 position complemented the growth defect. The EPA-less mutant became filamentous, and multiple nucleoids were observed in a single cell at 4 degrees C, indicating that the mutant has a defect in cell division. Electron microscopy of the cells by high-pressure freezing and freeze-substitution revealed abnormal intracellular membranes in the EPA-less mutant at 4 degrees C. We also found that the amounts of several membrane proteins were affected by the depletion of EPA. While polyunsaturated fatty acids are often considered to increase the fluidity of the hydrophobic membrane core, diffusion of a small hydrophobic molecule, pyrene, in the cell membranes and large unilamellar vesicles prepared from the lipid extracts was very similar between the EPA-less mutant and the parental strain. These results suggest that EPA in S. livingstonensis Ac10 is not required for bulk bilayer fluidity but plays a beneficial role in membrane organization and cell division at low temperatures, possibly through specific interaction between EPA and proteins involved in these cellular processes.
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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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Gao H, Pattison D, Yan T, Klingeman DM, Wang X, Petrosino J, Hemphill L, Wan X, Leaphart AB, Weinstock GM, Palzkill T, Zhou J. Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display. PLoS One 2008; 3:e2983. [PMID: 18714347 PMCID: PMC2500165 DOI: 10.1371/journal.pone.0002983] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/28/2008] [Indexed: 12/02/2022] Open
Abstract
A comprehensive gene collection for S. oneidensis was constructed using the lambda recombinase (Gateway) cloning system. A total of 3584 individual ORFs (85%) have been successfully cloned into the entry plasmids. To validate the use of the clone set, three sets of ORFs were examined within three different destination vectors constructed in this study. Success rates for heterologous protein expression of S. oneidensis His- or His/GST- tagged proteins in E. coli were approximately 70%. The ArcA and NarP transcription factor proteins were tested in an in vitro binding assay to demonstrate that functional proteins can be successfully produced using the clone set. Further functional validation of the clone set was obtained from phage display experiments in which a phage encoding thioredoxin was successfully isolated from a pool of 80 different clones after three rounds of biopanning using immobilized anti-thioredoxin antibody as a target. This clone set complements existing genomic (e.g., whole-genome microarray) and other proteomic tools (e.g., mass spectrometry-based proteomic analysis), and facilitates a wide variety of integrated studies, including protein expression, purification, and functional analyses of proteins both in vivo and in vitro.
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Affiliation(s)
- Haichun Gao
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Donna Pattison
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Tingfen Yan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dawn M. Klingeman
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaohu Wang
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Petrosino
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Lisa Hemphill
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiufeng Wan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Adam B. Leaphart
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Timothy Palzkill
- Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (TP); (JZ)
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail: (TP); (JZ)
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Abstract
The shewanellae are aquatic microorganisms with worldwide distribution. Their hallmark features include unparalleled respiratory diversity and the capacity to thrive at low temperatures. As a genus the shewanellae are physiologically diverse, and this review provides an overview of the varied roles they serve in the environment and describes what is known about how they might survive in such extreme and harsh environments. In light of their fascinating physiology, these organisms have several biotechnological uses, from bioremediation of chlorinated compounds, radionuclides, and other environmental pollutants to energy-generating biocatalysis. The ecology and biotechnology of these organisms are intertwined, with genomics playing a key role in our understanding of their physiology.
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Affiliation(s)
- Heidi H Hau
- Department of Microbiology and The BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, USA
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Chourey K, Thompson MR, Morrell-Falvey J, Verberkmoes NC, Brown SD, Shah M, Zhou J, Doktycz M, Hettich RL, Thompson DK. Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1. Appl Environ Microbiol 2006; 72:6331-44. [PMID: 16957260 PMCID: PMC1563591 DOI: 10.1128/aem.00813-06] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The biological impact of 24-h ("chronic") chromium(VI) [Cr(VI) or chromate] exposure on Shewanella oneidensis MR-1 was assessed by analyzing cellular morphology as well as genome-wide differential gene and protein expression profiles. Cells challenged aerobically with an initial chromate concentration of 0.3 mM in complex growth medium were compared to untreated control cells grown in the absence of chromate. At the 24-h time point at which cells were harvested for transcriptome and proteome analyses, no residual Cr(VI) was detected in the culture supernatant, thus suggesting the complete uptake and/or reduction of this metal by cells. In contrast to the untreated control cells, Cr(VI)-exposed cells formed apparently aseptate, nonmotile filaments that tended to aggregate. Transcriptome profiling and mass spectrometry-based proteomic characterization revealed that the principal molecular response to 24-h Cr(VI) exposure was the induction of prophage-related genes and their encoded products as well as a number of functionally undefined hypothetical genes that were located within the integrated phage regions of the MR-1 genome. In addition, genes with annotated functions in DNA metabolism, cell division, biosynthesis and degradation of the murein (peptidoglycan) sacculus, membrane response, and general environmental stress protection were upregulated, while genes encoding chemotaxis, motility, and transport/binding proteins were largely repressed under conditions of 24-h chromate treatment.
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Affiliation(s)
- Karuna Chourey
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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29
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Abstract
Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the recently formed and destroyed operons in E. coli. This allowed us to determine how operons form, how they become closely spaced, and how they die. Our findings suggest that operon evolution may be driven by selection on gene expression patterns. First, both operon creation and operon destruction lead to large changes in gene expression patterns. For example, the removal of lysA and ruvA from ancestral operons that contained essential genes allowed their expression to respond to lysine levels and DNA damage, respectively. Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. Third, although genes within operons are usually closely spaced because of a neutral bias toward deletion and because of selection against large overlaps, genes in highly expressed operons tend to be widely spaced because of regulatory fine-tuning by intervening sequences. Although operon evolution may be adaptive, it need not be optimal: new operons often comprise functionally unrelated genes that were already in proximity before the operon formed.
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Affiliation(s)
- Morgan N Price
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Virtual Institute for Microbial Stress and Survival, University of California San Francisco, San Francisco, California, United States of America
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Virtual Institute for Microbial Stress and Survival, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
| | - Eric J Alm
- Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Virtual Institute for Microbial Stress and Survival, University of California San Francisco, San Francisco, California, United States of America
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30
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Brown SD, Thompson MR, Verberkmoes NC, Chourey K, Shah M, Zhou J, Hettich RL, Thompson DK. Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress. Mol Cell Proteomics 2006; 5:1054-71. [PMID: 16524964 DOI: 10.1074/mcp.m500394-mcp200] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Temporal genomic profiling and whole-cell proteomic analyses were performed to characterize the dynamic molecular response of the metal-reducing bacterium Shewanella oneidensis MR-1 to an acute chromate shock. The complex dynamics of cellular processes demand the integration of methodologies that describe biological systems at the levels of regulation, gene and protein expression, and metabolite production. Genomic microarray analysis of the transcriptome dynamics of midexponential phase cells subjected to 1 mm potassium chromate (K(2)CrO(4)) at exposure time intervals of 5, 30, 60, and 90 min revealed 910 genes that were differentially expressed at one or more time points. Strongly induced genes included those encoding components of a TonB1 iron transport system (tonB1-exbB1-exbD1), hemin ATP-binding cassette transporters (hmuTUV), TonB-dependent receptors as well as sulfate transporters (cysP, cysW-2, and cysA-2), and enzymes involved in assimilative sulfur metabolism (cysC, cysN, cysD, cysH, cysI, and cysJ). Transcript levels for genes with annotated functions in DNA repair (lexA, recX, recA, recN, dinP, and umuD), cellular detoxification (so1756, so3585, and so3586), and two-component signal transduction systems (so2426) were also significantly up-regulated (p < 0.05) in Cr(VI)-exposed cells relative to untreated cells. By contrast, genes with functions linked to energy metabolism, particularly electron transport (e.g. so0902-03-04, mtrA, omcA, and omcB), showed dramatic temporal alterations in expression with the majority exhibiting repression. Differential proteomics based on multidimensional HPLC-MS/MS was used to complement the transcriptome data, resulting in comparable induction and repression patterns for a subset of corresponding proteins. In total, expression of 2,370 proteins were confidently verified with 624 (26%) of these annotated as hypothetical or conserved hypothetical proteins. The initial response of S. oneidensis to chromate shock appears to require a combination of different regulatory networks that involve genes with annotated functions in oxidative stress protection, detoxification, protein stress protection, iron and sulfur acquisition, and SOS-controlled DNA repair mechanisms.
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Affiliation(s)
- Steven D Brown
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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