101
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Early gene expression in Pseudomonas fluorescens exposed to a polymetallic solution. Cell Biol Toxicol 2015; 31:39-81. [DOI: 10.1007/s10565-015-9294-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/23/2015] [Indexed: 11/27/2022]
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102
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Joutey NT, Sayel H, Bahafid W, El Ghachtouli N. Mechanisms of hexavalent chromium resistance and removal by microorganisms. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2015; 233:45-69. [PMID: 25367133 DOI: 10.1007/978-3-319-10479-9_2] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Chromium has been and is extensively used worldwide in multiple industrial processes and is routinely discharged to the environment from such processes. Therefore, this heavy metal is a potential threat to the environment and to public health, primarily because it is non-biodegradable and environmentally persistent. Chromium exists in several oxidation states, the most stable of which are trivalent Cr(Ill) and hexavalent Cr(VI) species. Each species possesses its own individual chemical characteristics and produces its own biological effects. For example, Cr (Ill) is an essential oligoelement for humans, whereas Cr(VI) is carcinogenic and mutagenic. Several chemical methods are used to remove Cr(VI) from contaminated sites. Each of these methods has advantages and disadvantages. Currently, bioremediation is often the preferred method to deal with Cr contaminated sites, because it is eco-friendly, cost-effective and is a "natural" technology. Many yeast, bacterial and fungal species have been assessed for their suitability to reduce or remove Cr(VI) contamination. The mechanisms by which these microorganisms resist and reduce Cr(VI) are variable and are species dependent. There are several Cr-resistance mechanisms that are displayed by microorganisms. These include active efflux of Cr compounds, metabolic reduction of Cr(VI) to Cr (ill), and either intercellular or extracellular prec1p1tation. Microbial Cr (VI) removal typically involves three stages: binding of chromium to the cell surface, translocation of chromium into the cell, and reduction of Cr(VI) to Cr (ill). Cr(VI) reduction by microorganisms may proceed on the cell surface, outside the cell, or intracellularly, either directly via chromate reductase enzymes, or indirectly via metabolite reduction of Cr(VI). The uptake of chromium ions is a biphasic process. The primary step is known as biosorption, a metabolic energyindependent process. Thereafter, bioaccumulation occurs, but is much slower, and is dependent on cell metabolic activity. Choosing an appropriate bioremediation strategy for Cr is extremely important and must involve investigating and understanding the key mechanisms that are involved in microbial resistance to and removal of Cr(VI).
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Affiliation(s)
- Nezha Tahri Joutey
- Microbial Biotechnology Laboratory, Faculty of Sciences and Techniques, Sidi Mohamed Ben Abdellah University, Route Immouzer, 2202, Fez, Morocco
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103
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104
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Thatoi H, Das S, Mishra J, Rath BP, Das N. Bacterial chromate reductase, a potential enzyme for bioremediation of hexavalent chromium: a review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2014; 146:383-399. [PMID: 25199606 DOI: 10.1016/j.jenvman.2014.07.014] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 07/03/2014] [Accepted: 07/10/2014] [Indexed: 05/14/2023]
Abstract
Hexavalent chromium is mobile, highly toxic and considered as a priority environmental pollutant. Chromate reductases, found in chromium resistant bacteria are known to catalyse the reduction of Cr(VI) to Cr(III) and have recently received particular attention for their potential use in bioremediation process. Different chromate reductases such as ChrR, YieF, NemA and LpDH, have been identified from bacterial sources which are located either in soluble fractions (cytoplasm) or bound to the membrane of the bacterial cell. The reducing conditions under which these enzymes are functional can either be aerobic or anaerobic or sometimes both. Enzymatic reduction of Cr(VI) to Cr(III) involves transfer of electrons from electron donors like NAD(P)H to Cr(VI) and simultaneous generation of reactive oxygen species (ROS). Based on the steps involved in electron transfer to Cr(VI) and the subsequent amount of ROS generated, two reaction mechanisms, namely, Class I "tight" and Class II "semi tight" have been proposed. The present review discusses on the types of chromate reductases found in different bacteria, their mode of action and potential applications in bioremediation of hexavalent chromium both under free and immobilize conditions. Besides, techniques used in characterization of the Cr (VI) reduced products were also discussed.
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Affiliation(s)
- Hrudayanath Thatoi
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Techno-Campus, Ghatikia, Bhubaneswar 751003, Odisha, India.
| | - Sasmita Das
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Techno-Campus, Ghatikia, Bhubaneswar 751003, Odisha, India
| | - Jigni Mishra
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Techno-Campus, Ghatikia, Bhubaneswar 751003, Odisha, India
| | - Bhagwat Prasad Rath
- Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Techno-Campus, Ghatikia, Bhubaneswar 751003, Odisha, India
| | - Nigamananda Das
- Department of Chemistry, North Orissa University, Takatpur, Baripada 757003, Odisha, India
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105
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Orellana R, Hixson KK, Murphy S, Mester T, Sharma ML, Lipton MS, Lovley DR. Proteome of Geobacter sulfurreducens in the presence of U(VI). Microbiology (Reading) 2014; 160:2607-2617. [DOI: 10.1099/mic.0.081398-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Geobacter species often play an important role in the in situ bioremediation of uranium-contaminated groundwater, but little is known about how these microbes avoid uranium toxicity. To evaluate this further, the proteome of Geobacter sulfurreducens exposed to 100 µM U(VI) acetate was compared to control cells not exposed to U(VI). Of the 1363 proteins detected from these cultures, 203 proteins had higher abundance during exposure to U(VI) compared with the control cells and 148 proteins had lower abundance. U(VI)-exposed cultures expressed lower levels of proteins involved in growth, protein and amino acid biosynthesis, as well as key central metabolism enzymes as a result of the deleterious effect of U(VI) on the growth of G. sulfurreducens. In contrast, proteins involved in detoxification, such as several efflux pumps belonging to the RND (resistance–nodulation–cell division) family, and membrane protection, and other proteins, such as chaperones and proteins involved in secretion systems, were found in higher abundance in cells exposed to U(VI). Exposing G. sulfurreducens to U(VI) resulted in a higher abundance of many proteins associated with the oxidative stress response, such as superoxide dismutase and superoxide reductase. A strain in which the gene for superoxide dismutase was deleted grew more slowly than the WT strain in the presence of U(VI), but not in its absence. The results suggested that there is no specific mechanism for uranium detoxification. Rather, multiple general stress responses are induced, which presumably enable Geobacter species to tolerate high uranium concentrations.
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Affiliation(s)
- Roberto Orellana
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Kim K. Hixson
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sean Murphy
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Tünde Mester
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Manju L. Sharma
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Mary S. Lipton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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106
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Zhang X, Wu W, Virgo N, Zou L, Liu P, Li X. Global transcriptome analysis of hexavalent chromium stress responses in Staphylococcus aureus LZ-01. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:1534-1545. [PMID: 25086489 DOI: 10.1007/s10646-014-1294-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/16/2014] [Indexed: 06/03/2023]
Abstract
Staphylococcus aureus strain LZ-01, isolated from the Lanzhou reaches of the Yellow River, is capable of reducing Cr(VI) to Cr(III) aerobically. We employed transcriptome sequencing analysis to identify genes involved in Cr(VI) stress responses in S. aureus LZ-01. Our results showed that 512 of the 2,370 predicted genes displayed up-regulation (>2-fold), and 49 genes were down-regulated (<50 %) after Cr(VI) exposure. Among up-regulated genes, 128 genes were annotated to encode proteins involved in cellular processes; 68 were categorized to transport and binding proteins; 26 were involved in DNA repair and 32 were associated with regulatory functions. To further elucidate the Cr(VI) resistance and reduction mechanism, we carried out physiological tests and quantitative PCR analysis. Both RNA-seq and qRT-PCR data showed genes encoding a thioredoxin reductase and main subunits of cytochrome c oxidase complex were up-regulated upon Cr(VI) treatment. Either cadmium or NaN3 treatment could inhibit Cr(VI) reduction which indicates that thioredoxin and cytochrome are involved in Cr(VI) reduction strain LZ-01. 29 ABC-type metal/multidrug transporters and efflux pumps were up-regulated, suggesting that they are involved in Cr(VI) resistance by pumping chromium ions out of cells. The up-regulation of 26 DNA repair genes demonstrate that Cr(VI) is toxic to DNA and those DNA protection proteins need to be responded for Cr(VI) stress. Based on these results, the mechanism of strain LZ-01 resists and reduces Cr(VI) is revealed.
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Affiliation(s)
- Xiaowei Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, 222 South Tianshui Road, Lanzhou, Gansu, 730000, People's Republic of China
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107
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Martínez-Trujillo M, Méndez-Bravo A, Ortiz-Castro R, Hernández-Madrigal F, Ibarra-Laclette E, Ruiz-Herrera LF, Long TA, Cervantes C, Herrera-Estrella L, López-Bucio J. Chromate alters root system architecture and activates expression of genes involved in iron homeostasis and signaling in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2014; 86:35-50. [PMID: 24928490 DOI: 10.1007/s11103-014-0210-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 06/04/2014] [Indexed: 06/03/2023]
Abstract
Soil contamination by hexavalent chromium [Cr(VI) or chromate] due to anthropogenic activities has become an increasingly important environmental problem. To date few studies have been performed to elucidate the signaling networks involved on adaptive responses to (CrVI) toxicity in plants. In this work, we report that depending upon its concentration, Cr(VI) alters in different ways the architecture of the root system in Arabidopsis thaliana seedlings. Low concentrations of Cr (20-40 µM) promoted primary root growth, while concentrations higher than 60 µM Cr repressed growth and increased formation of root hairs, lateral root primordia and adventitious roots. We analyzed global gene expression changes in seedlings grown in media supplied with 20 or 140 µM Cr. The level of 731 transcripts was significantly modified in response to Cr treatment with only five genes common to both Cr concentrations. Interestingly, 23 genes related to iron (Fe) acquisition were up-regulated including IRT1, YSL2, FRO5, BHLH100, BHLH101 and BHLH039 and the master controllers of Fe deficiency responses PYE and BTS were specifically activated in pericycle cells. It was also found that increasing concentration of Cr in the plant correlated with a decrease in Fe content, but increased both acidification of the rhizosphere and activity of the ferric chelate reductase. Supply of Fe to Cr-treated Arabidopsis allowed primary root to resume growth and alleviated toxicity symptoms, indicating that Fe nutrition is a major target of Cr stress in plants. Our results show that low Cr levels are beneficial to plants and that toxic Cr concentrations activate a low-Fe rescue system.
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Affiliation(s)
- Miguel Martínez-Trujillo
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio R, Ciudad Universitaria, C. P. 58030, Morelia, Michoacán, Mexico
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108
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Zou L, Chen Z, Zhang X, Liu P, Li X. Phosphate promotes uranium (VI) adsorption in Staphylococcus aureus LZ-01. Lett Appl Microbiol 2014; 59:528-34. [PMID: 25065820 DOI: 10.1111/lam.12310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/03/2014] [Accepted: 07/23/2014] [Indexed: 11/26/2022]
Abstract
UNLABELLED Staphylococcus aureus LZ-01 was isolated from the Yellow River upstream from Lanzhou which can resist and reduce chromium (VI) to chromium (III). In this study, strain LZ-01's uranium (VI) resistance and adsorption abilities were investigated. Our results showed that it can resist 2 mmol l(-1) U(VI) and adsorb 96% of 2 mmol l(-1) U(VI) after 6 h incubation. Transmission electron microscopy (TEM) images showed that precipitates were formed on the surface of the cells. Energy dispersive X-ray spectroscopy (EDX) analysis indicated that the precipitates contained uranium and phosphorus. The U(VI) adsorption rate of strain LZ-01 was promoted by 20 mmol l(-1) phosphate. It adsorbed 45% of 2·5 mmol l(-1) U(VI) in 30 min compared to 36% without phosphate (P < 0·05). Strain LZ-01 can resist heavy metals and survive in nuclear waste-contaminated environments. Strain LZ-01 might be a potential candidate for nuclear waste remediation with phosphate added. SIGNIFICANCE AND IMPACT OF THE STUDY Staphylococcus aureus LZ-01 can resist 2 mmol l(-1) U(VI). It could adsorb more than 90% of the 2 mmol l(-1) U(VI) in 6 h. Uranium is precipitated with phosphorus on the surface of the cells. Phosphate promotes uranium adsorption in strain LZ-01, and its U(VI) adsorption capacity is related to its cell availability. These results indicate that the strain LZ-01 might be a potential candidate for remediation of nuclear waste when phosphate is added.
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Affiliation(s)
- L Zou
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, Gansu, China
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109
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Shamim S, Rehman A, Qazi MH. Cadmium-resistance mechanism in the bacteria Cupriavidus metallidurans CH34 and Pseudomonas putida mt2. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2014; 67:149-157. [PMID: 24595738 DOI: 10.1007/s00244-014-0009-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
Cupriavidus metallidurans CH34 and Pseudomonas putida mt2 were used as cadmium (Cd)-resistant and -sensitive bacteria, respectively, to study Cd uptake, sorption, intracellular accumulation, metallothionein (MT) induction, and bioremediation potential of both isolates. According to this research work, Cd had a stimulatory effect on the growth of CH34 cells (OD578 = 1.43) compared with mt2 cells (OD578 = 0.8). Addition of N,N'-dicyclohexylcarbodiimide (DCCD) and 2,4-dinitrophenol (DNP) along with Cd resulted in more cell growth in mt2 (OD578 = 0.71) compared with CH34 (OD578 = 0.34). DCCD and DNP inhibited this active uptake only in CH34 but not in mt2. Greater Cd interaction with the cell surface was observed in mt2 cells compared with CH34 cells. Intracellular Cd accumulation was interrupted by DCCD and DNP in CH34 (only 1.81 ± 0.04 μg L(-1) at 5 h) but not in mt2 (24.41 ± 0.01 μg L(-1) at 5 h). Intracellular Cd uptake was observed in even killed mt2 cells (7.11 ± 0.05 μg L(-1) at 5 h) compared with CH34 cells (2.50 ± 0.08 μg L(-1) at 5 h). This result showed that the Cd accumulation mechanism in CH34 is ATPase-dependent, whereas in mt2 uptake mechanism is not ATPase-dependent because mt2 ATPase was not inhibited by DCCD and DNP. CH34 removed 93 mg L(-1) of Cd after 8 days from original industrial effluent, which was more than Cd removal by CH34 from distilled water (i.e. 90 mg L(-1) after 8 days). mt2 was able to remove 80 mg L(-1) of Cd after 8 days from original industrial effluent, which was more than Cd removal by mt2 from distilled water (i.e. 77 mg L(-1) after 8 days). Cd did not induce any MT in CH34, but it did so in mt2 (14 kDa), which was thought to be a Cd-resistance mechanism operative in mt2.
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Affiliation(s)
- Saba Shamim
- Department of Microbiology and Molecular Genetics, University of the Punjab, New Campus, Lahore, 54590, Pakistan,
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110
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Modulation of medium pH by Caulobacter crescentus facilitates recovery from uranium-induced growth arrest. Appl Environ Microbiol 2014; 80:5680-8. [PMID: 25002429 DOI: 10.1128/aem.01294-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments.
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111
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Role of Bacillus subtilis error prevention oxidized guanine system in counteracting hexavalent chromium-promoted oxidative DNA damage. Appl Environ Microbiol 2014; 80:5493-502. [PMID: 24973075 DOI: 10.1128/aem.01665-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromium pollution is potentially detrimental to bacterial soil communities, compromising carbon and nitrogen cycles that are essential for life on earth. It has been proposed that intracellular reduction of hexavalent chromium [Cr(VI)] to trivalent chromium [Cr(III)] may cause bacterial death by a mechanism that involves reactive oxygen species (ROS)-induced DNA damage; the molecular basis of the phenomenon was investigated in this work. Here, we report that Bacillus subtilis cells lacking a functional error prevention oxidized guanine (GO) system were significantly more sensitive to Cr(VI) treatment than cells of the wild-type (WT) strain, suggesting that oxidative damage to DNA is involved in the deleterious effects of the oxyanion. In agreement with this suggestion, Cr(VI) dramatically increased the ROS concentration and induced mutagenesis in a GO-deficient B. subtilis strain. Alkaline gel electrophoresis (AGE) analysis of chromosomal DNA of WT and ΔGO mutant strains subjected to Cr(VI) treatment revealed that the DNA of the ΔGO strain was more susceptible to DNA glycosylase Fpg attack, suggesting that chromium genotoxicity is associated with 7,8-dihydro-8-oxodeoxyguanosine (8-oxo-G) lesions. In support of this notion, specific monoclonal antibodies detected the accumulation of 8-oxo-G lesions in the chromosomes of B. subtilis cells subjected to Cr(VI) treatment. We conclude that Cr(VI) promotes mutagenesis and cell death in B. subtilis by a mechanism that involves radical oxygen attack of DNA, generating 8-oxo-G, and that such effects are counteracted by the prevention and repair GO system.
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112
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Gómez-Sagasti MT, Becerril JM, Martín I, Epelde L, Garbisu C. cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals. Cell Biol Toxicol 2014; 30:207-32. [DOI: 10.1007/s10565-014-9281-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/12/2014] [Indexed: 12/30/2022]
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113
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Homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism. Indian J Microbiol 2014; 54:450-8. [PMID: 25320445 DOI: 10.1007/s12088-014-0482-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/06/2014] [Indexed: 10/25/2022] Open
Abstract
Superoxide dismutase (SOD), a well known antioxidant enzyme, is known to exert its presence across bacteria to humans. Apart from their well-known antioxidant defense mechanisms, their association with various extremophiles in response to various stress conditions is poorly understood. Here, we have discussed the conservation and the prevalence of SODs among 21 representative extremophiles. A systematic investigation of aligned amino acid sequences of SOD from all the selected extremophiles revealed a consensus motif D-[VLE]-[FW]-E-H-[AS]-Y-[YM]. To computationally predict the correlation of SOD with the various stress conditions encountered by these extremophiles, Exiguobacterium was selected as a model organism which is known to survive under various adverse extremophilic conditions. Interestingly, our phylogenetic study based on SOD homology revealed that Exiguobacterium sibiricum was one of the closest neighbors of Deinococcus radiodurans and Thermus thermophilus. Next, we sought to predict 3-D model structure of SOD for E. sibiricum (PMDB ID: 0078260), which showed >95 % similarity with D. radiodurans R1 SOD. The reliability of the predicted SOD model was checked by using various validation metrics, including Ramachandran plot, Z-score and normalized qualitative model energy analysis score. Further, various physicochemical properties of E. sibiricum SOD were calculated using different prominent resources.
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114
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Biomineralization of uranium by PhoY phosphatase activity aids cell survival in Caulobacter crescentus. Appl Environ Microbiol 2014; 80:4795-804. [PMID: 24878600 DOI: 10.1128/aem.01050-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus is known to tolerate high levels of uranium [U(VI)], but its detoxification mechanism is poorly understood. Here we show that C. crescentus is able to facilitate U(VI) biomineralization through the formation of U-Pi precipitates via its native alkaline phosphatase activity. The U-Pi precipitates, deposited on the cell surface in the form of meta-autunite structures, have a lower U/Pi ratio than do chemically produced precipitates. The enzyme that is responsible for the phosphatase activity and thus the biomineralization process is identified as PhoY, a periplasmic alkaline phosphatase with broad substrate specificity. Furthermore, PhoY is shown to confer a survival advantage on C. crescentus toward U(VI) under both growth and nongrowth conditions. Results obtained in this study thus highlight U(VI) biomineralization as a resistance mechanism in microbes, which not only improves our understanding of bacterium-mineral interactions but also aids in defining potential ecological niches for metal-resistant bacteria.
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115
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Yang S, Wen X, Zhao L, Shi Y, Jin H. Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route. PLoS One 2014; 9:e96552. [PMID: 24794099 PMCID: PMC4008593 DOI: 10.1371/journal.pone.0096552] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/08/2014] [Indexed: 11/25/2022] Open
Abstract
The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.
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Affiliation(s)
- Sizhong Yang
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
- * E-mail:
| | - Xi Wen
- College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, Gansu, China
| | - Liang Zhao
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Yulan Shi
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
| | - Huijun Jin
- State Key Laboratory of Frozen Soils Engineering (SKLFSE), Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences, Lanzhou, Gansu, China
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116
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Krumova E, Pashova S, Dolashka-Angelova P, Angelova M. Adaptive Response ofHumicola Luteato Copper Exposure. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2011.0114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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117
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Transcriptional Response of Selenopolypeptide Genes and Selenocysteine Biosynthesis Machinery Genes in Escherichia coli during Selenite Reduction. Int J Microbiol 2014; 2014:394835. [PMID: 24839442 PMCID: PMC4009273 DOI: 10.1155/2014/394835] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 02/28/2014] [Accepted: 03/16/2014] [Indexed: 01/05/2023] Open
Abstract
Bacteria can reduce toxic selenite into less toxic, elemental selenium (Se0), but the mechanism on how bacterial cells reduce selenite at molecular level is still not clear. We used Escherichia coli strain K12, a common bacterial strain, as a model to study its growth response to sodium selenite (Na2SeO3) treatment and then used quantitative real-time PCR (qRT-PCR) to quantify transcript levels of three E. coli selenopolypeptide genes and a set of machinery genes for selenocysteine (SeCys) biosynthesis and incorporation into polypeptides, whose involvements in the selenite reduction are largely unknown. We determined that 5 mM Na2SeO3 treatment inhibited growth by ∼50% while 0.001 to 0.01 mM treatments stimulated cell growth by ∼30%. Under 50% inhibitory or 30% stimulatory Na2SeO3 concentration, selenopolypeptide genes (fdnG, fdoG, and fdhF) whose products require SeCys but not SeCys biosynthesis machinery genes were found to be induced ≥2-fold. In addition, one sulfur (S) metabolic gene iscS and two previously reported selenite-responsive genes sodA and gutS were also induced ≥2-fold under 50% inhibitory concentration. Our findings provide insight about the detoxification of selenite in E. coli via induction of these genes involved in the selenite reduction process.
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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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Khemiri A, Carrière M, Bremond N, Ben Mlouka MA, Coquet L, Llorens I, Chapon V, Jouenne T, Cosette P, Berthomieu C. Escherichia coli response to uranyl exposure at low pH and associated protein regulations. PLoS One 2014; 9:e89863. [PMID: 24587082 PMCID: PMC3935937 DOI: 10.1371/journal.pone.0089863] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/23/2014] [Indexed: 11/18/2022] Open
Abstract
Better understanding of uranyl toxicity in bacteria is necessary to optimize strains for bioremediation purposes or for using bacteria as biodetectors for bioavailable uranyl. In this study, after different steps of optimization, Escherichia colicells were exposed to uranyl at low pH to minimize uranyl precipitation and to increase its bioavailability. Bacteria were adapted to mid acidic pH before exposure to 50 or 80 µM uranyl acetate for two hours at pH≈3. To evaluate the impact of uranium, growth in these conditions were compared and the same rates of cells survival were observed in control and uranyl exposed cultures. Additionally, this impact was analyzedby two-dimensional differential gel electrophoresis proteomics to discover protein actors specifically present or accumulated in contact with uranium.Exposure to uranium resulted in differential accumulation of proteins associated with oxidative stress and in the accumulation of the NADH/quinone oxidoreductase WrbA. This FMN dependent protein performs obligate two-electron reduction of quinones, and may be involved in cells response to oxidative stress. Interestingly, this WrbA protein presents similarities with the chromate reductase from E. coli, which was shown to reduce uranyl in vitro.
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Affiliation(s)
- Arbia Khemiri
- CEA, DSV, IBEB, Commissariat à l'Energie Atomique, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France ; CNRS, UMR Biologie Végétale et Microbiologie Environnementales 7265, Saint-Paul-lez-Durance, France ; Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Marie Carrière
- UMR E3 CEA-Université Joseph Fourier, Service de Chimie Inorganique et Biologique, Laboratoire Lésions des Acides Nucléiques (LAN), Grenoble, France
| | - Nicolas Bremond
- CEA, DSV, IBEB, Commissariat à l'Energie Atomique, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France ; CNRS, UMR Biologie Végétale et Microbiologie Environnementales 7265, Saint-Paul-lez-Durance, France ; Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Mohamed Amine Ben Mlouka
- UMR 6270 CNRS, Plateforme Protéomique PISSARO, IRIB -Université de Rouen, Mont Saint Aignan, France
| | - Laurent Coquet
- UMR 6270 CNRS, Plateforme Protéomique PISSARO, IRIB -Université de Rouen, Mont Saint Aignan, France
| | - Isabelle Llorens
- ESRF-CRG-FAME beamline, Polygone Scientifique Louis Néel, Grenoble, France ; Commissariat à l'Energie Atomique CEA, DSM, INAC, Laboratoire Nanostructure et Rayonnement Synchrotron, Grenoble, France
| | - Virginie Chapon
- CEA, DSV, IBEB, Commissariat à l'Energie Atomique, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France ; CNRS, UMR Biologie Végétale et Microbiologie Environnementales 7265, Saint-Paul-lez-Durance, France ; Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
| | - Thierry Jouenne
- UMR 6270 CNRS, Plateforme Protéomique PISSARO, IRIB -Université de Rouen, Mont Saint Aignan, France
| | - Pascal Cosette
- UMR 6270 CNRS, Plateforme Protéomique PISSARO, IRIB -Université de Rouen, Mont Saint Aignan, France
| | - Catherine Berthomieu
- CEA, DSV, IBEB, Commissariat à l'Energie Atomique, Laboratoire des Interactions Protéine-Métal, Saint-Paul-lez-Durance, France ; CNRS, UMR Biologie Végétale et Microbiologie Environnementales 7265, Saint-Paul-lez-Durance, France ; Université d'Aix-Marseille, Saint-Paul-lez-Durance, France
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Bacterial mechanisms for Cr(VI) resistance and reduction: an overview and recent advances. Folia Microbiol (Praha) 2014; 59:321-32. [PMID: 24470188 DOI: 10.1007/s12223-014-0304-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 01/12/2014] [Indexed: 01/16/2023]
Abstract
Chromium pollution is increasing incessantly due to continuing industrialization. Of various oxidation states, Cr(6+) is very toxic due to its carcinogenic and mutagenic nature. It also has deleterious effects on different microorganisms as well as on plants. Many species of bacteria thriving in the Cr(6+)-contaminated environments have evolved novel strategies to cope with Cr(6+) toxicity. Generally, decreased uptake or exclusion of Cr(6+) compounds through the membranes, biosorption, and the upregulation of genes associated with oxidative stress response are some of the resistance mechanisms in bacterial cells to overcome the Cr(6+) stress. In addition, bacterial Cr(6+) reduction into Cr(3+) is also a mechanism of specific significance as it transforms toxic and mobile chromium derivatives into reduced species which are innocuous and immobile. Ecologically, the bacterial trait of reductive immobilization of Cr(6+) derivatives is of great advantage in bioremediation. The present review is an effort to underline the bacterial resistance and reducing mechanisms to Cr(6+) compounds with recent development in order to garner a broad perspective.
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121
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Gonzalez D, Kozdon JB, McAdams HH, Shapiro L, Collier J. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. Nucleic Acids Res 2014; 42:3720-35. [PMID: 24398711 PMCID: PMC3973325 DOI: 10.1093/nar/gkt1352] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.
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Affiliation(s)
- Diego Gonzalez
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, CH 1015, Switzerland, Department of Developmental Biology, Stanford University, CA 94305, USA and Department of Chemistry, Stanford University, CA 94305, USA
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122
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Störmer R, Wichels A, Gerdts G. Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment. MARINE POLLUTION BULLETIN 2013; 77:113-122. [PMID: 24229782 DOI: 10.1016/j.marpolbul.2013.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 06/02/2023]
Abstract
The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.
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Affiliation(s)
- Rebecca Störmer
- Microbial Ecology Group Alfred Wegener, Institute for Polar and Marine Research, Kurpromenade 201, 27498 Helgoland, Germany.
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123
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Viti C, Marchi E, Decorosi F, Giovannetti L. Molecular mechanisms of Cr(VI) resistance in bacteria and fungi. FEMS Microbiol Rev 2013; 38:633-59. [PMID: 24188101 DOI: 10.1111/1574-6976.12051] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/13/2013] [Accepted: 10/28/2013] [Indexed: 11/28/2022] Open
Abstract
Hexavalent chromium [Cr(VI)] contamination is one of the main problems of environmental protection because the Cr(VI) is a hazard to human health. The Cr(VI) form is highly toxic, mutagenic, and carcinogenic, and it spreads widely beyond the site of initial contamination because of its mobility. Cr(VI), crossing the cellular membrane via the sulfate uptake pathway, generates active intermediates Cr(V) and/or Cr(IV), free radicals, and Cr(III) as the final product. Cr(III) affects DNA replication, causes mutagenesis, and alters the structure and activity of enzymes, reacting with their carboxyl and thiol groups. To persist in Cr(VI)-contaminated environments, microorganisms must have efficient systems to neutralize the negative effects of this form of chromium. The systems involve detoxification or repair strategies such as Cr(VI) efflux pumps, Cr(VI) reduction to Cr(III), and activation of enzymes involved in the ROS detoxifying processes, repair of DNA lesions, sulfur metabolism, and iron homeostasis. This review provides an overview of the processes involved in bacterial and fungal Cr(VI) resistance that have been identified through 'omics' studies. A comparative analysis of the described molecular mechanisms is offered and compared with the cellular evidences obtained using classical microbiological approaches.
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Affiliation(s)
- Carlo Viti
- Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente - sezione di Microbiologia, Università degli Studi di Firenze, Florence, Italy
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124
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Acharya C, Apte SK. Insights into the interactions of cyanobacteria with uranium. PHOTOSYNTHESIS RESEARCH 2013; 118:83-94. [PMID: 24101170 DOI: 10.1007/s11120-013-9928-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 09/23/2013] [Indexed: 06/02/2023]
Abstract
Due to various activities associated with nuclear industry, uranium is migrated to aquatic environments like groundwater, ponds or oceans. Uranium forms stable carbonate complexes in the oxic waters of pH 7-10 which results in a high degree of uranium mobility. Microorganisms employ various mechanisms which significantly influence the mobility and the speciation of uranium in aquatic environments. Uranyl bioremediation studies, this far, have generally focussed on low pH conditions and related to adsorption of positively charged UO2 (2+) onto negatively charged microbial surfaces. Sequestration of anionic uranium species, i.e. [UO2(CO3) 2 (2-) ] and [UO2(CO3) 3 (4-) ] onto microbial surfaces has received only scant attention. Marine cyanobacteria are effective metal adsorbents and represent an important sink for metals in aquatic environment. This article addresses the cyanobacterial interactions with toxic metals in general while stressing on uranium. It focusses on the possible mechanisms employed by cyanobacteria to sequester uranium from aqueous solutions above circumneutral pH where negatively charged uranyl carbonate complexes dominate aqueous uranium speciation. The mechanisms demonstrated by cyanobacteria are important components of biogeochemical cycle of uranium and are useful for the development of appropriate strategies, either to recover or remediate uranium from the aquatic environments.
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Affiliation(s)
- Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India,
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125
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da Silva Neto JF, Lourenço RF, Marques MV. Global transcriptional response of Caulobacter crescentus to iron availability. BMC Genomics 2013; 14:549. [PMID: 23941329 PMCID: PMC3751524 DOI: 10.1186/1471-2164-14-549] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 08/09/2013] [Indexed: 01/22/2023] Open
Abstract
Background In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. Results In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility. Conclusions Using a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.
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Affiliation(s)
- José F da Silva Neto
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av Prof Lineu Prestes 1374, 05508-000 São Paulo, Brazil.
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Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals. GENOME ANNOUNCEMENTS 2013; 1:1/3/e00322-13. [PMID: 23792749 PMCID: PMC3675514 DOI: 10.1128/genomea.00322-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here.
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127
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Valencia EY, Braz VS, Guzzo C, Marques MV. Two RND proteins involved in heavy metal efflux in Caulobacter crescentus belong to separate clusters within proteobacteria. BMC Microbiol 2013; 13:79. [PMID: 23578014 PMCID: PMC3637150 DOI: 10.1186/1471-2180-13-79] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 03/21/2013] [Indexed: 11/15/2022] Open
Abstract
Background Heavy metal Resistance-Nodulation-Division (HME-RND) efflux systems help Gram-negative bacteria to keep the intracellular homeostasis under high metal concentrations. These proteins constitute the cytoplasmic membrane channel of the tripartite RND transport systems. Caulobacter crescentus NA1000 possess two HME-RND proteins, and the aim of this work was to determine their involvement in the response to cadmium, zinc, cobalt and nickel, and to analyze the phylogenetic distribution and characteristic signatures of orthologs of these two proteins. Results Expression assays of the czrCBA operon showed significant induction in the presence of cadmium and zinc, and moderate induction by cobalt and nickel. The nczCBA operon is highly induced in the presence of nickel and cobalt, moderately induced by zinc and not induced by cadmium. Analysis of the resistance phenotype of mutant strains showed that the ΔczrA strain is highly sensitive to cadmium, zinc and cobalt, but resistant to nickel. The ΔnczA strain and the double mutant strain showed reduced growth in the presence of all metals tested. Phylogenetic analysis of the C. crescentus HME-RND proteins showed that CzrA-like proteins, in contrast to those similar to NczA, are almost exclusively found in the Alphaproteobacteria group, and the characteristic protein signatures of each group were highlighted. Conclusions The czrCBA efflux system is involved mainly in response to cadmium and zinc with a secondary role in response to cobalt. The nczCBA efflux system is involved mainly in response to nickel and cobalt, with a secondary role in response to cadmium and zinc. CzrA belongs to the HME2 subfamily, which is almost exclusively found in the Alphaproteobacteria group, as shown by phylogenetic analysis. NczA belongs to the HME1 subfamily which is more widespread among diverse Proteobacteria groups. Each of these subfamilies present distinctive amino acid signatures.
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Affiliation(s)
- Estela Y Valencia
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av, Prof, Lineu Prestes 1374, São Paulo, SP, 05508-900, Brazil
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Mukherjee A, Wheaton GH, Blum PH, Kelly RM. Uranium extremophily is an adaptive, rather than intrinsic, feature for extremely thermoacidophilic Metallosphaera species. Proc Natl Acad Sci U S A 2012; 109:16702-7. [PMID: 23010932 PMCID: PMC3478614 DOI: 10.1073/pnas.1210904109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermoacidophilic archaea are found in heavy metal-rich environments, and, in some cases, these microorganisms are causative agents of metal mobilization through cellular processes related to their bioenergetics. Given the nature of their habitats, these microorganisms must deal with the potentially toxic effect of heavy metals. Here, we show that two thermoacidophilic Metallosphaera species with nearly identical (99.99%) genomes differed significantly in their sensitivity and reactivity to uranium (U). Metallosphaera prunae, isolated from a smoldering heap on a uranium mine in Thüringen, Germany, could be viewed as a "spontaneous mutant" of Metallosphaera sedula, an isolate from Pisciarelli Solfatara near Naples. Metallosphaera prunae tolerated triuranium octaoxide (U(3)O(8)) and soluble uranium [U(VI)] to a much greater extent than M. sedula. Within 15 min following exposure to "U(VI) shock," M. sedula, and not M. prunae, exhibited transcriptomic features associated with severe stress response. Furthermore, within 15 min post-U(VI) shock, M. prunae, and not M. sedula, showed evidence of substantial degradation of cellular RNA, suggesting that transcriptional and translational processes were aborted as a dynamic mechanism for resisting U toxicity; by 60 min post-U(VI) shock, RNA integrity in M. prunae recovered, and known modes for heavy metal resistance were activated. In addition, M. sedula rapidly oxidized solid U(3)O(8) to soluble U(VI) for bioenergetic purposes, a chemolithoautotrophic feature not previously reported. M. prunae, however, did not solubilize solid U(3)O(8) to any significant extent, thereby not exacerbating U(VI) toxicity. These results point to uranium extremophily as an adaptive, rather than intrinsic, feature for Metallosphaera species, driven by environmental factors.
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Affiliation(s)
- Arpan Mukherjee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Garrett H. Wheaton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
| | - Paul H. Blum
- Beadle Center for Genetics, University of Nebraska-Lincoln, Lincoln, NE 68588-0666
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; and
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129
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Response of P. aeruginosa E1 Gene Expression to Cadmium Stress. Curr Microbiol 2012; 65:799-804. [DOI: 10.1007/s00284-012-0224-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 08/07/2012] [Indexed: 11/25/2022]
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130
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Kohler C, Lourenço RF, Avelar GM, Gomes SL. Extracytoplasmic function (ECF) sigma factor σF is involved in Caulobacter crescentus response to heavy metal stress. BMC Microbiol 2012; 12:210. [PMID: 22985357 PMCID: PMC3511200 DOI: 10.1186/1471-2180-12-210] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/10/2012] [Indexed: 11/26/2022] Open
Abstract
Background The α-proteobacterium Caulobacter crescentus inhabits low-nutrient environments and can tolerate certain levels of heavy metals in these sites. It has been reported that C. crescentus responds to exposure to various heavy metals by altering the expression of a large number of genes. Results In this work, we show that the ECF sigma factor σF is one of the regulatory proteins involved in the control of the transcriptional response to chromium and cadmium. Microarray experiments indicate that σF controls eight genes during chromium stress, most of which were previously described as induced by heavy metals. Surprisingly, σF itself is not strongly auto-regulated under metal stress conditions. Interestingly, σF-dependent genes are not induced in the presence of agents that generate reactive oxygen species. Promoter analyses revealed that a conserved σF-dependent sequence is located upstream of all genes of the σF regulon. In addition, we show that the second gene in the sigF operon acts as a negative regulator of σF function, and the encoded protein has been named NrsF (Negative regulator of sigma F). Substitution of two conserved cysteine residues (C131 and C181) in NrsF affects its ability to maintain the expression of σF-dependent genes at basal levels. Furthermore, we show that σF is released into the cytoplasm during chromium stress and in cells carrying point mutations in both conserved cysteines of the protein NrsF. Conclusion A possible mechanism for induction of the σF-dependent genes by chromium and cadmium is the inactivation of the putative anti-sigma factor NrsF, leading to the release of σF to bind RNA polymerase core and drive transcription of its regulon.
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Affiliation(s)
- Christian Kohler
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av, Prof, Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
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Yang Y, Mathieu JM, Chattopadhyay S, Miller JT, Wu T, Shibata T, Guo W, Alvarez PJJ. Defense mechanisms of Pseudomonas aeruginosa PAO1 against quantum dots and their released heavy metals. ACS NANO 2012; 6:6091-6098. [PMID: 22632375 DOI: 10.1021/nn3011619] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The growing use of quantum dots (QDs) in numerous applications increases the possibility of their release to the environment. Bacteria provide critical ecosystem services, and understanding their response to QDs is important to assess the potential environmental impacts of such releases. Here, we analyze the microbial response to sublethal exposure to commercial QDs, and investigate potential defense and adaptation mechanisms in the model bacterium Pseudomonas aeruginosa PAO1. Both intact and weathered QDs, as well as dissolved metal constituents, up-regulated czcABC metal efflux transporters. Weathered QDs also induced superoxide dismutase gene sodM, which likely served as a defense against oxidative stress. Interestingly, QDs also induced antibiotic resistance (ABR) genes and increased antibiotic minimum inhibitory concentrations by 50 to 100%, which suggests up-regulation of global stress defense mechanisms. Extracellular synthesis of nanoparticles (NPs) was observed after exposure to dissolved Cd(NO(3))(2) and SeO(2). With extended X-ray absorption fine structure (EXAFS), we discerned biogenic NPs such as CdO, CdS, CdSe, and selenium sulfides. These results show that bacteria can mitigate QD toxicity by turning on energy-dependent heavy-metal ion efflux systems and by mediating the precipitation of dissolved metal ions as less toxic and less bioavailable insoluble NPs.
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Affiliation(s)
- Yu Yang
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
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132
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Yergeau E, Sanschagrin S, Beaumier D, Greer CW. Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS One 2012; 7:e30058. [PMID: 22253877 PMCID: PMC3256217 DOI: 10.1371/journal.pone.0030058] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 12/09/2011] [Indexed: 11/19/2022] Open
Abstract
As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons.
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Affiliation(s)
- Etienne Yergeau
- National Research Council Canada, Biotechnology Research Institute, Montreal, Quebec, Canada.
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133
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Zhan Y, Yan Y, Zhang W, Chen M, Lu W, Ping S, Lin M. Comparative analysis of the complete genome of an Acinetobacter calcoaceticus strain adapted to a phenol-polluted environment. Res Microbiol 2012; 163:36-43. [DOI: 10.1016/j.resmic.2011.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/19/2011] [Indexed: 11/28/2022]
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134
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Babu MMG, Sridhar J, Gunasekaran P. Global transcriptome analysis of Bacillus cereus ATCC 14579 in response to silver nitrate stress. J Nanobiotechnology 2011; 9:49. [PMID: 22071005 PMCID: PMC3247866 DOI: 10.1186/1477-3155-9-49] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/10/2011] [Indexed: 11/30/2022] Open
Abstract
Silver nanoparticles (AgNPs) were synthesized using Bacillus cereus strains. Earlier, we had synthesized monodispersive crystalline silver nanoparticles using B. cereus PGN1 and ATCC14579 strains. These strains have showed high level of resistance to silver nitrate (1 mM) but their global transcriptomic response has not been studied earlier. In this study, we investigated the cellular and metabolic response of B. cereus ATCC14579 treated with 1 mM silver nitrate for 30 & 60 min. Global expression profiling using genomic DNA microarray indicated that 10% (n = 524) of the total genes (n = 5234) represented on the microarray were up-regulated in the cells treated with silver nitrate. The majority of genes encoding for chaperones (GroEL), nutrient transporters, DNA replication, membrane proteins, etc. were up-regulated. A substantial number of the genes encoding chemotaxis and flagellar proteins were observed to be down-regulated. Motility assay of the silver nitrate treated cells revealed reduction in their chemotactic activity compared to the control cells. In addition, 14 distinct transcripts overexpressed from the 'empty' intergenic regions were also identified and proposed as stress-responsive non-coding small RNAs.
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Affiliation(s)
- Malli Mohan Ganesh Babu
- Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Tamil Nadu, India
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135
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Decorosi F, Lori L, Santopolo L, Tatti E, Giovannetti L, Viti C. Characterization of a Cr(VI)-sensitive Pseudomonas corrugata 28 mutant impaired in a pyridine nucleotide transhydrogenase gene. Res Microbiol 2011; 162:747-55. [PMID: 21807093 DOI: 10.1016/j.resmic.2011.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 06/23/2011] [Indexed: 11/29/2022]
Abstract
Bacteria are known to adopt complex metabolic strategies in an effort to counteract the impact of numerous toxic compounds. In this study, a Cr(VI)-sensitive mutant of the Cr(VI)-hyperresistant bacterium Pseudomonas corrugata 28, obtained by insertional mutagenesis using the EZ-Tn5™ <R6Kγori/KAN-2>Tnp, was employed to gain a greater understanding of Cr(VI) resistance in bacteria. The insertion of the transposon, which occurred 16 bp upstream from the start codon of an ORF encoding a soluble pyridine nucleotide transhydrogenase (STH), negatively affected expression of the sth gene. The compromised expression of the sth gene in the mutant had two main effects on the pyridine nucleotide pools: (i) a decrease in NADPH and NADH fractions with a consequent shift in the redox state toward oxidation; and (ii) a decrease in the total concentration of the pyridine nucleotides. In the absence of a suitable pool of NADPH, the mutant failed to sustain an effective defense against the oxidative stress induced by Cr(VI).
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Affiliation(s)
- Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sezione di Microbiologia and Laboratorio Genexpress, Università degli Studi di Firenze, Piazzale delle Cascine, 24, I-50144 Florence, Italy
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136
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Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N]DNA-based stable isotope probing and pyrosequencing. Appl Environ Microbiol 2011. [PMID: 21498745 DOI: 10.1128/aem.00172‐11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for ∼2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [(15)N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using large-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in (15)N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments.
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137
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Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N]DNA-based stable isotope probing and pyrosequencing. Appl Environ Microbiol 2011; 77:4163-71. [PMID: 21498745 DOI: 10.1128/aem.00172-11] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for ∼2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [(15)N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using large-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in (15)N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments.
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138
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Regulatory response to carbon starvation in Caulobacter crescentus. PLoS One 2011; 6:e18179. [PMID: 21494595 PMCID: PMC3073932 DOI: 10.1371/journal.pone.0018179] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 02/22/2011] [Indexed: 11/19/2022] Open
Abstract
Bacteria adapt to shifts from rapid to slow growth, and have developed strategies for long-term survival during prolonged starvation and stress conditions. We report the regulatory response of C. crescentus to carbon starvation, based on combined high-throughput proteome and transcriptome analyses. Our results identify cell cycle changes in gene expression in response to carbon starvation that involve the prominent role of the FixK FNR/CAP family transcription factor and the CtrA cell cycle regulator. Notably, the SigT ECF sigma factor mediates the carbon starvation-induced degradation of CtrA, while activating a core set of general starvation-stress genes that respond to carbon starvation, osmotic stress, and exposure to heavy metals. Comparison of the response of swarmer cells and stalked cells to carbon starvation revealed four groups of genes that exhibit different expression profiles. Also, cell pole morphogenesis and initiation of chromosome replication normally occurring at the swarmer-to-stalked cell transition are uncoupled in carbon-starved cells.
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139
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Morais PV, Branco R, Francisco R. Chromium resistance strategies and toxicity: what makes Ochrobactrum tritici 5bvl1 a strain highly resistant. Biometals 2011; 24:401-10. [DOI: 10.1007/s10534-011-9446-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 03/24/2011] [Indexed: 11/30/2022]
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140
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Isolation and characterization of a chromium-resistant bacterium Serratia sp. Cr-10 from a chromate-contaminated site. Appl Microbiol Biotechnol 2011; 90:1163-9. [DOI: 10.1007/s00253-011-3120-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/07/2011] [Accepted: 01/08/2011] [Indexed: 10/18/2022]
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141
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Kovarik ML, Brown PJB, Kysela DT, Berne C, Kinsella AC, Brun YV, Jacobson SC. Microchannel-nanopore device for bacterial chemotaxis assays. Anal Chem 2010; 82:9357-64. [PMID: 20961116 DOI: 10.1021/ac101977f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motile bacteria bias the random walk of their motion in response to chemical gradients by the process termed chemotaxis, which allows cells to accumulate in favorable environments and disperse from less favorable ones. In this work, we describe a simple microchannel-nanopore device that establishes a stable chemical gradient for chemotaxis assays in ≤1 min. Chemoattractant is dispensed by diffusion through 10 nm diameter pores at the intersection of two microchannels. This design requires no external pump and minimizes the effect of transmembrane pressure, resulting in a stable, reproducible gradient. The microfluidic platform facilitates microscopic observation of individual cell trajectories, and chemotaxis is quantified by monitoring changes in cell swimming behavior in the vicinity of the intersection. We validate this system by measuring the chemotactic response of an aquatic bacterium, Caulobacter crescentus, to xylose concentrations from 1.3 μM to 1.3 M. Additionally, we make an unanticipated observation of increased turn frequency in a chemotaxis-impaired mutant which provides new insight into the chemotaxis pathway in C. crescentus.
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Affiliation(s)
- Michelle L Kovarik
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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142
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Isolation and physiology of bacteria from contaminated subsurface sediments. Appl Environ Microbiol 2010; 76:7413-9. [PMID: 20870785 DOI: 10.1128/aem.00376-10] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The majority of environmental microorganisms cannot be grown by traditional techniques. Here we employed, and contrasted with conventional plating, an alternative approach based on cultivation of microorganisms inside diffusion chambers incubated within natural samples, followed by subculturing in petri dishes. Using this approach, we isolated microorganisms from subsurface sediments from the Field Research Center (FRC) in Oak Ridge, TN. The sediments were acidic and highly contaminated with uranium, heavy metals, nitrate, and organic pollutants. Phylogenetic analysis of 16S rRNA gene sequences revealed clear differences between diversity of isolates obtained by the diffusion chamber approach and those obtained by conventional plating. The latter approach led to isolation of members of the Alpha- and Gammaproteobacteria, Actinobacteria, and Verrucomicrobia. Isolates obtained via the diffusion chamber approach represented the Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Notably, one-third of the isolates obtained by the new method were closely related to species known from previous molecular surveys conducted in the FRC area. Since the initial growth of microorganisms inside diffusion chambers occurred in the presence of the environmental stress factors, we expected the isolates we obtained to be tolerant of these factors. We investigated the physiologies of selected isolates and discovered that the majority were indeed capable of growth under low pH and/or high concentrations of heavy metals and nitrate. This indicated that in contrast to conventional isolation, the diffusion chamber-based approach leads to isolation of species that are novel, exhibit tolerance to extant environmental conditions, and match some of the species previously discovered by molecular methods.
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143
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Chromate reductase activity of the Paracoccus denitrificans ferric reductase B (FerB) protein and its physiological relevance. Arch Microbiol 2010; 192:919-26. [PMID: 20821194 DOI: 10.1007/s00203-010-0622-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 08/07/2010] [Accepted: 08/18/2010] [Indexed: 10/19/2022]
Abstract
The homodimeric flavoprotein FerB of Paracoccus denitrificans catalyzed the reduction of chromate with NADH as electron donor. When present, oxygen was reduced concomitantly with chromate. The recombinant enzyme had a maximum activity at pH 5.0. The stoichiometric ratio of NADH oxidized to chromate reduced was found to be 1.53 ± 0.09 (O(2) absent) or > 2 (O(2) present), the apparent K (M) value for chromate amounted to 70 ± 10 μM with the maximum rate of 2.9 ± 0.3 μmol NADH s(-1) (mg protein)(-1). Diode-array spectrophotometry and experiments with one-electron acceptors provided evidence for oxygen consumption being due to a flavin semiquinone, formed transiently during the interaction of FerB with chromate. At the whole-cell level, a ferB mutant strain displayed only slightly diminished rate of chromate reduction when compared to the wild-type parental strain. Anaerobically grown cells were more active than cells grown aerobically. The activity could be partly inhibited by antimycin, suggesting an involvement of the respiratory chain. Chromate concentrations above ten micromolars transiently slowed or halted culture growth, with the effect being more pronounced for the mutant strain. It appears, therefore, that, rather than directly reducing chromate, FerB confers a protection of cells against the oxidative stress accompanying chromate reduction. With a strain carrying the chromosomally integrated ferB promoter-lacZ fusion, it was shown that the ferB gene is not inducible by chromate.
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144
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CztR, a LysR-type transcriptional regulator involved in zinc homeostasis and oxidative stress defense in Caulobacter crescentus. J Bacteriol 2010; 192:5480-8. [PMID: 20709896 DOI: 10.1128/jb.00496-10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caulobacter crescentus is a free-living alphaproteobacterium that has 11 predicted LysR-type transcriptional regulators (LTTRs). Previously, a C. crescentus mutant strain with a mini-Tn5lacZ transposon inserted into a gene encoding an LTTR was isolated; this mutant was sensitive to cadmium. In this work, a mutant strain with a deletion was obtained, and the role of this LTTR (called CztR here) was evaluated. The transcriptional start site of this gene was determined by primer extension analysis, and its promoter was cloned in front of a lacZ reporter gene. β-galactosidase activity assays, performed with the wild-type and mutant strains, indicated that this gene is 2-fold induced when cells enter stationary phase and that it is negatively autoregulated. Moreover, this regulator is essential for the expression of the divergent cztA gene at stationary phase, in minimal medium, and in response to zinc depletion. This gene encodes a hypothetical protein containing 10 predicted transmembrane segments, and its expression pattern suggests that it encodes a putative zinc transporter. The cztR strain was also shown to be sensitive to superoxide (generated by paraquat) and to hydrogen peroxide but not to tert-butyl hydroperoxide. The expression of katG and ahpC, but not that of the superoxide dismutase genes, was increased in the cztR mutant. A model is proposed to explain how CztR binding to the divergent regulatory regions could activate cztA expression and repress its own transcription.
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145
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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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146
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Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S. Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems. Mol Microbiol 2010; 77:236-51. [PMID: 20487277 DOI: 10.1111/j.1365-2958.2010.07207.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Toxin-antitoxin (TA) gene cassettes are widely distributed across bacteria, archaea and bacteriophage. The chromosome of the alpha-proteobacterium, Caulobacter crescentus, encodes eight ParE/RelE-superfamily toxins that are organized into operons with their cognate antitoxins. A systematic genetic analysis of these parDE and relBE TA operons demonstrates that seven encode functional toxins. The one exception highlights an example of a non-functional toxin pseudogene. Chromosomally encoded ParD and RelB proteins function as antitoxins, inhibiting their adjacently encoded ParE and RelE toxins. However, these antitoxins do not functionally complement each other, even when overexpressed. Transcription of these paralogous TA systems is differentially regulated under distinct environmental conditions. These data support a model in which multiple TA paralogs encoded by a single bacterial chromosome form independent functional units with insulated protein-protein interactions. Further characterization of the parDE(1) system at the single-cell level reveals that ParE(1) toxin functions to inhibit cell division but not cell growth; residues at the C-terminus of ParE(1) are critical for its stability and toxicity. While continuous ParE(1) overexpression results in a substantial loss in cell viability at the population level, a fraction of cells escape toxicity, providing evidence that ParE(1) toxicity is not uniform within clonal cell populations.
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Affiliation(s)
- Aretha Fiebig
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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147
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Vanengelen MR, Field EK, Gerlach R, Lee BD, Apel WA, Peyton BM. UO(2) 2+ speciation determines uranium toxicity and bioaccumulation in an environmental Pseudomonas sp. isolate. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2010; 29:763-769. [PMID: 20821504 DOI: 10.1002/etc.126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In the present study, experiments were performed to investigate how representative cellulosic breakdown products, when serving as growth substrates under aerobic conditions, affect hexavalent uranyl cation (UO(2) (2+)) toxicity and bioaccumulation within a Pseudomonas sp. isolate (designated isolate A). Isolate A taken from the Cold Test Pit South (CTPS) region of the Idaho National Laboratory (INL), Idaho Falls, ID, USA. The INL houses low-level uranium-contaminated cellulosic material and understanding how this material, and specifically its breakdown products, affect U-bacterial interactions is important for understanding UO(2) (2+) fate and mobility. Toxicity was modeled using a generalized Monod expression. Butyrate, dextrose, ethanol, and lactate served as growth substrates. The potential contribution of bicarbonate species present in high concentrations was also investigated and compared with toxicity and bioaccumulation patterns seen in low-bicarbonate conditions. Isolate A was significantly more sensitive to UO(2) (2+) and accumulated significantly more UO(2) (2+) in low-bicarbonate concentrations. In addition, UO(2) (2+) growth inhibition and bioaccumulation varied depending on the growth substrate. In the presence of high bicarbonate concentrations, sensitivity to UO(2) (2+) inhibition was greatly mitigated, and did not vary between the four substrates tested. The extent of UO(2) (2+) accumulation was also diminished. The observed patterns were related to UO(2) (2+) aqueous complexation, as predicted by MINTEQ (ver. 2.52) (Easton, PA, USA). In the low- bicarbonate medium, the presence of positively charged and unstable UO(2) (2+)-hydroxide complexes explained both the greater sensitivity of isolate A to UO(2) (2+), and the ability of isolate A to accumulate significant amounts of UO(2) (2+). The exclusive presence of negatively charged and stable UO(2) (2+)-carbonate complexes in the high bi-carbonate medium explained the diminished sensitivity of isolate A to UO(2) (2+) toxicity, and limited ability of isolate A to accumulate UO(2) (2+).
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Affiliation(s)
- Michael R Vanengelen
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717-3920, USA
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148
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Xu Z, Lei Y, Patel J. Bioremediation of soluble heavy metals with recombinant Caulobacter crescentus. Bioeng Bugs 2010; 1:207-12. [PMID: 21326927 DOI: 10.4161/bbug.1.3.11246] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 01/05/2010] [Accepted: 01/06/2010] [Indexed: 01/22/2023] Open
Abstract
To achieve one-step separation of heavy metal ions from contaminated water, we have developed a novel bioremediation technology based on self-immobilization of the Caulobacter crescentus recombinant strain JS4022/p723-6H, which overexpresses hexahistidine peptide on the surface of the bacterial cells and serves as a whole-cell adsorbent for dissolved heavy metals. Biofilms formed by JS4022/p723-6H are effective at retaining cadmium from bacterial growth media or environmental water samples. Here we provide additional experiment data discussing the application potential of this new technology. Supplementation of calcium to the growth media produced robust JS4022/p723-6H cells by alleviating their sensitivity to chelators. After growth in the presence of 0.3% CaCl(2)·2H(2)O, double the amount of JS4022/p723-6H cells survived the treatment with 2 mM EDTA. Free cells of JS4022/p723-6H effectively sequestered 51% of the total cadmium from a Lake Erie water sample at pH 5.4, compared to 37% retrieved by the control strain. Similar levels of adsorption were observed at pH 4.2 as well. Cells of JS4022/p723-6H were tolerant of acid treatment for 90 min at pH ≥1.1 or 120 min at pH ≥2.5, which provides an avenue for the convenient regeneration of the bacterial cells metal-binding capacity with acidic solutions. Designs of possible bioreactors and an operation system are also presented.
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Affiliation(s)
- Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA.
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149
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Kavamura VN, Esposito E. Biotechnological strategies applied to the decontamination of soils polluted with heavy metals. Biotechnol Adv 2010; 28:61-9. [PMID: 19778598 DOI: 10.1016/j.biotechadv.2009.09.002] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 09/14/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
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150
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Decorosi F, Tatti E, Mini A, Giovannetti L, Viti C. Characterization of two genes involved in chromate resistance in a Cr(VI)-hyper-resistant bacterium. Extremophiles 2009; 13:917-23. [PMID: 19768364 DOI: 10.1007/s00792-009-0279-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 08/26/2009] [Indexed: 11/30/2022]
Abstract
Mechanisms underlying chromate resistance in Cr(VI)-hyper-resistant Pseudomonas corrugata strain 28, isolated from a highly Cr(VI) polluted soil, were studied by analyzing its two Cr(VI)-sensitive mutants obtained by insertion mutagenesis. The mutants, namely Crg3 and Crg96, were characterized by the identification of disrupted genes, and by the high-throughput approach called Phenotype MicroArray (PM), which permitted the assay of 1,536 phenotypes simultaneously. Crg3 and Crg96 mutants were affected in a malic enzyme family gene and in a gene encoding for a RecG helicase, respectively. The application of PM provided a wealth of new information relating to the disrupted genes and permitted to establish that chromate resistance in P. corrugata strain 28 also depends on supply on NADPH required in repairing damage induced by chromate and on DNA integrity maintenance.
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Affiliation(s)
- Francesca Decorosi
- Dipartimento di Biotecnologie Agrarie, Sez. Microbiologia, Università degli Studi di Firenze, Florence, Italy
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