Unique and overlapping pollutant stress proteins of Escherichia coli

Understanding GroEL and DnaK Stress Response Proteins as Antigens for Bacterial Diseases

Bacteria do not simply express a constitutive panel of proteins but they instead undergo dynamic changes in their protein repertoire in response to changes in nutritional status and when exposed to different environments. These differentially expressed proteins may be suitable to use for vaccine antigens if they are virulence factors. Immediately upon entry into the host organism, bacteria are exposed to a different environment, which includes changes in temperature, osmotic pressure, pH, etc. Even when an organism has already penetrated the blood or lymphatics and it then enters another organ or a cell, it can respond to these new conditions by increasing the expression of virulence factors to aid in bacterial adherence, invasion, or immune evasion. Stress response proteins such as heat shock proteins and chaperones are some of the proteins that undergo changes in levels of expression and/or changes in cellular localization from the cytosol to the cell surface or the secretome, making them potential immunogens for vaccine development. Herein we highlight literature showing that intracellular chaperone proteins GroEL and DnaK, which were originally identified as playing a role in protein folding, are relocated to the cell surface or are secreted during invasion and therefore may be recognized by the host immune system as antigens. In addition, we highlight literature showcasing the immunomodulation effects these proteins can have on the immune system, also making them potential adjuvants or immunotherapeutics.

Endophytic Bacillus megaterium BM18-2 mutated for cadmium accumulation and improving plant growth in Hybrid Pennisetum

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The endophytic Bacillus megaterium isolated from Hybrid Pennisetum is promising isolate for Cd bioremediation.

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The mutated strain BM18-2 showed higher capacity to resist Cd until 70 μM and improving plant growth.

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Six different genes of BM18-2 are involved in Cd resistance mechanism.

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Hybrid Pennisetum inoculated with BM18-2 showed higher amount of growth and toleranc to Cd toxicity than uninoculated plants.

Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach L.) is a tall and rapidly growing perennial C₄ bunch grass. It has been considered as a promising plant for phytoremediation of heavy metal-contaminated soil due to its high biomass, high resistance to environmental stress, pests and diseases. Heavy metal bioavailability level is the most important parameter for measurement of the phytoremediation efficiency. Endophytic bacteria were used to further enhance phytoremediation of heavy metals through bioaccumulation or bioabsorption process. In the present study, the endophytic Bacillus megaterium strain ‘BM18’ isolated from hybrid Pennisetum was screened under 10-70 μM cadmium (Cd) stress for Cd-resistant mutant colonies. And one such mutant colony‘BM18-2’ was obtained from the screen. Comparably, ‘BM18-2’ was more Cd-tolerant and had higher Cd removal ability than the original strain‘BM18’. The amount of IAA and ammonia production, and phosphate solubilization were 1.09, 1.23 and 1.24 times in ‘BM18-2’ than those of ‘BM18’, respectively. Full genome sequencing of these two strains revealed 6 different genes: BM18GM000901, BM18GM005669 and BM18GM005870 encoding heavy metal efflux pumps, BM18GM003487 and BM18GM005818 encoding transcriptional regulators for metal stress biosensor and BM18GM001335 encoding a replication protein. Inoculation with ‘BM18-2’ or ‘BM18’ both significantly reduced the toxic effect of Cd on hybrid Pennisetum, while the effect of ‘BM18-2’ on plant growth promotion in the presence of Cd was significantly better that of ‘BM18’. Therefore, the mutated strain ‘BM18-2’ could be used as a potential agent for Cd bioremediation, improving growth and Cd absorption of hybrid Pennisetum in Cd contaminated soil.

Blood lead and cadmium levels associated with hematological and hepatic functions in patients from an e-waste-polluted area

Chronic exposures to toxic trace metals have hazardous effects on human health, especially exposure to lead (Pb) and cadmium (Cd). Blood Pb and Cd reflect toxicity on human health. A total of 267 hospitalized patients, of which 158 were from Guiyu (exposed group) in China, and 109 from Jinping (reference group), were recruited in this study. Blood Pb and Cd were measured by graphite furnace atomic absorption spectrometry. Blood Pb and Cd levels from the exposed group were both higher than in the reference group. Blood Pb levels are positively associated with blood Cd levels from the two groups. Blood Pb and Cd levels are associated with elevated hematological and hepatic parameters in patients from the exposed and reference groups. The results suggest toxic trace metals may increase liver metabolic burden, inducing abnormal liver function.

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.

Assessment of physicochemical parameters and prevalence of virulent and multiple-antibiotic-resistant Escherichia coli in treated effluent of two wastewater treatment plants and receiving aquatic milieu in Durban, South Africa

The poor operational status of some wastewater treatment plants often result in the discharge of inadequately treated effluent into receiving surface waters. This is of significant public health concern as there are many informal settlement dwellers (ISDs) that rely on these surface waters for their domestic use. This study investigated the treatment efficiency of two independent wastewater treatment plants (WWTPs) in Durban, South Africa and determined the impact of treated effluent discharge on the physicochemical and microbial quality of the receiving water bodies over a 6-month period. Presumptive Escherichia coli isolates were identified using biochemical tests and detection of the mdh gene via PCR. Six major virulence genes namely eae, hly, fliC, stx1, stx2, and rfbE were also detected via PCR while antibiotic resistance profiles of the isolates were determined using Kirby-Bauer disc diffusion assay. The physicochemical parameters of the wastewater samples ranged variously between 9 and 313.33 mg/L, 1.52 and 76.43 NTUs, and 6.30 and 7.87 for COD, turbidity, and pH respectively, while the E. coli counts ranged between 0 and 31.2 × 10(3) CFU/ml. Of the 200 selected E. coli isolates, the hly gene was found in 28 %, fliC in 20 %, stx2 in 17 %, eae in 14 %, with stx1 and rfbE in only 4 % of the isolates. Notable resistance was observed toward trimethoprim (97 %), tetracycline (56 %), and ampicillin (52.5 %). These results further highlight the poor operational status of these WWTPs and outline the need for improved water quality monitoring and enforcement of stringent guidelines.

Cadmium Chloride Induces DNA Damage and Apoptosis of Human Liver Carcinoma Cells via Oxidative Stress

Cadmium is a heavy metal that has been shown to cause its toxicity in humans and animals. Many documented studies have shown that cadmium produces various genotoxic effects such as DNA damage and chromosomal aberrations. Ailments such as bone disease, renal damage, and several forms of cancer are attributed to overexposure to cadmium. Although there have been numerous studies examining the effects of cadmium in animal models and a few case studies involving communities where cadmium contamination has occurred, its molecular mechanisms of action are not fully elucidated. In this research, we hypothesized that oxidative stress plays a key role in cadmium chloride-induced toxicity, DNA damage, and apoptosis of human liver carcinoma (HepG₂) cells. To test our hypothesis, cell viability was determined by MTT assay. Lipid hydroperoxide content stress was estimated by lipid peroxidation assay. Genotoxic damage was tested by the means of alkaline single cell gel electrophoresis (Comet) assay. Cell apoptosis was measured by flow cytometry assessment (Annexin-V/PI assay). The result of MTT assay indicated that cadmium chloride induces toxicity to HepG₂ cells in a concentration-dependent manner, showing a 48 hr-LD50 of 3.6 µg/mL. Data generated from lipid peroxidation assay resulted in a significant (p < 0.05) increase of hydroperoxide production, specifically at the highest concentration tested. Data obtained from the Comet assay indicated that cadmium chloride causes DNA damage in HepG₂ cells in a concentration-dependent manner. A strong concentration-response relationship (p < 0.05) was recorded between annexin V positive cells and cadmium chloride exposure. In summary, these in vitro studies provide clear evidence that cadmium chloride induces oxidative stress, DNA damage, and programmed cell death in human liver carcinoma (HepG₂) cells.

Cadmium Chloride Induces DNA Damage and Apoptosis of Human Liver Carcinoma Cells via Oxidative Stress

Cadmium is a heavy metal that has been shown to cause its toxicity in humans and animals. Many documented studies have shown that cadmium produces various genotoxic effects such as DNA damage and chromosomal aberrations. Ailments such as bone disease, renal damage, and several forms of cancer are attributed to overexposure to cadmium. Although there have been numerous studies examining the effects of cadmium in animal models and a few case studies involving communities where cadmium contamination has occurred, its molecular mechanisms of action are not fully elucidated. In this research, we hypothesized that oxidative stress plays a key role in cadmium chloride-induced toxicity, DNA damage, and apoptosis of human liver carcinoma (HepG₂) cells. To test our hypothesis, cell viability was determined by MTT assay. Lipid hydroperoxide content stress was estimated by lipid peroxidation assay. Genotoxic damage was tested by the means of alkaline single cell gel electrophoresis (Comet) assay. Cell apoptosis was measured by flow cytometry assessment (Annexin-V/PI assay). The result of MTT assay indicated that cadmium chloride induces toxicity to HepG₂ cells in a concentration-dependent manner, showing a 48 hr-LD50 of 3.6 µg/mL. Data generated from lipid peroxidation assay resulted in a significant (p < 0.05) increase of hydroperoxide production, specifically at the highest concentration tested. Data obtained from the Comet assay indicated that cadmium chloride causes DNA damage in HepG₂ cells in a concentration-dependent manner. A strong concentration-response relationship (p < 0.05) was recorded between annexin V positive cells and cadmium chloride exposure. In summary, these in vitro studies provide clear evidence that cadmium chloride induces oxidative stress, DNA damage, and programmed cell death in human liver carcinoma (HepG₂) cells.

Heavy metal toxicity and the environment

Heavy metals are naturally occurring elements that have a high atomic weight and a density at least five times greater than that of water. Their multiple industrial, domestic, agricultural, medical, and technological applications have led to their wide distribution in the environment, raising concerns over their potential effects on human health and the environment. Their toxicity depends on several factors including the dose, route of exposure, and chemical species, as well as the age, gender, genetics, and nutritional status of exposed individuals. Because of their high degree of toxicity, arsenic, cadmium, chromium, lead, and mercury rank among the priority metals that are of public health significance. These metallic elements are considered systemic toxicants that are known to induce multiple organ damage, even at lower levels of exposure. They are also classified as human carcinogens (known or probable) according to the US Environmental Protection Agency and the International Agency for Research on Cancer. This review provides an analysis of their environmental occurrence, production and use, potential for human exposure, and molecular mechanisms of toxicity, genotoxicity, and carcinogenicity.

Proteomic analysis of uropathogenic Escherichia coli

Urinary tract infections (UTIs) are among the most common of bacterial infections in humans. Although a number of Gram-negative bacteria can cause UTIs, most cases are due to infection by uropathogenic E. coli (UPEC). Genomic studies have shown that UPEC encode a number of specialized activities that allow the bacteria to initiate and maintain infections in the environment of the urinary tract. Proteomic analyses have complemented the genomic data and have documented differential patterns of protein synthesis for bacteria growing ex vivo in human urine or recovered directly from the urinary tracts of infected mice. These studies provide valuable insights into the molecular basis of UPEC pathogenesis and have aided the identification of putative vaccine targets. Despite the substantial progress that has been achieved, many future challenges remain in the application of proteomics to provide a comprehensive view of bacterial pathogenesis in both acute and chronic UTIs.

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1

Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, where bacteria using oxygen-independent enzymes likely play an important role in decomposition. We have used transcriptomics and proteomics to examine the observed increased growth of SCF1 grown on media amended with lignin compared to unamended growth. Proteomics suggested accelerated xylose uptake and metabolism under lignin-amended growth, with up-regulation of proteins involved in lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase (GST) proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. This suggested the use of lignin as terminal electron acceptor. We detected significant lignin degradation over time by absorbance, and also used metabolomics to demonstrate moderately significant decreased xylose concentrations as well as increased metabolic products acetate and formate in stationary phase in lignin-amended compared to unamended growth conditions. Our data show the advantages of a multi-omics approach toward providing insights as to how lignin may be used in nature by microorganisms coping with poor carbon availability.

A cometabilic kinetics model incorporating enzyme inhbition, inactivation, and recovery: I. Model development, analysis, and testing

Cometabolic biodegradation prcesses are important for bioremediation of hazardous waste sites. However, these proceeses are not well understood and have not been modeled thoroughly. Traditional Michaelis-Menten kinetics models often are used, but toxic effects and bacterial responses to toxicity may cause changes in enzyme levels, rendering such models inappropriate. In this article, a conceptual and mathematical model of cometabolic enzyme kinetics i described. Model derivation is based on enzyme/growth-substrate/nongrowth-substrate interaction and incorporates enzyme inhibition (caused by the presence of a cometabolic compound), inactivation (resulting from toxicity of a cometabolic product), and recovery (associated with bacterial synthesis of new enbzyme in response to inactivation). The mathematical model consists of a system of two, nonlinear ordinary differential equations that can be solved implicitly using numerical methods, providing estimates of model parameters. Model analysis shows that growth substraate adn nongrowth substrate oxidation rates are related by a dimensionless constant. Reliability of tehy model solution prcedure is verifiedl by abnalyzing data ses, containing random error, from simulated experimentss with trichhloroethyylene (TCE) degradation by ammonia-oxidizing bacterialunder various conditions. Estimation of the recovery rate contant is deterimined to be sensitive to intial TCE concentration. Model assumptions are evaluated in a companion article using data from TCE degradation experiments with amoniaoxidizing bacteria. (c) 1995 John Wiley & Sons, Inc.

Heavy metal toxicity and the environment

Heavy metals are naturally occurring elements that have a high atomic weight and a density at least five times greater than that of water. Their multiple industrial, domestic, agricultural, medical, and technological applications have led to their wide distribution in the environment, raising concerns over their potential effects on human health and the environment. Their toxicity depends on several factors including the dose, route of exposure, and chemical species, as well as the age, gender, genetics, and nutritional status of exposed individuals. Because of their high degree of toxicity, arsenic, cadmium, chromium, lead, and mercury rank among the priority metals that are of public health significance. These metallic elements are considered systemic toxicants that are known to induce multiple organ damage, even at lower levels of exposure. They are also classified as human carcinogens (known or probable) according to the US Environmental Protection Agency and the International Agency for Research on Cancer. This review provides an analysis of their environmental occurrence, production and use, potential for human exposure, and molecular mechanisms of toxicity, genotoxicity, and carcinogenicity.

Finding biomarkers is getting easier

Single biomarkers are rarely accurate. Even suites of biomarkers can give conflicting results. Ideally potent combinations of variables are isolated which accurately identify specific analytes and their level of toxicity. The search for such combinations can be done by reducing the thousands of candidate variables to the small number necessary for treatment classification. When the key variables are recognized by machine learning (ML) the results are quite surprising, given the apparent failure of other searching methods to produce good diagnostics. Proteins seem especially useful for portable field tests of a variety of adverse conditions. This review shows how ML, in particular artificial neural networks, can find potent biomarkers embedded in any type of expression data, mainly proteins in this article. A computer does multiple iterations to produce sets of proteins which systematically identify (to near 100% accuracy) the treatment classes of interest. Whether these proteins are useful in actual diagnoses is tested by presenting the computer model with unknown classes. Finding the biomarkers is getting easier but there still must be confirmation, by multivariable statistics and with field studies.

Fish metalloproteins as biomarkers of environmental contamination

Fish are well-recognized bioindicators of environmental contamination. Several recent proteomic studies have demonstrated the validity and value of using fish in the search and discovery of new biomarkers. Certain analytical tools, such as comparative protein expression analyses, both in field and lab exposure studies, have been used to improve the understanding of the potential for chemical pollutants to cause harmful effects. The metallomic approach is in its early stages of development, but has already shown great potential for use in ecological and environmental monitoring contexts. Besides discovering new metalloproteins that may be used as biomarkers for environmental contamination, metallomics can be used to more comprehensively elucidate existing biomarkers, which may enhance their effectiveness. Unfortunately, metallomic profiling for fish has not been explored, because only a few fish metalloproteins have thus far been discovered and studied. Of those that have, some have shown ecological importance, and are now successfully used as biomarkers of environmental contamination. These biomarkers have been shown to respond to several types of environmental contamination, such as cyanotoxins, metals, and sewage effluents, although many do not yet possess any known function. Examples of successes include MMPs, superoxide dismutases, selenoproteins, and iron-bound proteins. Unfortunately, none of these have, as yet, been extensively studied. As data are developed for them, valuable new information on their roles in fish physiology and in inducing environmental effects should become available.

Heavy metal toxicity and the environment

Heavy metals are naturally occurring elements that have a high atomic weight and a density at least five times greater than that of water. Their multiple industrial, domestic, agricultural, medical, and technological applications have led to their wide distribution in the environment, raising concerns over their potential effects on human health and the environment. Their toxicity depends on several factors including the dose, route of exposure, and chemical species, as well as the age, gender, genetics, and nutritional status of exposed individuals. Because of their high degree of toxicity, arsenic, cadmium, chromium, lead, and mercury rank among the priority metals that are of public health significance. These metallic elements are considered systemic toxicants that are known to induce multiple organ damage, even at lower levels of exposure. They are also classified as human carcinogens (known or probable) according to the US Environmental Protection Agency and the International Agency for Research on Cancer. This review provides an analysis of their environmental occurrence, production and use, potential for human exposure, and molecular mechanisms of toxicity, genotoxicity, and carcinogenicity.

Hydrophobic substances induce water stress in microbial cells

Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes – metabolites that protect against osmotic and chaotrope‐induced stresses – ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope‐induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.

Comparative transcriptomics of the response of Escherichia coli to the disinfectant monochloramine and to growth conditions inducing monochloramine resistance

Escherichia coli growth in biofilms and growth at a suboptimal temperature of 20 °C have been shown to decrease sensitivity to monochloramine (Berry, D., C. Xi, L. Raskin. 2009. Environ. Sci. Technol. 43, 884-889). In order to better understand why growth conditions affect sensitivity to monochloramine, a comparative transcriptomic approach was used to identify common patterns of differentially-expressed genes under these growth conditions and during monochloramine exposure. This approach revealed a set of differentially-expressed genes shared under multiple conditions (planktonic growth at 20 °C, biofilm growth, and exposure of planktonic cells to monochloramine), with nine genes shared under all three conditions. Functional gene categories enriched in the shared gene sets included: general metabolic inhibition, redox and oxidoreductase response, cell envelope integrity response, control of iron and sulfur transport metabolism and several genes of unknown function. Single gene deletion mutant analyses verified that loss of 15 of the 24 genes up-regulated during monochloramine exposure as well as during other tested conditions increased E. coli sensitivity to monochloramine up to two fold. Constitutive expression of down-regulated genes in single gene mutants yielded mixed results, indicating that the expression of some down-regulated genes actually decreases sensitivity to monochloramine. These results contribute to the understanding of the bacterial response to disinfectants by characterizing the overlap between growth condition associated stress responses and monochloramine-associated stress responses. This characterization highlights the bacterial responses responsible for decreased sensitivity to monochloramine under different growth conditions.

Cometabolism of chlorinated solvents by nitrifying bacteria: kinetics, substrate interactions, toxicity effects, and bacterial response

Pure cultures of ammonia-oxidizing bacteria, Nitrosomonas europaea, were exposed to trichloroethylene (TCE), 1,1-dichloroethylene (1,1-DCE), chloroform (CF), 1,2-dichloroethane (1,2-DCA), or carbon tetrachloride (CT), in the presence of ammonia, in a quasi-steady-state bioreactor. Estimates of enzyme kinetics constants, solvent inactivation constants, and culture recovery constants were obtained by simultaneously fitting three model curves to experimental data using nonlinear optimization techniques and an enzyme kinetics model, referred to as the inhibition, inactivation, and recovery (IIR) model, that accounts for inhibition of ammonia oxidation by the solvent, enzyme inactivation by solvent product toxicity, and respondent synthesis of new enzyme (recovery). Results showed relative enzyme affinities for ammonia monooxygenase (AMO) of 1,1-DCE approximately TCE > CT > NH(3) > CF > 1,2-DCA. Relative maximum specific substrate transformation rates were NH(3) > 1,2-DCA > CF > TCE approximately 1,1-DCE > CT (=0). The TCE, CF, and 1,1-DCE inactivated the cells, with 1,1-DCE being about three times more potent than TCE or CF. Under the conditions of these experiments, inactivating injuries caused by TCE and 1,1-DCE appeared limited primarily to the AMO enzyme, but injuries caused by CF appeared to be more generalized. The CT was not oxidized by N. europaea while 1,2-DCA was oxidized quite readily and showed no inactivation effects. Recovery capabilities were demonstrated with all solvents except CF. A method for estimating protein yield, the relationship between the transformation capacity model and the IIR model, and a condition necessary for sustainable cometabolic treatment of inactivating substrates are presented. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 520-534, 1997.

Protein expression profiling

Protein expression profiling is defined in general as identifying the proteins expressed in a particular tissue, under a specified set of conditions and at a particular time, usually compared to expression in reference samples. This information is useful in drug discovery and diagnosis as well as in understanding response mechanisms at the protein level. We may identify all the proteins responding to a particular stimulus and select those whose expression changes most. Or we may isolate significant protein variables and then identify them. These definitive sets of proteins (protein expression signatures; PES) are specific to diseases, toxicants, physical stresses, and to degrees of stress severity. Here we describe a method, based on machine learning, for isolating the sets of proteins, before identifying them by name, which classify accurately the treatment classes in a study. The principle in this chapter is that if proteins associated with known classes of interest can be used to identify unknown classes then the proteins are definitive for diagnosis.The proteins in each class, including controls, are converted to digital data and serve as input to artificial neural network (ANN) models. Multiple two-dimensional electrophoresis (2DE) gel patterns are included in each treatment class. A training subset of digitized individual, not composite, gel images is used to construct an ANN model which is then applied to a test set of images. Successful classification of the unknown (test) data confirms that the variables included in the model are indeed significant in discrimination among the classes. In the study described here the misclassifications were 5% or less using the ANN models. The ANN method seems to be a useful complement to image analysis, described in Chapter "Troubleshooting Image Analysis in 2DE". The reduction in protein variables permits multivariable statistics such as cluster and discriminant analyses.

Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB

Rhodococcus sp. strain TFB is a versatile gram-positive bacterium able to grow on a wide variety of aromatic compounds as carbon and energy sources. Since the strain is refractory to genetic analysis, a proteomic approach was used to study the metabolic pathways involved in the catabolism of such compounds by analyzing differentially induced proteins. The most marked difference was observed when the proteome profiles of phthalate-grown cells were compared with those cultured in the presence of tetralin- or naphthalene, suggesting that different metabolic pathways are involved in the degradation of mono- and polyaromatic compounds. Comparison with the proteome of glucose-grown cells indicated that each pathway was specifically induced by the corresponding aromatic compound. A combination of proteomics and molecular biology led to the identification of 14 proteins (65-80% identical to known Pht proteins) that describe a complete pathway for the catabolism of phthalate to central metabolites via intradiol cleavage of protochatechuic acid. Chaperonins were also induced in phthalate-grown cells, indicating that growth on this compound induces a stress response. Absence of catabolite repression by glucose was observed by both transcriptional and proteome analysis, suggesting that Rhodococcus sp. strain TFB may have advantages over other tightly regulated strains in bioremediation.

Changes in microbiological metabolism under chemical stress

Chemical stress may alter microbiological metabolism and this, in turn, may affect the natural and engineered systems where these organisms function. The impact of chemical stress on microbiological metabolism was investigated using model chemicals 2,4-dinitrophenol (DNP), pentachlorophenol (PCP), and N-ethylmaleimide (NEM). Biological activity of Pseudomonas aeruginosa was measured in batch systems, with and without stressors at sub-lethal concentrations. Stressor DNP, between 49 and 140 mg l(-1), and PCP, at 15 and 38 mg l(-1), caused decreases in biomass growth yields, but did not inhibit substrate utilization rates. These effects increased with stressor concentrations, showing as much as a 10% yield reduction at the highest DNP concentration. This suggests that a portion of carbon and energy resources are diverted from growth and used in stress management and protection. Stressor DNP, between 300 and 700 mg l(-1), and PCP at 85 mg l(-1) caused decreases in growth yields and substrate utilization rates. This suggests an inhibition of both anabolism and catabolism. Stressor NEM was the most potent, inhibiting biological activity at concentrations as low as 2.7 mg l(-1). These findings will ultimately be useful in better monitoring and management of biological treatment operations and contaminated natural systems.

Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress

Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole-genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole-cell acetate uptake rates (WAURs) and cell viability and for gene expression changes by Affymetrix GeneChip technology and real-time reverse transcriptase PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multidrug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant.

Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress

We report the effects of 4-chlorobiphenyl and biphenyl on the physiology, morphology and proteome of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400. The exposure to 4-chlorobiphenyl decreases the growth of LB400 on glucose, and cells exhibit irregular outer membranes, a larger periplasmic space and electron-dense granules in the cytoplasm. Additionally, lysis of cells was observed during incubation with 4-chlorobiphenyl or biphenyl. Proteome of B. xenovorans LB400 exposed to biphenyl and 4-chlorobiphenyl were analysed by two-dimensional gel electrophoresis. Besides induction of the Bph enzymes of biphenyl catabolic pathways, incubation with 4-chlorobiphenyl or biphenyl results in the induction of the molecular chaperones DnaK and GroEL. Induction of these chaperones, which were also induced during heat shock, strongly suggests that exposure to (chloro)biphenyls constitutes stress conditions for LB400. During growth of LB400 on biphenyl, oxidative stress was evidenced by the induction of alkyl hydroperoxide reductase AhpC, which was also induced during exposure to H(2)O(2). 4-chlorobiphenyl and biphenyl induced catechol 1,2-dioxygenase, as well as polypeptides involved in energy production, amino acid metabolism and transport.

The alternative sigma factor RpoH2 is required for salt tolerance in Sinorhizobium sp. strain BL3

The objectives of this investigation were to isolate the rpoH2 gene encoding an alternative sigma factor from Sinorhizobium sp. BL3 and to determine its role in exopolysaccharide (EPS) synthesis, salt tolerance and symbiosis with Phaseolus lathyroides. The rpoH2 gene of Rhizobium sp. strain TAL1145 is known to be required for EPS synthesis and effective nodulation of Leucaena leucocephala. Three overlapping cosmid clones containing the rpoH2 gene of BL3 were isolated by complementing an rpoH2 mutant of TAL1145 for EPS production. From one of these cosmids, rpoH2 of BL3 was identified within a 3.0-kb fragment by subcloning and sequencing. The cloned rpoH2 gene of BL3 restored both EPS production and nodulation defects of the TAL1145 rpoH2 mutants. Three rpoH2 mutants of BL3 were constructed by transposon-insertion mutagenesis. These mutants of BL3 grew normally in complete or minimal medium and were not defective in EPS synthesis, nodulation and nitrogen fixation, but they failed to grow in salt stress conditions. The mutants complemented with cloned rpoH2 from either BL3 or TAL1145 showed higher levels of salt tolerance than BL3. The expression of rpoH2 in BL3 started increasing during the exponential phase and reached the highest level in the mid-stationary phase. These results indicate that RpoH2 is required for salt tolerance in Sinorhizobium sp. BL3, and it may have additional roles during the stationary phase.

Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be cyclic and predictable from year to year and that there are interactive effects between nutrients and the contaminant hexadecane.

Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400

Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC) and the megaplasmid (boxM). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the DeltabenABCD::kan mutant), the boxC pathway (the DeltaboxABC::kan mutant), and both pathways (the DeltabenABCDDelta boxABC::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the DeltabenABCD::kan and DeltabenABCD DeltaboxABC::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the DeltabenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400.

Mytilus trossulus hsp70 as a biomarker for arsenic exposure in the marine environment: laboratory and real-world results

The highly conserved heat shock protein 70 (hsp70) is induced by heat and chemical toxins, particularly heavy metals such as arsenic (As). The use of Mytilus trossulus (bay mussel) hsp70 as a 'screening' biomarker for marine heavy metals contamination was assessed. Some studies have found high hsp70 sensitivity to heavy metals, while others have found the opposite. Few studies have realistically used low heavy metals exposures, and fewer have used real-world contamination exposures. Clean sub-tidal mussels from the Puget Sound, Washington State (WA), USA, were acclimatized for 2 weeks and exposed for 24 h to As-spiked seawater (n=9) or to contaminated seawater from an arsenical pesticide plant in Tacoma, WA (n=10) followed by a Western blot for hsp70. Hsp70 inductions were insignificant at 10 microg l(-1) As(III), but were strong at 100 microg l(-1) (p<0.05) and 1000 microg l(-1) (p<0.01), with the induction threshold estimated at 30-50 microg l(-1) As(III). Hsp70 induction roughly correlated with arsenical toxicity, with As(III) > As(V) > (CH(3))(2)As(V). Altogether, the inter-individual variability of hsp70 levels tends to mask inductions at low As concentrations, making it a crude toxicity biomarker. In addressing this problem, the following options could prove promising: (1) pre- or post-stressing specimens for greater hsp70 sensitivity, (2) use of internal protein controls such as actin, (3) use of hsp70-reporter gene constructs, and (4) detection with hsp60, heme oxygenase-1, metallothionein, CYP450, MXR or GPx.

2-D PAGE analysis of pesticide-induced stress proteins of E. coli

Logarithmically growing batch cultures of Escherichia coli were exposed to sublethal concentrations of pyrethroid and carbamate pesticides of four different technical grades. This induced 17-20 stress proteins, as observed using two-dimensional polyacrylamide gel electrophoresis. An E. coli culture growing exponentially in Luria Bertani medium (cell density approximately 2.3x10(9) cells/ml) was exposed to predetermined sublethal doses of individual pesticides. The cells were harvested after 30 minutes of induction and the stress response was developed in fresh LB medium for three hours under the same growth conditions. Cell pellets were obtained and stored in sonication buffer. Two-dimensional polyacrylamide gel electrophoresis was performed to resolve the proteins. Visualization of the protein spots by rapid silver staining showed 17-20 stress proteins which were absent in the standard protein profile of E. coli. On average 29% of these stress proteins were unique to the pollutant, while the remaining stress proteins overlapped with those of other pesticides. The iso-electric points (PIs) and molecular weights of the proteins were determined by comparing with protein markers with known PIs and molecular weights. Furthermore, upon comparing the pesticide-induced proteins within the same class and between the two different classes (pyrethroid and carbamate), it was apparent that the general nature of the stress remained the same throughout, which indirectly proved that the gene or set of genes responsible for stress expression are also the same, irrespective of the chemical nature of the substituents of the pesticides.

Global gene expression responses to cadmium toxicity in Escherichia coli

Genome-wide analysis of temporal gene expression profiles in Escherichia coli following exposure to cadmium revealed a shift to anaerobic metabolism and induction of several stress response systems. Disruption in the transcription of genes encoding ribosomal proteins and zinc-binding proteins may partially explain the molecular mechanisms of cadmium toxicity.

Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods

Protein profiles of Mycobacterium vanbaalenii PYR-1 grown in the presence of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) were examined by two-dimensional gel electrophoresis (2-DE). Cultures of M. vanbaalenii PYR-1 were incubated with pyrene, pyrene-4,5-quinone (PQ), phenanthrene, anthracene, and fluoranthene. Soluble cellular protein fractions were analyzed and compared, using immobilized pH gradient (IPG) strips. More than 1000 gel-separated proteins were detected using a 2-DE analysis program within the window of isoelectric point (pI) 4-7 and a molecular mass range of 10-100 kDa. We observed variations in the protein composition showing the upregulation of multiple proteins for the five PAH treatments compared with the uninduced control sample. By N-terminal sequencing or mass spectrometry, we further analyzed the proteins separated by 2-DE. Due to the lack of genome sequence information for this species, protein identification provided an analytical challenge. Several PAH-induced proteins were identified including a catalase-peroxidase, a putative monooxygenase, a dioxygenase small subunit, a small subunit of naphthalene-inducible dioxygenase, and aldehyde dehydrogenase. We also identified proteins related to carbohydrate metabolism (enolase, 6-phosphogluconate dehydrogenase, indole-3-glycerol phosphate synthase, and fumarase), DNA translation (probable elongation factor Tsf), heat shock proteins, and energy production (ATP synthase). Many proteins from M. vanbaalenii PYR-1 showed similarity with protein sequences from M. tuberculosis and M. leprae. Some proteins were detected uniquely upon exposure to a specific PAH whereas others were common to more than one PAH, which indicates that induction triggers not only specific responses but a common response in this strain.

Stress responsive bacteria: biosensors as environmental monitors

The delicate and dynamic balance of the physiological steady state and its maintenance is well characterized by studies of bacterial stress response. Through the use of genetic analysis, numerous stress regulons, their physiological regulators and their biochemical processes have been delineated. In particular, transcriptionally activated stress regulons are subjects of study and application. These regulons include those that respond to macromolecular damage and toxicity as well as to nutrient starvation. The convenience of reporter gene fusions has allowed the creation of biosensor strains, resulting from the fusion of stress-responsive promoters with a variety of reporter genes. Such cellular biosensors are being used for monitoring dynamic systems and can report the presence of environmental stressors in real time. They provide a greater range of sensitivity, e.g. to sub-lethal concentrations of toxicants, than the simple assessment of cell viability. The underlying physiological context of the reporter strains results in the detection of bioavailable concentrations of both toxicants and nutrients. Culture conditions and host strain genotypes can be customized so as to maximize the sensitivity of the strain for a particular application. Collections of specific strains that are grouped in panels are used to diagnose targets or mode of action for unknown toxicants. Further application in massive by parallel DNA and gene fusion arrays greatly extends the information available for diagnosis of modes of action and may lead to development of novel high-throughput screens. Future studies will include more panels, arrays, as well as single reporter cell detection for a better understanding of the population heterogeneity during stress response. New knowledge of physiology gained from further studies of novel systems, or using innovative methods of analysis, will undoubtedly yield still more useful and informative environmental biosensors.

Treatment of Salmonella enterica serovar Enteritidis with a sublethal concentration of trisodium phosphate or alkaline pH induces thermotolerance

The responses of Salmonella enterica serovar Enteritidis to a sublethal dose of trisodium phosphate (TSP) and its equivalent alkaline pH made with NaOH were examined. Pretreatment of S. enterica serovar Enteritidis cells with 1.5% TSP or pH 10.0 solutions resulted in a significant increase in thermotolerance, resistance to 2.5% TSP, resistance to high pH, and sensitivity to acid and H(2)O(2). Protein inhibition studies with chloramphenicol revealed that thermotolerance, unlike resistance to high pH, was dependent on de novo protein synthesis. Two-dimensional polyacrylamide gel electrophoresis (PAGE) of total cellular proteins from untreated control cells resolved as many as 232 proteins, of which 22 and 15% were absent in TSP- or alkaline pH-pretreated cells, respectively. More than 50% of the proteins that were either up- or down-regulated by TSP pretreatment were also up- or down-regulated by alkaline pH pretreatment. Sodium dodecyl sulfate-PAGE analysis of detergent-insoluble outer membrane proteins revealed the up-regulation of at least four proteins. Mass spectrometric analysis showed the up-regulated proteins to include those involved in the transport of small hydrophilic molecules across the cytoplasmic membrane and those that act as chaperones and aid in the export of newly synthesized proteins by keeping them in open conformation. Other up-regulated proteins included common housekeeping proteins like those involved in amino acid biosynthesis, nucleotide metabolism, and aminoacyl-tRNA biosynthesis. In addition to the differential expression of proteins following TSP or alkaline pH treatment, changes in membrane fatty acid composition were also observed. Alkaline pH- or TSP-pretreated cells showed a higher saturated and cyclic to unsaturated fatty acid ratio than did the untreated control cells. These results suggest that the cytoplasmic membrane could play a significant role in the induction of thermotolerance and resistance to other stresses following TSP or alkaline pH treatment.

Regulation of catabolic enzymes during long-term exposure of Delftia acidovorans MC1 to chlorophenoxy herbicides

Delftia acidovorans MC1 is able to grow on chlorophenoxy herbicides such as 2,4-dichlorophenoxypropionic acid (2,4-DCPP) and 2,4-dichlorophenoxyacetic acid as sole sources of carbon and energy. High concentrations of the potentially toxic organics inhibit the productive degradation and poison the organism. To discover the target of chlorophenoxy herbicides in D. acidovorans MC1 and to recognize adaptation mechanisms, the response to chlorophenoxy acids at the level of proteins was analysed. The comparison of protein patterns after chemostatic growth on pyruvate and 2,4-DCPP facilitated the discovery of several proteins induced and repressed due to the substrate shifts. Many of the induced enzymes, for example two chlorocatechol 1,2-dioxygenases, are involved in the metabolism of 2,4-DCPP. A stronger induction of some catabolic enzymes (chlorocatechol 1,2-dioxygenase TfdC(II), chloromuconate cycloisomerase TfdD) caused by an instant increase in the concentration of 2,4-DCPP resulted in increased rates of productive detoxification and finally in resistance of the cells. Nevertheless, the decrease of the (S)-2,4-DCPP-specific 2-oxoglutarate-dependent dioxygenase in 2D gels reveals a potential bottleneck in 2,4-DCPP degradation. Well-known heat-shock proteins and oxidative-stress proteins play a minor role in adaptation, because apart from DnaK only a weak or no induction of the proteins GroEL, AhpC and SodA was observed. Moreover, the modification of elongation factor Tu (TufA), a strong decrease of asparaginase and the induction of the hypothetical periplasmic protein YceI point to additional resistance mechanisms against chlorophenoxy herbicides.

Proteomics in zebrafish exposed to endocrine disrupting chemicals

Embryonic zebrafish were examined for changes in protein expression following exposure to sublethal concentrations of 17beta-estradiol (E2) and the estrogen mimic 4-nonylphenol (4-NP). Protein Expression Signatures were derived from embryo homogenates by two-dimensional electrophoresis and digital imaging. In both experiments approximately 30% of the proteins sampled were specific to either E2 or 4-NP and about 33% were common to the control, 4-NP and E2. However, of the proteins induced by either E2 or 4-NP, 28% were common to both chemicals at 1 ppm but only 7% were common to both at 0.1 ppm. While there are many proteins that respond specifically to each chemical, relatively few are common to the two chemicals suggesting that the response pathways of the two chemicals are distinct.

Mode of bactericidal action of silver zeolite and its comparison with that of silver nitrate

The properties of the bactericidal action of silver zeolite as affected by inorganic salts and ion chelators were similar to those of silver nitrate. The results suggest that the contact of the bacterial cell with silver zeolite, the consequent transfer of silver ion to the cell, and the generation of reactive oxygen species in the cell are involved in the bactericidal activity of silver zeolite.

Virulence and the heat shock response

The major adaptive response to elevation in temperature is the heat shock response that involves the induction of many proteins--called heat shock proteins. These include chaperones, proteases, alternative sigma factors and other regulatory and structural proteins. The heat shock response is also turned on by other stress conditions, such as oxidative stress or pH changes. Bacterial entry into the host organism involves a significant environmental change, which is expected to induce the heat shock response. Indeed, some of the heat shock proteins are themselves virulence factors while others affect pathogenesis indirectly, by increasing bacterial resistance to host defenses or regulating virulence genes. The cross talk between heat shock and virulence genes is discussed.

Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout

The advent of DNA array technology and proteomics has revolutionised biology by allowing global analysis of cellular events. So far, the benefits from these new techniques have primarily been realised for well-characterised species. These organisms are rarely the most relevant for environmental biology and ecotoxicology. Thus, there is a need to explore new ways to exploit transcriptomics and proteomics for non-model species. In the present study, rainbow trout (Oncorhynchus mykiss) were exposed to a sublethal concentration of waterborne zinc for up to 6 days. The response in gill tissue was investigated by differential screening of a heterologous cDNA array and by protein profiling using Surface Enhanced Laser Desorption/Ionisation (SELDI). The cDNA array, which was a high-density spotted library of cDNA from Fugu rubripes gill, revealed differentially expressed genes related to energy production, protein synthesis, paracellular integrity, and inflammatory response. SELDI analysis yielded seven proteins that were consistently present only in zinc-exposed gills, and four proteins unique to gills from control fish. A further 11 proteins were differentially regulated. Identification of these proteins by bioinformatics proved difficult in spite of detailed information on molecular mass, charge and zinc-binding affinity. It is concluded that these approaches are viable to non-model species although both have clear limitations.

Protein expression signatures: an application of proteomics

The methods of proteomics, the study of the protein complement of the genome, are applicable to environmental testing. Sets of proteins specific to different stressors can be isolated using computer imaging software. Individual proteins can be identified by mass spectrometry. The Protein Expression Signatures (PES) obtained have potential in diagnosing adverse factors in the environment. The challenge is to demonstrate their feasibility in complex environments. We have shown that PES for three endocrine disrupting compounds in trout (Onchorhynchus mykiss), can be detected in mixed sewage effluent. Other studies support these results. As protein databases expand, identification becomes routine, and capture molecules specific to each protein are developed, the possibility of simple field tests for multiple stressors becomes real.

Assimilatory detoxification of herbicides by Delftia acidovorans MC1: induction of two chlorocatechol 1,2-dioxygenases as a response to chemostress

Proteome analysis of bacteria that can detoxify harmful organic compounds enables the discovery of enzymes involved in the biodegradation of these substances and proteins that protect the cell against poisoning. Exposure of Delftia acidovorans MC1 to 2,4-dichlorophenoxypropionic acid and its metabolites 2,4-dichlorophenol and 3,5-dichlorocatechol during growth on pyruvate as a source of carbon and energy induced several proteins. Contrary to the general hypothesis that lipophilic or reactive compounds induce heat shock or oxidative stress proteins, no induction of the GroEL, DnaK and AhpC proteins that were used as markers for the induction of heat shock and oxidative stress responses was observed. However, two chlorocatechol1,2-dioxygenases, identified by amino terminal sequence analysis, were induced. Both enzymes catalyse the conversion of 3,5-dichlorocatechol to 2,4-dichloro-cis,cis-muconate indicating that biodegradation is a major mechanism of resistance in the detoxifying bacterium D. acidovorans MC1.

Biodegradation of aromatic compounds by Escherichia coli

Although Escherichia coli has long been recognized as the best-understood living organism, little was known about its abilities to use aromatic compounds as sole carbon and energy sources. This review gives an extensive overview of the current knowledge of the catabolism of aromatic compounds by E. coli. After giving a general overview of the aromatic compounds that E. coli strains encounter and mineralize in the different habitats that they colonize, we provide an up-to-date status report on the genes and proteins involved in the catabolism of such compounds, namely, several aromatic acids (phenylacetic acid, 3- and 4-hydroxyphenylacetic acid, phenylpropionic acid, 3-hydroxyphenylpropionic acid, and 3-hydroxycinnamic acid) and amines (phenylethylamine, tyramine, and dopamine). Other enzymatic activities acting on aromatic compounds in E. coli are also reviewed and evaluated. The review also reflects the present impact of genomic research and how the analysis of the whole E. coli genome reveals novel aromatic catabolic functions. Moreover, evolutionary considerations derived from sequence comparisons between the aromatic catabolic clusters of E. coli and homologous clusters from an increasing number of bacteria are also discussed. The recent progress in the understanding of the fundamentals that govern the degradation of aromatic compounds in E. coli makes this bacterium a very useful model system to decipher biochemical, genetic, evolutionary, and ecological aspects of the catabolism of such compounds. In the last part of the review, we discuss strategies and concepts to metabolically engineer E. coli to suit specific needs for biodegradation and biotransformation of aromatics and we provide several examples based on selected studies. Finally, conclusions derived from this review may serve as a lead for future research and applications.

Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress

The proteins induced in Acinetobacter calcoaceticus by the potentially toxic growth substrates phenol and catechol were analyzed by 2D-electrophoresis of cell extracts and compared with those induced by heat shock and oxidative stress. Although both aromatic compounds are quite similar, the only difference being that catechol has an additional hydroxyl group, the responses obtained differed considerably. Phenol has greater lipophilicity and mainly induced heat shock proteins, whereas catechol, which causes the production of reactive oxygen species, predominantly induced oxidative stress proteins. Furthermore, some special proteins were induced by phenol or catechol, which might be useful as biomarkers for chemostress, and could be involved in the catalytic degradation of potentially toxic compounds.