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Bioremediation of an agricultural saline soil contaminated with endosulfan and Escherichia coli by an active surface agent induced in a Penicillium crustosum culture.
Landa-Faz, A, Rodríguez-Vázquez, R, Roldán-Carrillo, TG, Hidalgo-Lara, ME, Aguilar-López, R, Cebrián-García, ME
Preparative biochemistry & biotechnology. 2022;(3):292-301
Abstract
This study evaluates the production of a biological active surface agent (BASA) through its surface tension (ST) and emulsifying activity (E24) for endosulfan degradation (ED) and Escherichia coli growth inhibition (EcGI) in an agricultural saline soil. The fungus, identified as Penicillium crustosum was isolated from the Citrus sinensis peel (CsP), then the surface properties were evaluated in 9 culture media through a Taguchi L9 experimental design. The culture conditions included: stirring speed, pH, carbon (C) and nitrogen (N) sources; being glucose, NH4N03, 120 rpm and pH of 5, the most significant parameters in the BASA production. The BASA identified as a lipopeptide type, showed a ST = 38 mN m-1 and E24=71%. Both properties were stable at 80 °C, while ST presented stability in the pH range of 2 - 12, and a saline concentration of 200 g L-1; E24 was also stable at a pH between 8-12. Further application of BASA and fungal inoculum to a contaminated agricultural saline soil presented an EcGI of 99.8% on the 8th day, and ED of 92.9 ± 4.7% in 30 days, respectively; being the first report that uses this fungus for pesticide and bacteria elimination from an agricultural saline soil.
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A multistep enrichment process with custom growth medium improves resuscitation of chlorine-stressed coliforms from secondary sewage effluents.
Mobberley, JM, Cooley, SK, Widder, MW, Phillips, SM, Melville, AM, Brennan, LM, Divito, VT, van der Schalie, WH, Ozanich, RM, Hutchison, JR
Journal of microbiological methods. 2022;:106364
Abstract
Resuscitation and detection of stressed total coliforms in chlorinated water samples is needed to assess and prevent health effects from adverse exposure. In this study, we report that the addition of a growth enhancer mix consisting of trehalose, sodium pyruvate, magnesium chloride, and 1× trace mineral supplement improved growth of microorganisms from chlorinated secondary effluent in the base medium with Colilert-18. Improving growth of chlorine stressed microorganisms from secondary effluent is crucial to decreased detection time from 18 to 8 h.
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Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases.
Hartman, MCT
Chembiochem : a European journal of chemical biology. 2022;(1):e202100299
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Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Equilibrium properties of E. coli lactose permease symport-A random-walk model approach.
Sun, H
PloS one. 2022;(2):e0263286
Abstract
The symport of lactose and H+ is an important physiological process in E. coli, for it is closely related to cellular energy supply. In this paper, we review, extend and analyse a newly proposed cotransport model that takes the "leakage" phenomenon (uncoupled particle translocation) into account and also satisfies the static head equilibrium condition. Then, we use the model to study the equilibrium properties, including equilibrium solution and the time required to reach equilibrium, of the symport process of E. coli LacY protein, when varying the parameters of the initial state of cotransport system. It can be found that in our extended model, H+ and lactose will reach their equilibrium state separately, and when "leakage" exists, it linearly affects the equilibrium solution, which is a useful property that the original model does not have. We later investigated the effect of the volume of periplasm and cytoplasm on the equilibrium properties. For a certain E. coli cell, as it continues to lose water and contract, the time for cytoplasm pH to be stabilized by symport increases monotonically when the cell survives. Finally, we reproduce the experimental data from a literature to verify the validity of the extension in this symport process. The above phenomena and other findings in this paper may help us to not only further validate or improve the model, but also deepen our understanding of the cotransport process of E. coli LacY protein.
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Association of Pre-diagnostic Antibody Responses to Escherichia coli and Bacteroides fragilis Toxin Proteins with Colorectal Cancer in a European Cohort.
Butt, J, Jenab, M, Werner, J, Fedirko, V, Weiderpass, E, Dahm, CC, Tjønneland, A, Olsen, A, Boutron-Ruault, MC, Rothwell, JA, et al
Gut microbes. 2021;(1):1-14
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Abstract
Experimental evidence has implicated genotoxic Escherichia coli (E. coli) and enterotoxigenic Bacteroides fragilis (ETBF) in the development of colorectal cancer (CRC). However, evidence from epidemiological studies is sparse. We therefore assessed the association of serological markers of E. coli and ETBF exposure with odds of developing CRC in the European Prospective Investigation into Nutrition and Cancer (EPIC) study.Serum samples of incident CRC cases and matched controls (n = 442 pairs) were analyzed for immunoglobulin (Ig) A and G antibody responses to seven E. coli proteins and two isoforms of the ETBF toxin via multiplex serology. Multivariable-adjusted conditional logistic regression analyses were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association of sero-positivity to E. coli and ETBF with CRC.The IgA-positivity of any of the tested E. coli antigens was associated with higher odds of developing CRC (OR: 1.42; 95% CI: 1.05-1.91). Dual-positivity for both IgA and IgG to E. coli and ETBF was associated with >1.7-fold higher odds of developing CRC, with a significant association only for IgG (OR: 1.75; 95% CI: 1.04, 2.94). This association was more pronounced when restricted to the proximal colon cancers (OR: 2.62; 95% CI: 1.09, 6.29) compared to those of the distal colon (OR: 1.24; 95% CI: 0.51, 3.00) (pheterogeneity = 0.095). Sero-positivity to E. coli and ETBF was associated with CRC development, suggesting that co-infection of these bacterial species may contribute to colorectal carcinogenesis. These findings warrant further exploration in larger prospective studies and within different population groups.
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Discovery of an Unnatural DNA Modification Derived from a Natural Secondary Metabolite.
Wang, T, Kohli, RM
Cell chemical biology. 2021;(1):97-104.e4
Abstract
Despite widespread interest for understanding how modified bases have evolved their contemporary functions, limited experimental evidence exists for measuring how close an organism is to accidentally creating a new, modified base within the framework of its existing genome. Here, we describe the biochemical and structural basis for how a single-point mutation in E. coli's naturally occurring cytosine methyltransferase can surprisingly endow a neomorphic ability to create the unnatural DNA base, 5-carboxymethylcytosine (5cxmC), in vivo. Mass spectrometry, bacterial genetics, and structure-guided biochemistry reveal this base to be exclusively derived from the natural but sparse secondary metabolite carboxy-S-adenosyl-L-methionine (CxSAM). Our discovery of a new, unnatural DNA modification reveals insights into the substrate selectivity of DNA methyltransferase enzymes, offers a promising new biotechnological tool for the characterization of the mammalian epigenome, and provides an unexpected model for how neomorphic bases could arise in nature from repurposed host metabolites.
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Gender medicine: the impact of probiotics on male patients.
Pacifici, L, Santacroce, L, Dipalma, G, Haxhirexha, K, Topi, S, Cantore, S, Altini, V, Pacifici, A, De Vito, D, Pettini, F, et al
La Clinica terapeutica. 2021;(1):e8-e15
Abstract
PURPOSE Numerous studies in the literature confirm the importance of the use of probiotics in inflammatory states of the prostate in humans. Our pilot study aimed to test probiotics strains ability to improve urinary bacterial load in male subjects. METHODS Twenty healthy men aged 55-65 years, with recurrent urinatory infections were enrolled and randomized into 2 groups. Urine culturing to detect Enterobacteriaceae (Escherichia Coli and Enterococcus faecalis) was performed at baseline and at 12 weeks after the starting of the study. RESULTS We found that taking the probiotic reduces the bacterial load of E. coli and E. faecalis in urine cultures. The use of the probiotic in these inflammatory states does not affect the change in weight in the tested subjects. CONCLUSIONS Our data confirm and improve the main results reported in the scientific literature on the importance of taking probiotics in prostatitis.
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Studying bacterial chemosensory array with CryoEM.
Qin, Z, Zhang, P
Biochemical Society transactions. 2021;(5):2081-2089
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Abstract
Bacteria direct their movement in respond to gradients of nutrients and other stimuli in the environment through the chemosensory system. The behavior is mediated by chemosensory arrays that are made up of thousands of proteins to form an organized array near the cell pole. In this review, we briefly introduce the architecture and function of the chemosensory array and its core signaling unit. We describe the in vivo and in vitro systems that have been used for structural studies of chemosensory array by cryoEM, including reconstituted lipid nanodiscs, 2D lipid monolayer arrays, lysed bacterial ghosts, bacterial minicells and native bacteria cells. Lastly, we review recent advances in structural analysis of chemosensory arrays using state-of-the-art cryoEM and cryoET methodologies, focusing on the latest developments and insights with a perspective on current challenges and future directions.
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In situ EPR spectroscopy of a bacterial membrane transporter using an expanded genetic code.
Kugele, A, Ketter, S, Silkenath, B, Wittmann, V, Joseph, B, Drescher, M
Chemical communications (Cambridge, England). 2021;(96):12980-12983
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Abstract
The membrane transporter BtuB is site-directedly spin labelled on the surface of living Escherichia coli via Diels-Alder click chemistry of the genetically encoded amino acid SCO-L-lysine. The previously introduced photoactivatable nitroxide PaNDA prevents off-target labelling, is used for distance measurements, and the temporally shifted activation of the nitroxide allows for advanced experimental setups. This study describes significant evolution of Diels-Alder-mediated spin labelling on cellular surfaces and opens up new vistas for the the study of membrane proteins.
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Escherichia coli small molecule metabolism at the host-microorganism interface.
Gatsios, A, Kim, CS, Crawford, JM
Nature chemical biology. 2021;(10):1016-1026
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Abstract
Escherichia coli are a common component of the human microbiota, and isolates exhibit probiotic, commensal and pathogenic roles in the host. E. coli members often use diverse small molecule chemistry to regulate intrabacterial, intermicrobial and host-bacterial interactions. While E. coli are considered to be a well-studied model organism in biology, much of their chemical arsenal has only more recently been defined, and much remains to be explored. Here we describe chemical signaling systems in E. coli in the context of the broader field of metabolism at the host-bacteria interface and the role of this signaling in disease modulation.