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1.
The biosynthesis of the molybdenum cofactors in Escherichia coli.
Leimkühler, S
Environmental microbiology. 2020;(6):2007-2026
Abstract
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5'-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
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2.
Making iron-sulfur cluster: structure, regulation and evolution of the bacterial ISC system.
Baussier, C, Fakroun, S, Aubert, C, Dubrac, S, Mandin, P, Py, B, Barras, F
Advances in microbial physiology. 2020;:1-39
Abstract
Iron sulfur (Fe-S) clusters rank among the most ancient and conserved prosthetic groups. Fe-S clusters containing proteins are present in most, if not all, organisms. Fe-S clusters containing proteins are involved in a wide range of cellular processes, from gene regulation to central metabolism, via gene expression, RNA modification or bioenergetics. Fe-S clusters are built by biogenesis machineries conserved throughout both prokaryotes and eukaryotes. We focus mostly on bacterial ISC machinery, but not exclusively, as we refer to eukaryotic ISC system when it brings significant complementary information. Besides covering the structural and regulatory aspects of Fe-S biogenesis, this review aims to highlight Fe-S biogenesis facets remaining matters of discussion, such as the role of frataxin, or the link between fatty acid metabolism and Fe-S homeostasis. Last, we discuss recent advances on strategies used by different species to make and use Fe-S clusters in changing redox environmental conditions.
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3.
Enhanced antibacterial activity of calcium silicate-based hybrid cements for bone repair.
Lin, MC, Chen, CC, Wu, IT, Ding, SJ
Materials science & engineering. C, Materials for biological applications. 2020;:110727
Abstract
Calcium silicate cement has attracted much attention for bone defect repair and regeneration due to its osteogenic properties. Biomaterial-associated infections and washout have become a common clinical problem. In order to enhance the antibacterial and washout performance of calcium silicate cement to meet clinical needs, different types of chitosan, including chitosan polysaccharide (CTS), quaternary ammonium chitosan (QTS), and chitosan oligosaccharide (COS), as a liquid phase were added to the calcium silicate powder. The physicochemical properties, in vitro bioactivity, antibacterial efficacy, and osteogenic effects (MG63 cells) of the cement were evaluated. Antibacterial activity was conducted with Gram-negative Escherichia coli (E. coli) and a Gram-positive Staphylococcus aureus (S. aureus) bacteria. The amount of intracellular reactive oxygen species (ROS) produced in the bacteria cultured with the chitosan solution was also detected. The experimental results showed that the chitosan additive did not affect the crystalline phase of calcium silicate cement, but increased the setting time and strength of the cement in a concentration-dependent manner. Within the scope of this study, CTS and QTS solutions with a concentration of not <1 wt% improved the washout resistance of the control cement, while the COS solutions failed to strengthen the cement. When soaked in simulated body fluid (SBF) for 1 day, all cement samples formed apatite spherules. As the soaking time increased, the diametral tensile strength of all cements decreased and the porosity increased. The assays of MG63 cell function showed lower osteogenic activity of osteoblastic cells grown on the surfaces of the chitosan-incorporated cements in comparison with the control cement without chitosan. At the same 1% concentration, compared with QTS and COS cement, CTS cement had lower cell attachment, proliferation, differentiation, and mineralization. Conversely, the CTS cement resulted in the highest bacteriostasis ratio among the three hybrid cements against two bacteria. The ROS production followed the order of CTS > QTS > COS at the same 1% concentration. In conclusion, calcium silicate cement with 1% QTS may be a viable candidate for bone defect repair in view of anti-washout performance, setting time, antibacterial activity, and osteogenic activity shown in this study.
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4.
Synthesis and characterization of cellulose/TiO2 nanocomposite: Evaluation of in vitro antibacterial and in silico molecular docking studies.
M V, A, Harb, M, Sundaram, R
Carbohydrate polymers. 2020;:116868
Abstract
Cellulose/TiO2 nanocomposite was synthesized using coagulation in sodium hydroxide-thiourea-urea aqueous solution medium by precipitation method. This method was accomplished green and cost-effective for the fabrication of composite nanomaterials. Structure, morphology and optical properties of the nanocomposite were characterized by X-ray diffraction, energy dispersive X-ray spectroscopy, field emission scanning electron microscopy, transmission electron microscopy, and ultraviolet diffuse reflectance spectra respectively. XRD results showed the anatase structure of TiO2 while FESEM micrograph showed evidence of particle size ranging from 20 to 40 nm for cellulose/TiO2 nanocomposite. The Fourier transfer infrared spectroscopy investigation reveals that the TiO2 is bound to hydroxyl groups to the cellulose by hydrogen bonding. The optical energy bandgap is found to be 2.71 eV for nanocomposite from the UV-DRS. The mechanical strength of the composites gently escalated with the addition of TiO2 nanoparticles into cellulose polymer matrix. Cellulose/TiO2 nanocomposite was screened for their in vitro antibacterial activity against Staphylococcus aureus and Escherichia coli bacteria have been investigated. Additionally, the results obtained from in silico molecular docking studies confirm the interaction of nanocomposite with proteins, were in good agreement with the experimental data. This finding provides a novel and simple method for the synthesis of cellulose/TiO2 nanocomposite as functional biomaterials.
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5.
ZnO, AgCl and AgCl/ZnO nanocomposites incorporated chitosan in the form of hydrogel beads for photocatalytic degradation of MB, E. coli and S. aureus.
Taghizadeh, MT, Siyahi, V, Ashassi-Sorkhabi, H, Zarrini, G
International journal of biological macromolecules. 2020;:1018-1028
Abstract
Significant improvement of effective and low-cost decolorization and disinfecting technologies is required to address the problems created by dyes and dangerous microorganisms from water and wastewaters. This article expresses the degradation of methylene blue (MB), Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) as gram negative and positive bacteria via a chitosan/AgCl/ZnO (CS/AgCl/ZnO) nanocomposite hydrogel beads system as a photocatalyst under visible light irradiation. The techniques such as FT-IR, SEM, EDAX, TGA, and XRD were applied to recognize the synthesized beads. Decolorization and disinfection experimental results revealed that the hydrogel beads system effectively degrade MB and bacteria. Also, the effects of the initial amount of catalysts, pH, coions and initial concentration of dye on the photocatalytic decolorization were investigated. Moreover, kinetics analysis indicates that the photocatalytic degradation rate of MB and bacteria can be described by Langmuir-Hinshelwood (L-H) and Weibull inactivation models, respectively. We provide a reusable and recoverable effective organic/inorganic photocatalyst in the form of beads that could solve the disadvantages of powder photocatalytic, without reducing the efficiency.
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6.
Escherichia coli Extract-Based Cell-Free Expression System as an Alternative for Difficult-to-Obtain Protein Biosynthesis.
Smolskaya, S, Logashina, YA, Andreev, YA
International journal of molecular sciences. 2020;(3)
Abstract
Before utilization in biomedical diagnosis, therapeutic treatment, and biotechnology, the diverse variety of peptides and proteins must be preliminarily purified and thoroughly characterized. The recombinant DNA technology and heterologous protein expression have helped simplify the isolation of targeted polypeptides at high purity and their structure-function examinations. Recombinant protein expression in Escherichia coli, the most-established heterologous host organism, has been widely used to produce proteins of commercial and fundamental research interests. Nonetheless, many peptides/proteins are still difficult to express due to their ability to slow down cell growth or disrupt cellular metabolism. Besides, special modifications are often required for proper folding and activity of targeted proteins. The cell-free (CF) or in vitro recombinant protein synthesis system enables the production of such difficult-to-obtain molecules since it is possible to adjust reaction medium and there is no need to support cellular metabolism and viability. Here, we describe E. coli-based CF systems, the optimization steps done toward the development of highly productive and cost-effective CF methodology, and the modification of an in vitro approach required for difficult-to-obtain protein production.
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7.
Enzymatic reactions and microorganisms producing the various isomers of hydroxyproline.
Hara, R, Kino, K
Applied microbiology and biotechnology. 2020;(11):4771-4779
Abstract
Hydroxyproline is an industrially important compound with applications in the pharmaceutical, nutrition, and cosmetic industries. trans-4-Hydroxy-L-proline is recognized as the most abundant of the eight possible isomers (hydroxy group at C-3 or C-4, cis- or trans-configuration, and L- or D-form). However, little attention has been paid to the rare isomers, probably due to their limited availability. This mini-review provides an overview of recent advances in microbial and enzymatic processes to develop practical production strategies for various hydroxyprolines. Here, we introduce three screening strategies, namely, activity-, sequence-, and metabolite-based approaches, allowing identification of diverse proline-hydroxylating enzymes with different product specificities. All naturally occurring hydroxyproline isomers can be produced by using suitable hydroxylases in a highly regio- and stereo-selective manner. Furthermore, crystal structures of relevant hydroxylases provide much insight into their functional roles. Since hydroxylases acting on free L-proline belong to the 2-oxoglutarate-dependent dioxygenase superfamily, cellular metabolism of Escherichia coli coupled with a hydroxylase is a valuable source of 2-oxoglutarate, which is indispensable as a co-substrate in L-proline hydroxylation. Further, microbial hydroxyproline 2-epimerase may serve as a highly adaptable tool to convert L-hydroxyproline into D-hydroxyproline. KEY POINTS • Proline hydroxylases serve as powerful tools for selectivel-proline hydroxylation. • Engineered Escherichia coli are a robust platform for hydroxyproline production. • Hydroxyproline epimerase convertsl-hydroxyproline intod-hydroxyproline.
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8.
Use, Acceptability, Performance, and Health Impact of Hollow Fiber Ultrafilters for Water Treatment in Rural Kenyan Households, 2009-2011.
Fagerli, K, Gieraltowski, L, Nygren, B, Foote, E, Gaines, J, Oremo, J, Odhiambo, A, Kim, S, Quick, R
The American journal of tropical medicine and hygiene. 2020;(1):465-471
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Abstract
Diarrheal illness remains a leading cause of morbidity and mortality in children < 5 years in developing countries, and contaminated water contributes to diarrhea risk. To address this problem, a novel hollow fiber ultrafilter (HFU) was developed for household water treatment. To test its impact on water quality and infant health, we conducted a cluster-randomized longitudinal evaluation in 10 intervention and 10 comparison villages in Kenya, attempting to enroll all households with infants (< 12 months old). We conducted a baseline survey, distributed HFUs to intervention households, made biweekly home visits for 1 year to assess water treatment practices and diarrhea in infants, and tested water samples from both groups every 2 months for Escherichia coli. We enrolled 92 infants from intervention households and 74 from comparison households. During the 1-year study period, 45.7% of intervention households and 97.3% of comparison households had at least one stored water sample test positive for E. coli. Compared with comparison households, the odds of E. coli contamination in stored water was lower for intervention households (odds ratio [OR]: 0.42, 95% CI: 0.24, 0.74), but there was no difference in the odds of reported diarrhea in infants, adjusting for covariates (OR: 1.19, 95% CI: 0.74, 1.90). Although nearly all water samples obtained from unprotected sources and filtered by the HFU were free of E. coli contamination, HFUs alone were not effective at reducing diarrhea in infants.
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9.
Between computational predictions and high-throughput transcriptional profiling: in depth expression analysis of the OppB trans-membrane subunit of Escherichia coli OppABCDF oligopeptide transporter.
Masulis, IS, Sukharycheva, NA, Kiselev, SS, Andreeva, ZS, Ozoline, ON
Research in microbiology. 2020;(2):55-63
Abstract
Bacterial oligopeptide transporters encoded by arrays of opp genes are implicated in a wide variety of physiological functions including nutrient acquisition, cell-to-cell communication, host-pathogen interaction. Combining the five opp genes in one oppABCDF operon of Escherichia coli assumes unified principle of their transcriptional regulation, which should provide a comparable amounts of translated products. This, however, contradicts the experimentally detected disproportion in the abundance of periplasmic OppA and the trans-membrane subunits OppB and OppC. As a first step towards understanding differential regulation of intraoperonic genes we examined genomic region proximal to oppB for its competence to initiate RNA synthesis using in silico promoter predictions, data of high-throughput RNA sequencing and targeted transcription assay. A number of transcription start sites (TSSs), whose potency depends on the presence of cationic oligopeptide protamine in cultivation medium, was found at the end of oppA and in the early coding part of oppB. We also show that full-size OppB conjugated with EGFP is produced under the control of its own genomic regulatory region and may be detected in analytical quantities of bacterial cell culture.
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10.
Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway.
Li, Z, Wang, H, Ding, D, Liu, Y, Fang, H, Chang, Z, Chen, T, Zhang, D
Journal of industrial microbiology & biotechnology. 2020;(6-7):525-535
Abstract
The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.