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1.
Synthesis of non-canonical branched-chain amino acids in Escherichia coli and approaches to avoid their incorporation into recombinant proteins.
Reitz, C, Fan, Q, Neubauer, P
Current opinion in biotechnology. 2018;:248-253
Abstract
In E. coli the non-canonical amino acids acids norvaline, norleucine, and β-methylnorleucine, which derive from an off-pathway of the branched-chain amino acid synthesis route are synthesized and incorporated into cellular and recombinant proteins. The synthesis of these amino acids is supported by a high flux of glucose through the glycolytic pathway in combination with a derepression of the enzymes of the branched chain amino acid pathway, for example, when leucine-rich proteins are produced. Avoiding the synthesis and misincorporation of these amino acids has been challenging, especially in large-scale pharmaceutical processes where the problem is boosted by the typical fed-batch production and the technical limitation of mass transfer in the bioreactors. Despite its industrial importance, so far this issue has not been discussed comprehensively. Therefore this paper reviews, firstly, the specific pathway of the non-canonical branched chain amino acids starting at pyruvate, secondly, the molecular factors for their misincorporation, and thirdly, approaches to avoid this misincoporation. While the synthesis of these amino acids is difficult to prevent due to the broad promiscuity of the connected enzymes, recent studies on the control mechanisms of aminoacyl tRNA synthetases open new opportunities to avoid this misincorporation.
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2.
Variation on a theme: investigating the structural repertoires used by ferric uptake regulators to control gene expression.
Sarvan, S, Butcher, J, Stintzi, A, Couture, JF
Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine. 2018;(5):681-704
Abstract
In every living organism, the control of metal homoeostasis is a tightly regulated process coordinated by several intertwined biological pathways. In many bacteria, the ferric uptake regulator (Fur) family of transcriptional factors (TFs) are key factors in controlling the expression of genes involved in metal homeostasis and can also regulate the expression of genes involved in responses to oxidative stresses. Since the crystallization of Escherichia coli Fur DNA binding domain, the crystal structure of several metalloregulators have been reported. While the Fur family of proteins adopt similar structures, each contains unique structural features relating to their specific biological functions. Moreover, recent groundbreaking studies have provided additional insights into the mechanisms underlying the binding of DNA by these metalloregulators. In this review, we present a comprehensive overview of the crystal structure of Fur family metalloregulators with a specific focus on the new structures of these TFs bound to DNA.
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3.
Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing.
Chu, HY, Sprouffske, K, Wagner, A
BMC evolutionary biology. 2018;(1):54
Abstract
BACKGROUND Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. RESULTS At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. CONCLUSIONS To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.
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4.
Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis.
Vilkhovoy, M, Horvath, N, Shih, CH, Wayman, JA, Calhoun, K, Swartz, J, Varner, JD
ACS synthetic biology. 2018;(8):1844-1857
Abstract
Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence specific constraint based modeling to evaluate the performance of E. coli cell-free protein synthesis. A core E. coli metabolic network, describing glycolysis, the pentose phosphate pathway, energy metabolism, amino acid biosynthesis, and degradation was augmented with sequence specific descriptions of transcription and translation and effective models of promoter function. Model parameters were largely taken from literature; thus the constraint based approach coupled the transcription and translation of the protein product, and the regulation of gene expression, with the availability of metabolic resources using only a limited number of adjustable model parameters. We tested this approach by simulating the expression of two model proteins: chloramphenicol acetyltransferase and dual emission green fluorescent protein, for which we have data sets; we then expanded the simulations to a range of additional proteins. Protein expression simulations were consistent with measurements for a variety of cases. The constraint based simulations confirmed that oxidative phosphorylation was active in the CAT cell-free extract, as without it there was no feasible solution within the experimental constraints of the system. We then compared the metabolism of theoretically optimal and experimentally constrained CFPS reactions, and developed parameter free correlations which could be used to estimate productivity as a function of carbon number and promoter type. Lastly, global sensitivity analysis identified the key metabolic processes that controlled CFPS productivity and energy efficiency. In summary, sequence specific constraint based modeling of CFPS offered a novel means to a priori estimate the performance of a cell-free system, using only a limited number of adjustable parameters. While we modeled the production of a single protein in this study, the approach could easily be extended to multiprotein synthetic circuits, RNA circuits, or the cell-free production of small molecule products.
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5.
Ribosome Hibernation.
Prossliner, T, Skovbo Winther, K, Sørensen, MA, Gerdes, K
Annual review of genetics. 2018;:321-348
Abstract
Protein synthesis consumes a large fraction of available resources in the cell. When bacteria encounter unfavorable conditions and cease to grow, specialized mechanisms are in place to ensure the overall reduction of costly protein synthesis while maintaining a basal level of translation. A number of ribosome-associated factors are involved in this regulation; some confer an inactive, hibernating state of the ribosome in the form of 70S monomers (RaiA; this and the following are based on Escherichia coli nomenclature) or 100S dimers (RMF and HPF homologs), and others inhibit translation at different stages in the translation cycle (RsfS, YqjD and paralogs, SRA, and EttA). Stationary phase cells therefore exhibit a complex array of different ribosome subpopulations that adjusts the translational capacity of the cell to the encountered conditions and ensures efficient reactivation of translation when conditions improve. Here, we review the current state of research regarding stationary phase-specific translation factors, in particular ribosome hibernation factors and other forms of translational regulation in response to stress conditions.
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6.
A modern purification method for volatile sesquiterpenes produced by recombinant Escherichia coli carrying terpene synthase genes.
Shindo, K
Bioscience, biotechnology, and biochemistry. 2018;(6):935-939
Abstract
Most volatile sesquiterpenes had been purified from plants using distillation and preparative gas chromatography, which is not applicable to many laboratories that do not possess a needed facility. Thus, this review focuses on a modern purification method for volatile sesquiterpenes using Escherichia coli cells that functionally express terpene synthase (Tps) genes. It was recently developed that recombinant E. coli cells carrying Tps genes were cultured in two-layer media (n-octane/TB medium) without harming the cells, and the volatile hydrophobic compounds trapped in the n-octane were purified by two-phase partition (alkane/alkaline 50% MeOH), silica gel column chromatography, and reversed-phase preparative high-performance liquid chromatography (if necessary). Consequently, it was found that the volatile sesquiterpenes are easily purified, the structures of which can then be determined by nuclear magnetic resonance, [α]D and gas chromatography-mass spectrometry analyses. The antioxidant activities of several volatile sesquiterpenes are also presented in this review.
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7.
Adaptation of Escherichia coli to long-term batch culture in various rich media.
Westphal, LL, Lau, J, Negro, Z, Moreno, IJ, Ismail Mohammed, W, Lee, H, Tang, H, Finkel, SE, Kram, KE
Research in microbiology. 2018;(3):145-156
Abstract
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms. In contrast with other experimental evolution systems, because of cycling of nutrients and waste products, this is a heterogeneous environment, where selective pressures change over time, similar to natural environments. We determined that incubation in each environment leads to different adaptations by observing the growth advantage in stationary phase (GASP) phenotype. Re-sequencing whole genomes of populations identified both mutant alleles in a conserved set of genes and differences in evolutionary trajectories between environments. Reconstructing identified mutations in the parental strain background confirmed the adaptive advantage of some alleles, but also identified a surprising number of neutral or even deleterious mutations. This result indicates that complex epistatic interactions may be under positive selection within these heterogeneous environments.
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8.
Trypsin Binding with Copper Ions Scavenges Superoxide: Molecular Dynamics-Based Mechanism Investigation.
Li, X, Zhong, Y, Zhao, C
International journal of environmental research and public health. 2018;(1)
Abstract
Trypsin is a serine protease, which has been proved to be a novel superoxide scavenger. The burst of superoxide induced by polychlorinated biphenyls can be impeded by trypsin in both wild type and sod knockout mutants of Escherichia coli. The experimental results demonstrated that the activities of superoxide scavenging of trypsin were significantly accelerated by Cu ions. Also, with the addition of Cu ions, a new β-sheet (β7) transited from a random coil in the Cu(II)-trypsin (TP) system, which was favorable for the formation of more contacts with other sheets of trypsin. Residue-residue network analysis and the porcupine plots proved that the Cu ion in trypsin strengthened some native interactions among residues, which ultimately resulted in much greater stability of the Cu(II)-TP system. Moreover, compact and stable trypsin structures with Cu ions might be responsible for significantly provoking the activity of superoxide scavenging.
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9.
Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics.
Foik, IP, Tuszynska, I, Feder, M, Purta, E, Stefaniak, F, Bujnicki, JM
European journal of medicinal chemistry. 2018;:60-67
Abstract
In erythromycin-resistant bacteria, the N6 position of A2058 in 23S rRNA is mono- or dimethylated by Erm family methyltransferases. This modification results in cross-resistance to macrolides, lincosamides and streptogramin B. Most inhibitors of Erm methyltransferases developed up-to-date target the cofactor-binding pocket, resulting in a lack of selectivity whereas inhibitors that bind the substrate-binding pocket demonstrate low in vitro activity. In this study, a molecular docking approach followed by biochemical screening was applied to search for inhibitors targeting both cofactor- and substrate-binding pockets of ErmC' methyltransferase. Based on the results of the molecular docking-based virtual screening of the clean-leads subset of the ZINC database, 29 compounds were chosen for experimental verification. Among them inhibitor 28 (ZINC code 32747906), with an IC50 of 100 μM, decreased the minimal inhibitory concentration of erythromycin in the Escherichia coli strain overexpressing ErmC'. Docking analysis of 28 to the ErmC' structure and the competitive ligand binding assay revealed a non-competitive model of inhibition. Inhibitor 28 served as a template for similarity-based virtual screening, which resulted in the identification of two derivatives 3s (ZINC code 62022572) and 4s (ZINC code 49032257) with an IC50 of 116 μM and 110 μM, respectively. Our results provide a basis for the development of inhibitors against the Erm-family of enzymes.
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10.
Graphene-Oxide-Decorated Microporous Polyetheretherketone with Superior Antibacterial Capability and In Vitro Osteogenesis for Orthopedic Implant.
Ouyang, L, Deng, Y, Yang, L, Shi, X, Dong, T, Tai, Y, Yang, W, Chen, ZG
Macromolecular bioscience. 2018;(6):e1800036
Abstract
Due to its similar elastic modulus of human bones, polyetheretherketone (PEEK) has been considered as an excellent cytocompatible material. However, the bioinertness, poor osteoconduction, and weak antibacterial activity of PEEK limit its wide applications in clinics. In this study, a facile strategy is developed to prepare graphene oxide (GO) modified sulfonated polyetheretherketone (SPEEK) (GO-SPEEK) through a simple dip-coating method. After detailed characterization, it is found that the GO closely deposits on the surface of PEEK, which is attributed to the π-π stacking interaction between PEEK and GO. Antibacterial tests reveal that the GO-SPEEK exhibits excellent suppression toward Escherichia coli. In vitro cell attachment, growth, differentiation, alkaline phosphatase activity, quantitative real-time polymerase chain reaction analyses, and calcium mineral deposition all illustrate that the GO-SPEEK substrate can significantly accelerate the proliferation and osteogenic differentiation of osteoblast-like MG-63 cells compared with those on PEEK and SPEEK groups. These results suggest that the GO-SPEEK has an improved antibacterial activity and cytocompatibility in vitro, showing that the developed GO-SPEEK has a great potential as the bioactive implant material in bone tissue engineering.