The bacterial pathogenPseudomonas aeruginosaactivates expression of many virulence genes in a cell density-dependent manner by using an intricate quorum-sensing (QS) network. QS inP. aeruginosainvolves two acyl-homoserine-lactone circuits, LasI-LasR and RhlI-RhlR. LasI-LasR is required to activate many genes including those coding for RhlI-RhlR.P. aeruginosacauses chronic infections in the lungs of people with cystic fibrosis (CF). In these infections, LasR mutants are common, butrhlR-rhlIexpression has escaped LasR regulation in many CF isolates. To better understand the evolutionary trajectory ofP. aeruginosaQS in chronic infections, we grew LasR mutants of the well-studiedP. aeruginosastrain, PAO1, in conditions that recapitulate an environment where QS signal synthesis by other bacteria might still occur. When QS is required for growth, addition of the RhlI product butyryl-homoserine lactone (C4-HSL), or bacteria that produce C4-HSL, to LasR mutants results in the rapid emergence of a population with a LasR-independent RhlI-RhlR QS system. These evolved populations exhibit subsequent growth without added C4-HSL. The variants that emerge have mutations inmexT, which codes for a transcription factor that controls expression of multiple genes. LasR-MexT mutants have a competitive advantage over both the parent LasR mutant and a LasR-MexT-RhlR mutant. Our findings suggest a plausible evolutionary trajectory for QS inP. aeruginosaCF infections where LasR mutants arise during infection, but because these mutants are surrounded by C4-HSL–producingP. aeruginosa,variants rewired to have a LasR-independent RhlIR system quickly emerge.
Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work.
Cellulases acting on crystalline cellulose in synergistic mixtures have higher combined activities than the sum of their individual activities. The mechanisms by which different types of cellulases enhance each other's activities are complex and not completely understood, and the published data is often inconsistent. We discuss the role of the substrate and experimental factors in synergism experiments and consider the various modes of synergism that have been proposed. New oxidoreductase enzymes that participate in novel synergistic reactions are also discussed. Finally, we propose a general encompassing synergism model, based on the observations described in the review.
Dynamic light scattering, potentiometric titration, transmission electron microscopy and atomic force microscopy have been used to investigate the micellar behaviour and metal-nanoparticle formation in poly(ethylene oxide)-block-poly(2-vinylpyridine), PEO-b-P2VP, poly(hexa(ethylene glycol) methacrylate)-block-poly(2-(diethylamino)ethyl methacrylate), PHEGMA-b-PDEAEMA, and PEO-b-PDEAEMA amphiphilic diblock copolymers in water. The hydrophobic block of these copolymers (P2VP or PDEAEMA) is pH-sensitive: at low pH it can be protonated and becomes partially or completely hydrophilic leading to molecular solubility whereas at higher pH micelles are formed. These micelles consist of a P2VP or PDEAEMA core and a PEO or PHEGMA corona, respectively, where the core forming amine units can incorporate metal compounds due to coordination. The metal compounds (e.g., H2PtCl6, K2PtCl6) can either be introduced in a micellar solution, where they are incorporated within the micelle core via coordination with functional groups, or can be added to a unimer solution at low pH, where they lead to a metal-induced micellization. In these micellar nanoreactors, metal nanoparticles nucleate and grow upon reduction with sizes in the range of a few nanometers as observed by TEM. The effect of the metal incorporation method on the characteristics of the micelles and of the synthesized nanoparticles is investigated.
Lignocellulosic biomass is a potential source of renewable, low-carbon-footprint liquid fuels. Biomass recalcitrance and enzyme cost are key challenges associated with the large-scale production of cellulosic fuel. Kinetic modeling of enzymatic cellulose digestion has been complicated by the heterogeneous nature of the substrate and by the fact that a true steady state cannot be attained. We present a two-parameter kinetic model based on the Michaelis-Menten scheme (Michaelis L and Menten ML. (1913) Biochem Z 49:333–369), but with a time-dependent activity coefficient analogous to fractal-like kinetics formulated by Kopelman (Kopelman R. (1988) Science 241:1620–1626). We provide a mathematical derivation and experimental support to show that one of the parameters is a total activity coefficient and the other is an intrinsic constant that reflects the ability of the cellulases to overcome substrate recalcitrance. The model is applicable to individual cellulases and their mixtures at low-to-medium enzyme loads. Using biomass degrading enzymes from a cellulolytic bacterium Thermobifida fusca we show that the model can be used for mechanistic studies of enzymatic cellulose digestion. We also demonstrate that it applies to the crude supernatant of the widely studied cellulolytic fungus Trichoderma reesei and can thus be used to compare cellulases from different organisms. The two parameters may serve a similar role to Vmax, KM, and kcat in classical kinetics. A similar approach may be applicable to other enzymes with heterogeneous substrates and where a steady state is not achievable.
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