Relationship of the transcription factor MexT to quorum sensing and virulence in .

is an opportunistic bacterial pathogen. Many of its virulence genes are regulated by quorum sensing (QS), a form of cell-to-cell communication. QS consists of three interlinked circuits, LasI-R, Rhl-R, and quinolone signal (PQS).

Dynamics of cheater invasion in a cooperating population of Pseudomonas aeruginosa.

Pseudomonas aeruginosa quorum sensing (QS) regulates expression of dozens of genes in a cell density-dependent manner. Many QS-regulated genes code for production of extracellular factors, "public goods" that can benefit the entire population. This cooperation encourages individuals to cheat by using but not producing public goods.

Evolution of the quorum-sensing hierarchy.

The bacterial pathogen activates expression of many virulence genes in a cell density-dependent manner by using an intricate quorum-sensing (QS) network. QS in involves two acyl-homoserine-lactone circuits, LasI-LasR and RhlI-RhlR. LasI-LasR is required to activate many genes including those coding for RhlI-RhlR.

Modulation of Quorum Sensing by Glutathione.

uses quorum sensing (QS) to regulate the production of a battery of secreted products. At least some of these products are shared among the population and serve as public goods. When is grown on casein as the sole carbon and energy source, the QS-induced extracellular protease elastase is required for growth.

Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor.

The spiroindolones, a new class of antimalarial medicines discovered in a cellular screen, are rendered less active by mutations in a parasite P-type ATPase, PfATP4. We show here that S. cerevisiae also acquires mutations in a gene encoding a P-type ATPase (ScPMA1) after exposure to spiroindolones and that these mutations are sufficient for resistance.

Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies.

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.

Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling.

The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these organisms by identifying individually deletable regions using transposon mutagenesis and progressively clustering deleted genomic segments using meiotic recombination between the bacterial genomes harbored in yeast.

Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases.

Molecular dynamics simulations were used to study the possible catalytic role of an unusual conserved water-filled pore structure in the family 48 cellulase enzyme Cel48A from Thermobifida fusca. It was hypothesized that this pore serves as the pathway for the water molecules consumed in the hydrolysis catalyzed by the enzyme to reach the active site in a continuous stream to participate in the processive reactions. Theoretical mutants of this enzyme were created in which all of the residues lining the pore were made hydrophobic, which had the effect in molecular dynamics simulations of emptying the pore of water molecules and preventing any from passing through the pore on the simulation time scale.

Cel48A from Thermobifida fusca: structure and site directed mutagenesis of key residues.

Lignocellulosic biomass is a potential source of sustainable transportation fuels, but efficient enzymatic saccharification of cellulose is a key challenge in its utilization. Cellulases from the glycoside hydrolase (GH) family 48 constitute an important component of bacterial biomass degrading systems and structures of three enzymes from this family have been previously published. We report a new crystal structure of TfCel48A, a reducing end directed exocellulase from Thermobifida fusca, which shows that this enzyme shares important structural features with the other members of the GH48 family.

A distinct model of synergism between a processive endocellulase (TfCel9A) and an exocellulase (TfCel48A) from Thermobifida fusca.

Lignocellulosic biomass is digested in nature by the synergistic activities of enzymes with complementary properties, and understanding synergistic interactions will improve the efficiency of industrial biomass use for sustainable fuels and chemicals. Cel9A and Cel48A from a model bacterium, Thermobifida fusca (TfCel9A and TfCel48A, respectively), are two cellulases with different properties and have previously been shown to synergize well with each other. TfCel9A is a processive endocellulase with relatively high activity on crystalline cellulose.

Two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion.

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.

Cellulase processivity.

There are two types of processive cellulases, exocellulases and processive endoglucanases. There are also two classes of exocellulases, ones that attack the reducing ends of cellulose chains and ones that attack the nonreducing ends. There are a number of ways of assaying processivity but none of them are ideal.

Determination of the molecular states of the processive endocellulase Thermobifida fusca Cel9A during crystalline cellulose depolymerization.

Detailed understanding of cell wall degrading enzymes is important for their modeling and industrial applications, including in the production of biofuels. Here we used Cel9A, a processive endocellulase from Thermobifida fusca, to demonstrate that cellulases that contain a catalytic domain (CD) attached to a cellulose binding module (CBM) by a flexible linker exist in three distinct molecular states. By measuring the ability of a soluble competitor to reduce Cel9A activity on an insoluble substrate, we show that the most common state of Cel9A is bound via its CBM, but with its CD unoccupied by the insoluble substrate.

Determination of the catalytic base in family 48 glycosyl hydrolases.

The catalytic base in family 48 glycosyl hydrolases has not been previously established experimentally. Based on structural and modeling data published to date, we used site-directed mutagenesis and azide rescue activity assays to show definitively that the catalytic base in Thermobifida fusca Cel48A is aspartic acid 225. Of the tested mutants, only Cel48A with the D225E mutation retained partial activity on soluble and insoluble substrates.

Mixed Co/Fe oxide nanoparticles in block copolymer micelles.

Small iron oxide and Co-doped iron oxide nanoparticles (NPs) were synthesized in a commercial amphiphilic block copolymer, poly(ethylene oxide)-b-poly(methacrylic acid) (PEO 68-b-PMAA8), in aqueous solutions. The structure and composition of the micelles containing guest molecules (metal salts) or NPs (metal oxides) were studied using transmission electron microscopy, dynamic light scattering, X-ray photoelectron spectroscopy, and X-ray powder diffraction. The enlarged micelle cores after incorporation of metal salts are believed to be formed by both PMAA blocks containing metal species and penetrating PEO chains.

Transformations of poly(methoxy hexa(ethylene glycol) methacrylate)-b-(2-(diethylamino)ethyl methacrylate) block copolymer micelles upon metalation.

Micelle transformations upon metalation (i.e., incorporation of metal compounds and metal nanoparticle formation) in poly(methoxy hexa(ethylene glycol) methacrylate)-block-poly((2-(diethylamino)ethyl methacrylate)), PHEGMA-b-PDEAEMA, solutions have been studied using transmission electron microscopy (TEM) and photon correlation spectroscopy (PCS).

Core-shell nanostructures from single poly(N-vinylcaprolactam) macromolecules: stabilization and visualization.

Formation of core-shell poly(N-vinylcaprolactam) (PVCL) single-molecule nanostructures due to interaction of PVCL with metal ions was studied using transmission electron microscopy, 13C NMR, and light scattering. This study demonstrates that addition of CoCl2 to PVCL in its globular conformation yields unimolecular core-shell polymer particles with the core decorated with Co(II) ions. The crucial condition for formation of well-defined unimolecular nanostructures is the presence of stable globular aggregates in aqueous solution.

Micellization in pH-sensitive amphiphilic block copolymers in aqueous media and the formation of metal nanoparticles.

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.