The Escherichia coli Protein YfeX Functions as a Porphyrinogen Oxidase, Not a Heme Dechelatase

The protein YfeX from Escherichia coli has been proposed to be essential for the process of iron removal from heme by carrying out a dechelation of heme without cleavage of the porphyrin macrocycle. Since this proposed reaction is unique and would represent the first instance of the biological dechelation of heme, we undertook to characterize YfeX. Our data reveal that YfeX effectively decolorizes the dyes alizarin red and Cibacron blue F3GA and has peroxidase activity with pyrogallal but not guiacol. YfeX oxidizes protoporphyrinogen to protoporphyrin in vitro. However, we were unable to detect any dechelation of heme to free porphyrin with purified YfeX or in cellular extracts of E. coli overexpressing YfeX. Additionally, Vibrio fischeri, an organism that can utilize heme as an iron source when grown under iron limitation, is able to grow with heme as the sole source of iron when its YfeX homolog is absent. Plasmid-driven expression of YfeX in V. fischeri grown with heme did not result in accumulation of protoporphyrin. We propose that YfeX is a typical dye-decolorizing peroxidase (or DyP) and not a dechelatase. The protoporphyrin reported to accumulate when YfeX is overexpressed in E. coli likely arises from the intracellular oxidation of endogenously synthesized protoporphyrinogen and not from dechelation of exogenously supplied heme. Bioinformatic analysis of bacterial YfeX homologs does not identify any connection with iron acquisition but does suggest links to anaerobic-growth-related respiratory pathways. Additionally, some genes encoding homologs of YfeX have tight association with genes encoding a bacterial cytoplasmic encapsulating protein

Streptomyces Exploration is Triggered by Fungal Interactions and Volatile Signals

It has long been thought that the life cycle of Streptomyces bacteria encompasses three developmental stages: vegetative hyphae, aerial hyphae and spores. Here, we show interactions between Streptomyces and fungi trigger a previously unobserved mode of Streptomyces development. We term these Streptomyces cells ‘explorers’, for their ability to adopt a non-branching vegetative hyphal conformation and rapidly transverse solid surfaces. Fungi trigger Streptomyces exploratory growth in part by altering the composition of the growth medium, and Streptomyces explorer cells can communicate this exploratory behaviour to other physically separated streptomycetes using an airborne volatile organic compound (VOC). These results reveal that interkingdom interactions can trigger novel developmental behaviours in bacteria, here, causing Streptomyces to deviate from its classically-defined life cycle. Furthermore, this work provides evidence that VOCs can act as long-range communication signals capable of propagating microbial morphological switches

Formation and aging of incipient thin film wax-oil gels

A fundamental study of the deposition and aging of a thin incipient wax-oil gel that is formed during the flow of waxy oils in cooled pipes was performed. The solubility of high molecular weight paraffins in naphthenic, aromatic or paraffinic solvents is very low and decreases rapidly with decreasing temperature. This property of the paraffins leads to the formation of gels of complex morphology that deposit on the cold walls of the subsea pipelines during the flow of waxy crudes. This deposition reduces the pipe diameter and decreases the flow capacity of the pipe. These wax-oil gels contain a large fraction of oil trapped in a 3-D network structure of the wax crystals that behaves as a porous medium. After the incipient gel is formed, wax molecules continue to diffuse into this structure, thereby increasing its wax content. A model system of wax and oil mixture was used to understand the aging process of the wax-oil gels, which hardens the wax deposit with time. To understand the physics of the aging process for incipient thin-film deposits, a series of laboratory flow loop experiments was performed. The aging process was a counterdiffusion phenomenon with a critical carbon number above which wax molecules diffuse into the gel deposit and below which oil molecules diffuse out of the deposit. The aging rate of the gel deposit depends on the oil flow rate and the wall temperature. A mathematical model developed predicted the growth and wax content of the gel deposit on externally cooled pipe walls. The theory agreed with experiments excellently for thin gels.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34241/1/690460517_ftp.pd

Morphological evolution of thick wax deposits during aging

The presence of waxes in crude oil can lead to the formation of wax deposits on the walls of cold subsea pipelines, which restricts flow and can lead to plugging of the pipelines. This problem has recently become more significant as the production wells move further offshore causing the oil to be cooled below the cloud point before reaching shore. Wax deposition was studied in the laboratory under conditions simulating the deposition in a subsea pipeline. Wax deposition is initiated by the precipitation of wax directly on the pipe wall and the formation of a network of' wax crystals (wax-oil gel) with significant amounts of oil trapped in it. Radial diffusion of the wax molecules from the bulk solution to the gel deposit causes it to simultaneously grow and age with time. The wax molecules diffusing into the gel deposit precipitate near the interface resulting in a faster aging rate of the deposit new the interface than that near the wall. This nonuniform aging of the wax deposit causes the evolution of complex morphologies of the wax deposits. The diffusion of wax molecules into the gel matrix was analyzed theoretically during the growth of the wax deposit. This mathematical model predicted the radial variation of the morphology of the wax deposit observed in the laboratory flow loop experiments along with the deposit thickness as a function of time.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34242/1/690470103_ftp.pd

Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology

Élaboration et caractérisation d’une matrice polypropylène chimiquement modifiée et chargée GNP/graphène fonctionnalisés

In the last decade, the environmental awareness of the need to reduce human impact on the environment affects the research sector. Reducing the fuel consumption and the human gas emissions became a priority, the humanity needs to switch to more eco-efficient patterns of consumption. In the transport field, numerous new lines of research are possible, like lighter structure. Composite materials, like multi-layered steel/polymer, appeared to be the perfect candidates to reach that objective. The polymer part of such material needs to present good shock absorption and thermo-electrical properties, and good compatibility with a metallic surface. The objective of this thesis is the elaboration and characterization of a polymer material with such properties that can be produced at industrial scale. To obtain good compatibility with the metal surfaces, the isotactic polypropylene-grafted-Maleic anhydride was selected as the initial material. This matrix presents good chemical property, its major drawback is its brittleness. A crosslinking reaction based on the reaction between MAH and amine groups was used to modify the mechanical properties of the matrix. The PP-g-MAH were crosslinked by twin-screw reactive extrusion with different configurations. The reaction affects the microstructure and the mechanical behavior of the materials, with a switch from brittle to ductile. The switch is explained by the variation of micro-mechanism of deformation implied by the crosslinked network. The solution used to modify the thermo-electrical properties of the material is the dispersion of different carbon nano-fillers such as graphite. To raise the dispersion quality of the fillers, and the compatibility between the carbon filler and the polymer matrix, a new method of functionalization of the graphite, by plasma discharge was developed. This new method implied a diminution of the filler thickness and an oxidation of the graphene surface, without any significative degradation of the fillers quality. Two types of nanocomposites were produced, one with an unmodified graphite filler and another one with a graphite modified by plasma treatment. Even with high filler concentration no electrical percolation was obtained, a high fillers exfoliation process need to be obtained. The functionalization of the graphite implied a carbon dispersion improvement, thus a better compatibility between the filler and the matrix.Au cours de la dernière décennie, la prise de conscience écologique a impacté les domaines de la recherche. Pour diminuer la production de gaz à effet de serre de nombreux changements sont à apporter aux modes de consommations. Dans le domaine des transports, plusieurs pistes de recherche sont possibles comme l’allégement des structures. L’une des pistes pour permettre cet allégement est l’élaboration de nouveaux matériaux composites métal/polymère. Le polymère de ce composite doit présenter une bonne adhésion aux surfaces métalliques, de bonnes propriétés mécaniques, et de conductivité thermoélectrique. L’objectif de ce travail de thèse est l’élaboration d’une telle matrice par l’emploi de procédé facilement transposable à l’échelle industrielle. Afin d’assurer l’adhésion aux surfaces métalliques, la matrice sélectionnée est le polypropylène greffé anhydride maléique. Cette matrice grâce à ses greffons MAH présente des propriétés chimiques intéressantes au détriment de ses propriétés mécaniques. Pour contourner ce problème, une méthode de réticulation du PP-g-MAH par polyéther amine a été développée. Plusieurs configurations de réticulation ont été réalisées par extrusion réactive. L’évolution de la réticulation suivant le type d’élaboration et son impact sur les matrices ont été déterminés. Le principal changement est le passage d’un comportement mécanique fragile à ductile. Ce changement a été analysé de manière post mortem et in situ à un essai de traction uniaxial, ce qui a permis de mettre en évidence l’impact de la réticulation sur les micro-mécanismes de déformation des matrices. Les propriétés de conductivité thermoélectrique souhaitées sont assurée l’ajout d’une nano-charge de graphite lors de l’extrusion. Afin d’améliorer la dispersion du carbone et d’assurer une percolation mécanique et électrique à faible concentration, une nouvelle méthode d’exfoliation/fonctionnalisation du graphite par décharges plasma a été mise au point. Cette méthode de fonctionnalisation a permis la diminution de l’épaisseur des nanocharges ainsi que l’oxydation de leurs surfaces sans impliquer la création de défaut de structure. Deux gammes de nanocomposites ont été réalisées à l’aide de la nanocharge initiale et traitée. Bien que de hautes teneurs en carbone aient pu être atteintes, il n’a pas été possible d’atteindre la percolation électrique. Malgré cela, une meilleure dispersion de la charge traitée a été observée

Secretion of CyaA-PrtB and HlyA-PrtB fusion proteins in Escherichia coli: involvement of the glycine-rich repeat domain of Erwinia chrysanthemi protease B.

Protease B from Erwinia chrysanthemi was shown previously to have a C-terminal secretion signal located downstream of a domain that contains six glycine-rich repeats. This domain is conserved in all known bacterial proteins secreted by the signal peptide-independent pathway. The role of these repeats in the secretion process is controversial. We compared the secretion processes of various heterologous polypeptides fused either directly to the signal or separated from it by the glycine-rich domain. Although the repeats are not involved in the secretion of small truncated protease B carboxy-terminal peptides, they are required for the secretion of higher-molecular-weight fusion proteins. Secretion efficiency was also dependent on the size of the passenger polypeptide