title: Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation.
abstract: Polyethylene (PE), one of the most prominent synthetic polymers used worldwide, is very poorly biodegradable in the natural environment. Consequently, PE represents by itself more than half of all plastic wastes. PE biodegradation is achieved through the combination of abiotic and biotic processes. Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the Rhodococcus genus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a potent carbon source. However, most of them, if not all, fail to induce a clear-cut degradation of PE samples, showing that bottlenecks to reach optimal biodegradation clearly exist. To identify the pathways involved in PE consumption, we used in the present study a combination of RNA-sequencing and lipidomic strategies. We show that short-term exposure to various forms of PE, displaying different molecular weight distributions and oxidation levels, lead to an increase in the expression of 158 genes in a Rhodococcus representative, R. ruber. Interestingly, one of the most up-regulated pathways is related to alkane degradation and β-oxidation of fatty acids. This approach also allowed us to identify metabolic limiting steps, which could be fruitfully targeted for optimized PE consumption by R. ruber.
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Kévin
authors.initials: K
authors.lastname: Gravouil
authors.affiliation: Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Ferru-Clément
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Steven
authors.initials: S
authors.lastname: Colas
authors.affiliation: Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France.
authors.forename: Reynald
authors.initials: R
authors.lastname: Helye
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Linette
authors.initials: L
authors.lastname: Kadri
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Ludivine
authors.initials: L
authors.lastname: Bourdeau
authors.affiliation: Team Ecology, Evolution, Symbiosis, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Bouziane
authors.initials: B
authors.lastname: Moumen
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.
authors.forename: Anne
authors.identifier: http://orcid.org/0000-0002-6970-452X
authors.initials: A
authors.lastname: Mercier
authors.affiliation: Cooperative Laboratory ThanaplastSP-Carbios, Laboratory of Ecological and Biological Interactions, National Center for Scientific Research UMR 7267, University of Poitiers , Poitiers 86073, France.|Laboratory of Signalisation and Membrane Ionic Transports, National Center for Scientific Research STIM CNRS ERL 7368, University of Poitiers , Poitiers 86073, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Ferreira
mesh_terms: D001483:Base Sequence; D001673:Biodegradation, Environmental; D010084:Oxidation-Reduction; D020959:Polyethylene / Q000378:metabolism*; D012240:Rhodococcus / Q000378:metabolism*
chemical_list: D020959:Polyethylene