Comparative proteomic analysis of Arthrobacter phenanthrenivorans Sphe3 on phenanthrene, phthalate and glucose Elpiniki Vandera a , Martina Samiotaki b, ⁎ , Maria Parapouli a , George Panayotou b , Anna Irini Koukkou a, ⁎ a Sector of Organic Chemistry and Biochemistry, University of Ioannina, Greece b Biomedical Sciences Research Center “Alexander Fleming”, Vari, Athens, Greece ARTICLE INFO ABSTRACT Article history: Received 6 March 2014 Accepted 22 August 2014 In the present study, by applying comparative quantitative proteomics, we investigated the metabolic adaptation of Arthrobacter phenanthrenivorans Sphe3 when using phenanthrene, phthalate, glucose or glucose plus phenanthrene as sole carbon and energy sources. More than a third of the total Sphe3 proteins, with function prediction within the genome, were identified with confidence. Proteomic analysis data and annotated genomic information coincide, allowing us to clarify the phenanthrene catabolic pathway. We confirmed the implication of several proteins in aromatic substrate degradation by identifying those mediating the initial ring-hydroxylation and ring cleavage of phenan- threne to phthalate, phthalate degradation, as well as ortho- and meta-protocatechuate catabolism. Repression of catabolic genes by glucose was observed by both proteomic and transcriptional analyses. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in substrate and amino acid metabolism, stress response, detoxification and membrane and cell wall metabolism. Uptake and transport associated proteins differ in the substrates used, indicating the use of different uptake mechanisms for transport of each compound in the Sphe3 cells. Our results also suggest the activation of a glyoxylate shunt in the presence of aromatic compounds, based on the up-regulation of the key enzymes of this pathway. Biological significance A. phenanthrenivorans Sphe3, isolated from a creosote contaminated soil in Greece, can grow on phenanthrene as the sole source of carbon and energy. To explore the phenanthrene catabolic pathway by determining the key proteins involved in this pathway, as well as the global changes in proteins due to the adaptive response of Sphe3 cells grown on different substrates, we applied a gel-free quantitative proteomic analysis using nanoLC–MS/MS. To our knowledge this is the first study of comparative global proteomic changes occurring in the Sphe3 cells under exposure in different nutritional environments. The extended proteomic changes observed in Sphe3 grown on different substrates provide an insight in Keywords: Comparative quantitative proteomics Phenanthrene Biodegradation Arthrobacter phenanthrenivorans NanoLC–MS/MS Catabolite repression JOURNAL OF PROTEOMICS 113 (2015) 73 – 89 ⁎ Corresponding authors. E-mail addresses: samiotaki@fleming.gr (M. Samiotaki), akukku@cc.uoi.gr (A.I. Koukkou). http://dx.doi.org/10.1016/j.jprot.2014.08.018 1874-3919/© 2014 Elsevier B.V. All rights reserved. Available online at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/jprot