title: Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data.
abstract: The analysis of catabolic capacities of microorganisms is currently often achieved by cultivation approaches and by the analysis of genomic or metagenomic datasets. Recently, a microarray system designed from curated key aromatic catabolic gene families and key alkane degradation genes was designed. The collection of genes in the microarray can be exploited to indicate whether a given microbe or microbial community is likely to be functionally connected with certain degradative phenotypes, without previous knowledge of genome data. Herein, this microarray was applied to capture new insights into the catabolic capacities of copper-resistant actinomycete Amycolatopsis tucumanensis DSM 45259. The array data support the presumptive ability of the DSM 45259 strain to utilize single alkanes (n-decane and n-tetradecane) and aromatics such as benzoate, phthalate and phenol as sole carbon sources, which was experimentally validated by cultivation and mass spectrometry. Interestingly, while in strain DSM 45259 alkB gene encoding an alkane hydroxylase is most likely highly similar to that found in other actinomycetes, the genes encoding benzoate 1,2-dioxygenase, phthalate 4,5-dioxygenase and phenol hydroxylase were homologous to proteobacterial genes. This suggests that strain DSM 45259 contains catabolic genes distantly related to those found in other actinomycetes. Together, this study not only provided new insight into the catabolic abilities of strain DSM 45259, but also suggests that this strain contains genes uncommon within actinomycetes.
authors: Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.
authors: Natalia
authors: N
authors: Bourguignon
authors: Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain.
authors: Rafael
authors: R
authors: Bargiela
authors: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain.
authors: David
authors: D
authors: Rojo
authors: School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK.
authors: Tatyana N
authors: TN
authors: Chernikova
authors: Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
authors: Sara A López
authors: SA
authors: de Rodas
authors: Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
authors: Jesús
authors: J
authors: García-Cantalejo
authors: Institute for Microbiology, Biocentre, Goethe University, Frankfurt, Germany.
authors: Daniela J
authors: DJ
authors: Näther
authors: School of Biological Sciences, Bangor University, Gwynedd, LL57 2UW, UK.
authors: Peter N
authors: PN
authors: Golyshin
authors: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Monteprincipe, Boadilla del Monte, Madrid, Spain.
authors: Coral
authors: C
authors: Barbas
authors: Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Tucumán, Argentina.
authors: Marcela
authors: M
authors: Ferrero
authors: Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain. mferrer@icp.csic.es.
authors: Manuel
authors: http://orcid.org/0000-0003-4962-4714
authors: M
authors: Ferrer
mesh_terms: D039903:Actinobacteria / Q000235:genetics* / Q000378:metabolism; D000473:Alkanes / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001673:Biodegradation, Environmental; D003300:Copper / Q000378:metabolism; D019143:Evolution, Molecular; D008660:Metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D000473:Alkanes; D001426:Bacterial Proteins; D003300:Copper
keywords: Alkanes; Amycolatopsis tucumanensis; Aromatics; Catabolome; Degradation; Microarray