Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data

  • Natalia Bourguignon
  • Rafael Bargiela
  • David Rojo
  • Tatyana N. Chernikova
  • Sara A. López de Rodas
  • Jesús García-Cantalejo
  • Daniela J. Näther
  • Peter N. Golyshin
  • Coral Barbas
  • Marcela Ferrero
  • Manuel Ferrer
Original Paper

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.

Keywords

Alkanes Amycolatopsis tucumanensis Aromatics Catabolome Degradation Microarray 

Notes

Acknowledgments

This work was supported by the CSIC (Programa CSIC de Cooperación Científica para el Desarrollo i-COOP; ref. COOPB20077), the European Community project KILLSPILL (FP7-KBBE-2012-312139), and the Spanish Ministry of Economy and Competitiveness (CTQ2014-55279-R). N.B. is a recipient of a fellowship from the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina. We thank Drs. Dietmar H. Pieper and Ramiro Vilchez-Vargas for their support in providing resources for this study.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11274_2016_2163_MOESM1_ESM.xls (992 kb)
Supplementary material 1 (XLS 991 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Natalia Bourguignon
    • 1
  • Rafael Bargiela
    • 2
  • David Rojo
    • 3
  • Tatyana N. Chernikova
    • 4
  • Sara A. López de Rodas
    • 5
  • Jesús García-Cantalejo
    • 5
  • Daniela J. Näther
    • 6
  • Peter N. Golyshin
    • 4
  • Coral Barbas
    • 3
  • Marcela Ferrero
    • 1
  • Manuel Ferrer
    • 2
  1. 1.Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET)TucumánArgentina
  2. 2.Consejo Superior de Investigaciones Científicas (CSIC)Institute of CatalysisMadridSpain
  3. 3.Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de FarmaciaUniversidad CEU San PabloMadridSpain
  4. 4.School of Biological SciencesBangor UniversityGwyneddUK
  5. 5.Unidad de Genómica-Campus Moncloa, C.A.I. Genómica y Proteómica, Facultad CC. BiológicasUniversidad Complutense de MadridMadridSpain
  6. 6.Institute for Microbiology, BiocentreGoethe UniversityFrankfurtGermany

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